PDB Short entry for 6Z20 HEADER CELL ADHESION 14-MAY-20 6Z20 TITLE STRUCTURE OF THE EC2 DOMAIN OF CD9 IN COMPLEX WITH NANOBODY 4C8 COMPND MOL_ID: 1; COMPND 2 MOLECULE: CD9 ANTIGEN; COMPND 3 CHAIN: A, C; COMPND 4 SYNONYM: 5H9 ANTIGEN,CELL GROWTH-INHIBITING GENE 2 PROTEIN,LEUKOCYTE COMPND 5 ANTIGEN MIC3,MOTILITY-RELATED PROTEIN,MRP-1,TETRASPANIN-29,TSPAN-29, COMPND 6 P24; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: NANOBODY 4C8; COMPND 10 CHAIN: B, D; COMPND 11 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: CD9, MIC3, TSPAN29, GIG2; SOURCE 6 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 7 EXPRESSION_SYSTEM_COMMON: HUMAN; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 9 EXPRESSION_SYSTEM_CELL_LINE: HEK293EBNA; SOURCE 10 EXPRESSION_SYSTEM_ORGAN: KIDNEY; SOURCE 11 EXPRESSION_SYSTEM_CELL: EMBRYONIC; SOURCE 12 EXPRESSION_SYSTEM_PLASMID: 107.03; SOURCE 13 MOL_ID: 2; SOURCE 14 ORGANISM_SCIENTIFIC: LAMA GLAMA; SOURCE 15 ORGANISM_COMMON: LLAMA; SOURCE 16 ORGANISM_TAXID: 9844; SOURCE 17 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 18 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 19 EXPRESSION_SYSTEM_VARIANT: CODON PLUS (RIL); SOURCE 20 EXPRESSION_SYSTEM_VECTOR_TYPE: PHEN6 KEYWDS ANTIBODY-ANTIGEN COMPLEX, TETRASPANIN, CD9, EC2 DOMAIN, NANOBODY, KEYWDS 2 CELL ADHESION EXPDTA X-RAY DIFFRACTION AUTHOR W.OOSTERHEERT,J.MANSHANDE,N.M.PEARCE,M.LUTZ,P.GROS REVDAT 3 24-JAN-24 6Z20 1 REMARK REVDAT 2 30-SEP-20 6Z20 1 JRNL REVDAT 1 23-SEP-20 6Z20 0 JRNL AUTH W.OOSTERHEERT,K.T.XENAKI,V.NEVIANI,W.POS,S.DOULKERIDOU, JRNL AUTH 2 J.MANSHANDE,N.M.PEARCE,L.M.KROON-BATENBURG,M.LUTZ, JRNL AUTH 3 P.M.VAN BERGEN EN HENEGOUWEN,P.GROS JRNL TITL IMPLICATIONS FOR TETRASPANIN-ENRICHED MICRODOMAIN ASSEMBLY JRNL TITL 2 BASED ON STRUCTURES OF CD9 WITH EWI-F. JRNL REF LIFE SCI ALLIANCE V. 3 2020 JRNL REFN ESSN 2575-1077 JRNL PMID 32958604 JRNL DOI 10.26508/LSA.202000883 REMARK 2 REMARK 2 RESOLUTION. 2.68 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.68 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 60.71 REMARK 3 DATA CUTOFF (SIGMA(F)) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 83.5 REMARK 3 NUMBER OF REFLECTIONS : 14243 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : FREE R-VALUE REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : 0.208 REMARK 3 R VALUE (WORKING SET) : 0.206 REMARK 3 FREE R VALUE : 0.248 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.150 REMARK 3 FREE R VALUE TEST SET COUNT : 734 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.68 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.89 REMARK 3 REFLECTION IN BIN (WORKING SET) : 998 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 31.01 REMARK 3 BIN R VALUE (WORKING SET) : 0.3112 REMARK 3 BIN FREE R VALUE SET COUNT : 39 REMARK 3 BIN FREE R VALUE : 0.3700 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3104 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 13 REMARK 3 SOLVENT ATOMS : 6 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 66.57 