PDB Short entry for 6Z1V HEADER CELL ADHESION 14-MAY-20 6Z1V TITLE STRUCTURE OF THE EC2 DOMAIN OF CD9 IN COMPLEX WITH NANOBODY 4E8 COMPND MOL_ID: 1; COMPND 2 MOLECULE: CD9 ANTIGEN; COMPND 3 CHAIN: A; 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 4E8; COMPND 10 CHAIN: B; 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: PUPE 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 KEYWDS ANTIBODY-ANTIGEN COMPLEX, TETRASPANIN, EC2 DOMAIN, NANOBODY, CELL KEYWDS 2 ADHESION EXPDTA X-RAY DIFFRACTION AUTHOR W.OOSTERHEERT,N.M.PEARCE,P.GROS REVDAT 2 30-SEP-20 6Z1V 1 JRNL REVDAT 1 23-SEP-20 6Z1V 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. 1.33 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) : 1.33 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.72 REMARK 3 DATA CUTOFF (SIGMA(F)) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 69.7 REMARK 3 NUMBER OF REFLECTIONS : 32042 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) : 0.153 REMARK 3 R VALUE (WORKING SET) : 0.151 REMARK 3 FREE R VALUE : 0.190 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1570 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) : 1.33 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.37 REMARK 3 REFLECTION IN BIN (WORKING SET) : 371 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 9.49 REMARK 3 BIN R VALUE (WORKING SET) : 0.2693 REMARK 3 BIN FREE R VALUE SET COUNT : 20 REMARK 3 BIN FREE R VALUE : 0.5263 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1570 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 18 REMARK 3 SOLVENT ATOMS : 134 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 19.48 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.70 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): 0.137 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 : NULL 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: FOR THE CD9EC2 - 4E8 DATASET, THE REMARK 3 AUTOPROCESSED AND ANISOTROPICAL-TRUNCATED (AUTOPROC-STARANISO) REMARK 3 REFLECTION DATA FILE PROVIDED BY DLS WAS EMPLOYED. THE STRUCTURE REMARK 3 WAS SOLVED BY MOLECULAR REPLACEMENT USING PHASER WITH THE CD9EC2 REMARK 3 - 4C8 STRUCTURE AS SEARCH MODEL. THE 4C8 RESIDUES WERE REPLACED REMARK 3 WITH THE CORRESPONDING 4E8 RESIDUES AND THE CDR REGIONS OF THE REMARK 3 NANOBODY WERE MANUALLY BUILT IN COOT. THE STRUCTURE WAS THEN REMARK 3 ITERATIVELY REFINED USING REFMAC5 OR PHENIX, ALTERNATED WITH REMARK 3 MODEL IMPROVEMENT IN COOT. THE FINAL REFINEMENT IN PHENIX REMARK 3 YIELDED RWORK/RFREE = 15.1/19.0% REMARK 4 REMARK 4 6Z1V 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_1292108720. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-AUG-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I04-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9159 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 32044 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.330 REMARK 200 RESOLUTION RANGE LOW (A) : 44.720 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.0 REMARK 200 DATA REDUNDANCY : 6.400 REMARK 200 R MERGE (I) : 0.04000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 17.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.33 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.44 REMARK 200 COMPLETENESS FOR SHELL (%) : 68.9 REMARK 200 DATA REDUNDANCY IN SHELL : 6.10 REMARK 200 R MERGE FOR SHELL (I) : 0.98000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.500 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: STRUCTURE OF CD9EC2 BOUND TO NANOBODY 4C8 REMARK 200 REMARK 200 REMARK: 3D-DIAMOND LIKE SHAPE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 35.67 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.91 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M SODIUM ACETATE, 0.1 M TRIS PH REMARK 280 8.0, 30% (W/V) PEG 4,000 CRYOPROTECTED WITH RESERVOIR SOLUTION REMARK 280 SUPPLEMENTED WITH 20% (V/V) ETHYLENE GLYCOL., VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X+1/2,Y+1/2,-Z REMARK 290 4555 X+1/2,-Y+1/2,-Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 30.76050 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 44.72300 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 30.76050 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 44.72300 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1880 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9930 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 2.0 KCAL/MOL 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 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 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 HIS B 124 REMARK 465 GLY B 125 REMARK 465 SER B 126 REMARK 465 GLY B 127 REMARK 465 LEU B 128 REMARK 465 VAL B 129 REMARK 465 PRO B 130 REMARK 465 ARG B 131 REMARK 465 GLY B 132 REMARK 465 SER B 133 REMARK 465 GLY B 134 REMARK 465 GLY B 135 REMARK 465 GLY B 136 REMARK 465 HIS B 137 REMARK 465 HIS B 138 REMARK 465 HIS B 139 REMARK 465 HIS B 140 REMARK 465 HIS B 141 REMARK 465 HIS B 142 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 LYS A 119 CG CD CE NZ REMARK 470 LYS A 135 CG CD CE NZ REMARK 470 GLU A 141 CG CD OE1 OE2 REMARK 470 ARG B 27 CG CD NE CZ NH1 NH2 REMARK 470 GLU B 44 CG CD OE1 OE2 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 LYS A 135 26.08 84.46 REMARK 500 CYS A 153 118.04 -160.25 REMARK 500 VAL A 172 -68.32 -121.90 REMARK 500 ALA B 92 166.60 179.23 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 PGE A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO B 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACY B 202 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6RLR RELATED DB: PDB REMARK 900 STRUCTURE OF THE EC2 DOMAIN OF CD9 WITHOUT NANOBODY BOUND, THIS REMARK 900 STRUCTURE WAS UPLOADED TO THE PDB PREVIOUSLY DBREF 6Z1V A 114 191 UNP P21926 CD9_HUMAN 114 191 DBREF 6Z1V B 1 142 PDB 6Z1V 6Z1V 1 142 SEQADV 6Z1V GLY A 112 UNP P21926 EXPRESSION TAG SEQADV 6Z1V SER A 113 UNP P21926 EXPRESSION TAG SEQADV 6Z1V ALA A 192 UNP P21926 EXPRESSION TAG SEQADV 6Z1V ALA A 193 UNP P21926 EXPRESSION TAG SEQADV 6Z1V ALA A 194 UNP P21926 EXPRESSION TAG SEQADV 6Z1V HIS A 195 UNP P21926 EXPRESSION TAG SEQADV 6Z1V HIS A 196 UNP P21926 EXPRESSION TAG SEQADV 6Z1V HIS A 197 UNP P21926 EXPRESSION TAG SEQADV 6Z1V HIS A 198 UNP P21926 EXPRESSION TAG SEQADV 6Z1V HIS A 199 UNP P21926 EXPRESSION TAG SEQADV 6Z1V HIS A 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 142 GLU VAL GLN LEU VAL GLU SER GLY GLY ARG LEU VAL ARG SEQRES 2 B 142 THR GLY GLY SER LEU ARG LEU SER CYS ALA ALA SER GLY SEQRES 3 B 142 ARG THR PHE SER ASN TYR VAL MET GLY TRP PHE ARG GLN SEQRES 4 B 142 ALA PRO GLY LYS GLU ARG GLU VAL VAL ALA ALA ILE THR SEQRES 5 B 142 TRP SER GLY ASP ILE THR TRP HIS ALA ASP PHE VAL LYS SEQRES 6 B 142 GLY ARG PHE THR ILE SER ARG ASP ASN ALA LYS ASN THR SEQRES 7 B 142 VAL TYR LEU GLN MET ASN SER LEU LYS PRO GLU ASP THR SEQRES 8 B 142 ALA VAL TYR TYR CYS ALA ALA THR GLU ARG TRP GLY LEU SEQRES 9 B 142 ARG ALA PRO ALA ASP TRP GLY SER TRP GLY GLN GLY THR SEQRES 10 B 142 GLN VAL THR VAL SER SER HIS GLY SER GLY LEU VAL PRO SEQRES 11 B 142 ARG GLY SER GLY GLY GLY HIS HIS HIS HIS HIS HIS HET PGE A 301 24 HET EDO B 201 10 HET ACY B 202 7 HETNAM PGE TRIETHYLENE GLYCOL HETNAM EDO 1,2-ETHANEDIOL HETNAM ACY ACETIC ACID HETSYN EDO ETHYLENE GLYCOL FORMUL 3 PGE C6 H14 O4 FORMUL 4 EDO C2 H6 O2 FORMUL 5 ACY C2 H4 O2 FORMUL 6 HOH *134(H2 O) HELIX 1 AA1 SER A 113 THR A 134 1 22 HELIX 2 AA2 LYS A 135 PRO A 138 5 4 HELIX 3 AA3 GLN A 139 ASN A 151 1 13 HELIX 4 AA4 GLU A 160 CYS A 167 5 8 HELIX 5 AA5 VAL A 172 PHE A 176 5 5 HELIX 6 AA6 SER A 180 ASN A 191 1 12 HELIX 7 AA7 THR B 28 TYR B 32 5 5 HELIX 8 AA8 LYS B 87 THR B 91 5 5 HELIX 9 AA9 ALA B 106 TRP B 110 5 5 SHEET 1 AA1 4 LEU B 4 SER B 7 0 SHEET 2 AA1 4 LEU B 18 ALA B 24 -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 THR B 69 O GLN B 82 SHEET 1 AA2 6 LEU B 11 ARG B 13 0 SHEET 2 AA2 6 THR B 117 SER B 122 1 O THR B 120 N VAL B 12 SHEET 3 AA2 6 ALA B 92 THR B 99 -1 N ALA B 92 O VAL B 119 SHEET 4 AA2 6 VAL B 33 GLN B 39 -1 N VAL B 33 O THR B 99 SHEET 5 AA2 6 GLU B 46 ILE B 51 -1 O VAL B 48 N TRP B 36 SHEET 6 AA2 6 THR B 58 HIS B 60 -1 O TRP B 59 N ALA B 50 SHEET 1 AA3 4 LEU B 11 ARG B 13 0 SHEET 2 AA3 4 THR B 117 SER B 122 1 O THR B 120 N VAL B 12 SHEET 3 AA3 4 ALA B 92 THR B 99 -1 N ALA B 92 O VAL B 119 SHEET 4 AA3 4 SER B 112 TRP B 113 -1 O SER B 112 N ALA B 98 SSBOND 1 CYS A 152 CYS A 181 1555 1555 2.09 SSBOND 2 CYS A 153 CYS A 167 1555 1555 2.03 SSBOND 3 CYS B 22 CYS B 96 1555 1555 2.04 SITE 1 AC1 7 GLY A 112 GLU A 120 PHE A 124 ASP A 127 SITE 2 AC1 7 THR A 128 LYS A 131 GLN A 139 SITE 1 AC2 4 SER A 164 THR B 52 ASP B 56 HOH B 301 SITE 1 AC3 4 ARG B 10 LEU B 11 GLN B 118 THR B 120 CRYST1 61.521 89.446 35.684 90.00 90.00 90.00 P 21 21 2 4 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 0.016255 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011180 0.000000 0.00000 SCALE3 0.000000 0.000000 0.028024 0.00000