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 68.91 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): NULL REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.305 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : NULL REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): NULL ; NULL ; NULL REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): NULL ; NULL ; NULL REMARK 3 GENERAL PLANES REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : NULL NULL NULL NULL REMARK 3 ORIGIN FOR THE GROUP (A): 20.6221 11.8145 -22.5004 REMARK 3 T TENSOR REMARK 3 T11: 0.3552 T22: 0.4182 REMARK 3 T33: 0.3501 T12: 0.1309 REMARK 3 T13: -0.0451 T23: -0.0550 REMARK 3 L TENSOR REMARK 3 L11: 1.1013 L22: 1.9921 REMARK 3 L33: 1.1472 L12: -0.2208 REMARK 3 L13: 0.1672 L23: -0.6080 REMARK 3 S TENSOR REMARK 3 S11: -0.2596 S12: -0.1342 S13: 0.2217 REMARK 3 S21: 0.3679 S22: 0.4436 S23: 0.2352 REMARK 3 S31: -0.1704 S32: -0.1813 S33: 0.0363 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.11 REMARK 3 ION PROBE RADIUS : NULL REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6Z20 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 14-MAY-20. REMARK 100 THE DEPOSITION ID IS D_1292108736. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-MAY-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I03 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9763 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 XE 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DIALS REMARK 200 DATA SCALING SOFTWARE : STARANISO REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14256 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.680 REMARK 200 RESOLUTION RANGE LOW (A) : 88.490 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.9 REMARK 200 DATA REDUNDANCY : 6.700 REMARK 200 R MERGE (I) : 0.13000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 9.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.68 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.83 REMARK 200 COMPLETENESS FOR SHELL (%) : 55.8 REMARK 200 DATA REDUNDANCY IN SHELL : 7.30 REMARK 200 R MERGE FOR SHELL (I) : 1.78000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 6RLO REMARK 200 REMARK 200 REMARK: NEEDLE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 59.85 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.06 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.095 M SODIUM CITRATE PH 5.6, 5% REMARK 280 (V/V) GLYCEROL, 19% (V/V) ISOPROPANOL, 20% (W/V) PEG 4,000. THE REMARK 280 CRYSTAL WAS CRYOPROTECTED BY SOAKING IN RESERVOIR SOLUTION REMARK 280 SUPPLEMENTED WITH 25% GLYCEROL (FINAL CONCENTRATION)., VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X,-Y+1/2,Z REMARK 290 7555 -X+1/2,Y,-Z REMARK 290 8555 X,-Y,-Z+1/2 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 37.82250 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 64.62450 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 60.70750 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 64.62450 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 37.82250 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 60.70750 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 37.82250 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 60.70750 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 64.62450 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 60.70750 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 37.82250 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 64.62450 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, D REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 ASN A 191 REMARK 465 ALA A 192 REMARK 465 ALA A 193 REMARK 465 ALA A 194 REMARK 465 HIS A 195 REMARK 465 HIS A 196 REMARK 465 HIS A 197 REMARK 465 HIS A 198 REMARK 465 HIS A 199 REMARK 465 HIS A 200 REMARK 465 GLU B 1 REMARK 465 HIS B 122 REMARK 465 GLY B 123 REMARK 465 SER B 124 REMARK 465 GLY B 125 REMARK 465 LEU B 126 REMARK 465 VAL B 127 REMARK 465 PRO B 128 REMARK 465 ARG B 129 REMARK 465 GLY C 112 REMARK 465 ALA C 192 REMARK 465 ALA C 193 REMARK 465 ALA C 194 REMARK 465 HIS C 195 REMARK 465 HIS C 196 REMARK 465 HIS C 197 REMARK 465 HIS C 198 REMARK 465 HIS C 199 REMARK 465 HIS C 200 REMARK 465 GLU D 1 REMARK 465 HIS D 122 REMARK 465 GLY D 123 REMARK 465 SER D 124 REMARK 465 GLY D 125 REMARK 465 LEU D 126 REMARK 465 VAL D 127 REMARK 465 PRO D 128 REMARK 465 ARG D 129 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ARG B 27 CG CD NE CZ NH1 NH2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 CYS A 153 117.82 -168.00 REMARK 500 VAL A 172 -54.57 -122.68 REMARK 500 SER B 7 165.65 178.01 REMARK 500 ARG B 27 -178.46 -58.47 REMARK 500 SER B 30 1.33 -69.71 REMARK 500 VAL B 48 -62.46 -121.94 REMARK 500 ALA B 92 167.69 174.96 REMARK 500 SER B 120 -127.80 -125.38 REMARK 500 LYS C 135 36.60 70.22 REMARK 500 CYS C 153 115.71 -163.70 REMARK 500 VAL D 48 -54.78 -123.94 REMARK 500 LEU D 81 88.93 -151.20 REMARK 500 ALA D 92 171.26 174.97 REMARK 500 SER D 120 -92.34 -121.85 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL B 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL D 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL D 202 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6RLR RELATED DB: PDB REMARK 900 STRUCTURE OF THE EC2 DOMAIN OF CD9 WITH NO NANOBODY BOUND, THIS REMARK 900 STRUCTURE WAS UPLOADED TO THE PDB PREVIOUSLY REMARK 900 RELATED ID: 6Z1Z RELATED DB: PDB REMARK 900 STRUCTURE OF THE ANTI-CD9 NANOBODY 4C8 ALONE REMARK 900 RELATED ID: 6Z1V RELATED DB: PDB REMARK 900 STRUCTURE OF THE EC2 DOMAIN OF CD9 IN COMPLEX WITH NANOBODY 4E8, REMARK 900 THIS IS A DIFFERENT, BUT SIMILAR NANOBODY. DBREF 6Z20 A 114 191 UNP P21926 CD9_HUMAN 114 191 DBREF 6Z20 B 1 129 PDB 6Z20 6Z20 1 129 DBREF 6Z20 C 114 191 UNP P21926 CD9_HUMAN 114 191 DBREF 6Z20 D 1 129 PDB 6Z20 6Z20 1 129 SEQADV 6Z20 GLY A 112 UNP P21926 EXPRESSION TAG SEQADV 6Z20 SER A 113 UNP P21926 EXPRESSION TAG SEQADV 6Z20 ALA A 192 UNP P21926 EXPRESSION TAG SEQADV 6Z20 ALA A 193 UNP P21926 EXPRESSION TAG SEQADV 6Z20 ALA A 194 UNP P21926 EXPRESSION TAG SEQADV 6Z20 HIS A 195 UNP P21926 EXPRESSION TAG SEQADV 6Z20 HIS A 196 UNP P21926 EXPRESSION TAG SEQADV 6Z20 HIS A 197 UNP P21926 EXPRESSION TAG SEQADV 6Z20 HIS A 198 UNP P21926 EXPRESSION TAG SEQADV 6Z20 HIS A 199 UNP P21926 EXPRESSION TAG SEQADV 6Z20 HIS A 200 UNP P21926 EXPRESSION TAG SEQADV 6Z20 GLY C 112 UNP P21926 EXPRESSION TAG SEQADV 6Z20 SER C 113 UNP P21926 EXPRESSION TAG SEQADV 6Z20 ALA C 192 UNP P21926 EXPRESSION TAG SEQADV 6Z20 ALA C 193 UNP P21926 EXPRESSION TAG SEQADV 6Z20 ALA C 194 UNP P21926 EXPRESSION TAG SEQADV 6Z20 HIS C 195 UNP P21926 EXPRESSION TAG SEQADV 6Z20 HIS C 196 UNP P21926 EXPRESSION TAG SEQADV 6Z20 HIS C 197 UNP P21926 EXPRESSION TAG SEQADV 6Z20 HIS C 198 UNP P21926 EXPRESSION TAG SEQADV 6Z20 HIS C 199 UNP P21926 EXPRESSION TAG SEQADV 6Z20 HIS C 200 UNP P21926 EXPRESSION TAG SEQRES 1 A 89 GLY SER LYS ASP GLU VAL ILE LYS GLU VAL GLN GLU PHE SEQRES 2 A 89 TYR LYS ASP THR TYR ASN LYS LEU LYS THR LYS ASP GLU SEQRES 3 A 89 PRO GLN ARG GLU THR LEU LYS ALA ILE HIS TYR ALA LEU SEQRES 4 A 89 ASN CYS CYS GLY LEU ALA GLY GLY VAL GLU GLN PHE ILE SEQRES 5 A 89 SER ASP ILE CYS PRO LYS LYS ASP VAL LEU GLU THR PHE SEQRES 6 A 89 THR VAL LYS SER CYS PRO ASP ALA ILE LYS GLU VAL PHE SEQRES 7 A 89 ASP ASN ALA ALA ALA HIS HIS HIS HIS HIS HIS SEQRES 1 B 129 GLU VAL GLN LEU VAL GLU SER GLY GLY GLY LEU VAL GLN SEQRES 2 B 129 ALA GLY GLY SER LEU ARG LEU SER CYS ALA ALA SER GLY SEQRES 3 B 129 ARG THR PHE SER ASP TYR VAL MET GLY TRP PHE ARG GLN SEQRES 4 B 129 ALA PRO GLY LYS GLU ARG THR PHE VAL ALA ARG ILE GLY SEQRES 5 B 129 TRP SER GLY ASP LEU THR TYR TYR ALA ASP SER VAL LYS SEQRES 6 B 129 GLY ARG PHE THR ILE SER ARG ASP ASN ALA LYS ASN THR SEQRES 7 B 129 VAL TYR LEU GLN MET ASN SER LEU LYS PRO GLU ASP THR SEQRES 8 B 129 ALA ILE TYR TYR CYS ALA ALA ASP GLU ARG TRP GLY THR SEQRES 9 B 129 GLY GLY LYS PHE ASP TYR TRP GLY GLN GLY THR GLN VAL SEQRES 10 B 129 THR VAL SER SER HIS GLY SER GLY LEU VAL PRO ARG SEQRES 1 C 89 GLY SER LYS ASP GLU VAL ILE LYS GLU VAL GLN GLU PHE SEQRES 2 C 89 TYR LYS ASP THR TYR ASN LYS LEU LYS THR LYS ASP GLU SEQRES 3 C 89 PRO GLN ARG GLU THR LEU LYS ALA ILE HIS TYR ALA LEU SEQRES 4 C 89 ASN CYS CYS GLY LEU ALA GLY GLY VAL GLU GLN PHE ILE SEQRES 5 C 89 SER ASP ILE CYS PRO LYS LYS ASP VAL LEU GLU THR PHE SEQRES 6 C 89 THR VAL LYS SER CYS PRO ASP ALA ILE LYS GLU VAL PHE SEQRES 7 C 89 ASP ASN ALA ALA ALA HIS HIS HIS HIS HIS HIS SEQRES 1 D 129 GLU VAL GLN LEU VAL GLU SER GLY GLY GLY LEU VAL GLN SEQRES 2 D 129 ALA GLY GLY SER LEU ARG LEU SER CYS ALA ALA SER GLY SEQRES 3 D 129 ARG THR PHE SER ASP TYR VAL MET GLY TRP PHE ARG GLN SEQRES 4 D 129 ALA PRO GLY LYS GLU ARG THR PHE VAL ALA ARG ILE GLY SEQRES 5 D 129 TRP SER GLY ASP LEU THR TYR TYR ALA ASP SER VAL LYS SEQRES 6 D 129 GLY ARG PHE THR ILE SER ARG ASP ASN ALA LYS ASN THR SEQRES 7 D 129 VAL TYR LEU GLN MET ASN SER LEU LYS PRO GLU ASP THR SEQRES 8 D 129 ALA ILE TYR TYR CYS ALA ALA ASP GLU ARG TRP GLY THR SEQRES 9 D 129 GLY GLY LYS PHE ASP TYR TRP GLY GLN GLY THR GLN VAL SEQRES 10 D 129 THR VAL SER SER HIS GLY SER GLY LEU VAL PRO ARG HET GOL B 201 14 HET CL D 201 1 HET GOL D 202 14 HETNAM GOL GLYCEROL HETNAM CL CHLORIDE ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 5 GOL 2(C3 H8 O3) FORMUL 6 CL CL 1- FORMUL 8 HOH *6(H2 O) HELIX 1 AA1 SER A 113 THR A 134 1 22 HELIX 2 AA2 PRO A 138 ASN A 151 1 14 HELIX 3 AA3 GLU A 160 ASP A 165 1 6 HELIX 4 AA4 SER A 180 ASP A 190 1 11 HELIX 5 AA5 THR B 28 TYR B 32 5 5 HELIX 6 AA6 ASN B 74 LYS B 76 5 3 HELIX 7 AA7 LYS B 87 THR B 91 5 5 HELIX 8 AA8 LYS C 114 THR C 134 1 21 HELIX 9 AA9 LYS C 135 GLU C 137 5 3 HELIX 10 AB1 PRO C 138 ASN C 151 1 14 HELIX 11 AB2 GLU C 160 CYS C 167 5 8 HELIX 12 AB3 SER C 180 PHE C 189 1 10 HELIX 13 AB4 THR D 28 TYR D 32 5 5 HELIX 14 AB5 ASN D 74 LYS D 76 5 3 HELIX 15 AB6 LYS D 87 THR D 91 5 5 SHEET 1 AA1 4 GLN B 3 SER B 7 0 SHEET 2 AA1 4 LEU B 18 SER B 25 -1 O SER B 21 N SER B 7 SHEET 3 AA1 4 THR B 78 MET B 83 -1 O MET B 83 N LEU B 18 SHEET 4 AA1 4 PHE B 68 ASP B 73 -1 N SER B 71 O TYR B 80 SHEET 1 AA2 6 LEU B 11 VAL B 12 0 SHEET 2 AA2 6 THR B 115 VAL B 119 1 O THR B 118 N VAL B 12 SHEET 3 AA2 6 ALA B 92 ASP B 99 -1 N TYR B 94 O THR B 115 SHEET 4 AA2 6 VAL B 33 GLN B 39 -1 N VAL B 33 O ASP B 99 SHEET 5 AA2 6 ARG B 45 ILE B 51 -1 O ALA B 49 N TRP B 36 SHEET 6 AA2 6 THR B 58 TYR B 60 -1 O TYR B 59 N ARG B 50 SHEET 1 AA3 4 LEU B 11 VAL B 12 0 SHEET 2 AA3 4 THR B 115 VAL B 119 1 O THR B 118 N VAL B 12 SHEET 3 AA3 4 ALA B 92 ASP B 99 -1 N TYR B 94 O THR B 115 SHEET 4 AA3 4 TYR B 110 TRP B 111 -1 O TYR B 110 N ALA B 98 SHEET 1 AA4 4 LEU D 4 SER D 7 0 SHEET 2 AA4 4 LEU D 18 ALA D 24 -1 O SER D 21 N SER D 7 SHEET 3 AA4 4 THR D 78 MET D 83 -1 O MET D 83 N LEU D 18 SHEET 4 AA4 4 PHE D 68 ASP D 73 -1 N SER D 71 O TYR D 80 SHEET 1 AA5 6 GLY D 10 VAL D 12 0 SHEET 2 AA5 6 THR D 115 VAL D 119 1 O THR D 118 N VAL D 12 SHEET 3 AA5 6 ALA D 92 ASP D 99 -1 N TYR D 94 O THR D 115 SHEET 4 AA5 6 VAL D 33 GLN D 39 -1 N VAL D 33 O ASP D 99 SHEET 5 AA5 6 ARG D 45 ILE D 51 -1 O ILE D 51 N MET D 34 SHEET 6 AA5 6 THR D 58 TYR D 60 -1 O TYR D 59 N ARG D 50 SHEET 1 AA6 4 GLY D 10 VAL D 12 0 SHEET 2 AA6 4 THR D 115 VAL D 119 1 O THR D 118 N VAL D 12 SHEET 3 AA6 4 ALA D 92 ASP D 99 -1 N TYR D 94 O THR D 115 SHEET 4 AA6 4 TYR D 110 TRP D 111 -1 O TYR D 110 N ALA D 98 SSBOND 1 CYS A 152 CYS A 181 1555 1555 2.04 SSBOND 2 CYS A 153 CYS A 167 1555 1555 2.01 SSBOND 3 CYS B 22 CYS B 96 1555 1555 2.02 SSBOND 4 CYS C 152 CYS C 181 1555 1555 2.02 SSBOND 5 CYS C 153 CYS C 167 1555 1555 2.01 SSBOND 6 CYS D 22 CYS D 96 1555 1555 2.03 SITE 1 AC1 5 VAL B 64 LYS B 65 GLY B 66 PHE B 68 SITE 2 AC1 5 THR B 69 SITE 1 AC2 6 GLY D 52 TRP D 53 SER D 54 GLY D 55 SITE 2 AC2 6 ASP D 56 LEU D 57 SITE 1 AC3 7 TYR D 60 VAL D 64 LYS D 65 GLY D 66 SITE 2 AC3 7 ARG D 67 PHE D 68 THR D 69 CRYST1 75.645 121.415 129.249 90.00 90.00 90.00 I 21 21 21 16 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.013220 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008236 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007737 0.00000