PDB Short entry for 5UD8 HEADER IMMUNE SYSTEM 23-DEC-16 5UD8 TITLE CRYSTAL STRUCTURE OF MUTANT IG-LIKE DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRIGGERING RECEPTOR EXPRESSED ON MYELOID CELLS 2; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: TREM-2,TRIGGERING RECEPTOR EXPRESSED ON MONOCYTES 2; COMPND 5 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: TREM2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET24 KEYWDS IG-LIKE DOMAIN, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR A.SUDOM,X.MIN,Z.WANG REVDAT 2 17-APR-19 5UD8 1 JRNL REVDAT 1 04-APR-18 5UD8 0 JRNL AUTH A.SUDOM,S.TALREJA,J.DANAO,E.BRAGG,R.KEGEL,X.MIN, JRNL AUTH 2 J.RICHARDSON,Z.ZHANG,N.SHARKOV,E.MARCORA,S.THIBAULT, JRNL AUTH 3 J.BRADLEY,S.WOOD,A.C.LIM,H.CHEN,S.WANG,I.N.FOLTZ, JRNL AUTH 4 S.SAMBASHIVAN,Z.WANG JRNL TITL MOLECULAR BASIS FOR THE LOSS-OF-FUNCTION EFFECTS OF THE JRNL TITL 2 ALZHEIMER'S DISEASE-ASSOCIATED R47H VARIANT OF THE IMMUNE JRNL TITL 3 RECEPTOR TREM2. JRNL REF J. BIOL. CHEM. V. 293 12634 2018 JRNL REFN ESSN 1083-351X JRNL PMID 29794134 JRNL DOI 10.1074/JBC.RA118.002352 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.25 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 3 NUMBER OF REFLECTIONS : 17894 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. 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 (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 913 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 44.2658 - 3.4428 1.00 2627 135 0.1937 0.2263 REMARK 3 2 3.4428 - 2.7328 1.00 2512 127 0.2140 0.2325 REMARK 3 3 2.7328 - 2.3874 1.00 2420 144 0.2209 0.3219 REMARK 3 4 2.3874 - 2.1691 1.00 2441 121 0.2113 0.2380 REMARK 3 5 2.1691 - 2.0136 0.99 2408 137 0.1906 0.2293 REMARK 3 6 2.0136 - 1.8949 0.98 2359 130 0.2038 0.2554 REMARK 3 7 1.8949 - 1.8000 0.92 2214 119 0.2207 0.2556 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.180 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.600 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 14.29 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 11.43 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 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.006 1668 REMARK 3 ANGLE : 1.097 2259 REMARK 3 CHIRALITY : 0.083 261 REMARK 3 PLANARITY : 0.004 285 REMARK 3 DIHEDRAL : 15.993 588 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5UD8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-JAN-17. REMARK 100 THE DEPOSITION ID IS D_1000225683. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-OCT-13 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 : ALS REMARK 200 BEAMLINE : 5.0.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : SI REMARK 200 OPTICS : 3X3 CCD ARRAY REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA 3.3.20 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17947 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 44.250 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 200 DATA REDUNDANCY : 5.800 REMARK 200 R MERGE (I) : 0.12700 REMARK 200 R SYM (I) : 0.12700 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 9.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.90 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.6 REMARK 200 DATA REDUNDANCY IN SHELL : 3.90 REMARK 200 R MERGE FOR SHELL (I) : 0.35100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 33.84 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.86 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% PEG 6000, 0.1 M TRIS 8.0, PH 8.0, REMARK 280 EVAPORATION, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 2 21 21 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,Y+1/2,-Z+1/2 REMARK 290 4555 -X,-Y+1/2,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 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 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 31.26500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 62.63500 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 31.26500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 62.63500 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 ARG A 76 REMARK 465 ARG A 77 REMARK 465 TRP A 78 REMARK 465 ASN A 79 REMARK 465 GLY A 80 REMARK 465 SER A 81 REMARK 465 PHE B 74 REMARK 465 LEU B 75 REMARK 465 ARG B 76 REMARK 465 ARG B 77 REMARK 465 TRP B 78 REMARK 465 ASN B 79 REMARK 465 GLY B 80 REMARK 465 SER B 81 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 NZ LYS A 57 OE1 GLU B 56 1545 2.12 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5UD7 RELATED DB: PDB DBREF 5UD8 A 19 130 UNP Q9NZC2 TREM2_HUMAN 19 130 DBREF 5UD8 B 19 130 UNP Q9NZC2 TREM2_HUMAN 19 130 SEQADV 5UD8 HIS A 47 UNP Q9NZC2 ARG 47 ENGINEERED MUTATION SEQADV 5UD8 HIS B 47 UNP Q9NZC2 ARG 47 ENGINEERED MUTATION SEQRES 1 A 112 HIS ASN THR THR VAL PHE GLN GLY VAL ALA GLY GLN SER SEQRES 2 A 112 LEU GLN VAL SER CYS PRO TYR ASP SER MET LYS HIS TRP SEQRES 3 A 112 GLY ARG HIS LYS ALA TRP CYS ARG GLN LEU GLY GLU LYS SEQRES 4 A 112 GLY PRO CYS GLN ARG VAL VAL SER THR HIS ASN LEU TRP SEQRES 5 A 112 LEU LEU SER PHE LEU ARG ARG TRP ASN GLY SER THR ALA SEQRES 6 A 112 ILE THR ASP ASP THR LEU GLY GLY THR LEU THR ILE THR SEQRES 7 A 112 LEU ARG ASN LEU GLN PRO HIS ASP ALA GLY LEU TYR GLN SEQRES 8 A 112 CYS GLN SER LEU HIS GLY SER GLU ALA ASP THR LEU ARG SEQRES 9 A 112 LYS VAL LEU VAL GLU VAL LEU ALA SEQRES 1 B 112 HIS ASN THR THR VAL PHE GLN GLY VAL ALA GLY GLN SER SEQRES 2 B 112 LEU GLN VAL SER CYS PRO TYR ASP SER MET LYS HIS TRP SEQRES 3 B 112 GLY ARG HIS LYS ALA TRP CYS ARG GLN LEU GLY GLU LYS SEQRES 4 B 112 GLY PRO CYS GLN ARG VAL VAL SER THR HIS ASN LEU TRP SEQRES 5 B 112 LEU LEU SER PHE LEU ARG ARG TRP ASN GLY SER THR ALA SEQRES 6 B 112 ILE THR ASP ASP THR LEU GLY GLY THR LEU THR ILE THR SEQRES 7 B 112 LEU ARG ASN LEU GLN PRO HIS ASP ALA GLY LEU TYR GLN SEQRES 8 B 112 CYS GLN SER LEU HIS GLY SER GLU ALA ASP THR LEU ARG SEQRES 9 B 112 LYS VAL LEU VAL GLU VAL LEU ALA FORMUL 3 HOH *113(H2 O) HELIX 1 AA1 ASN A 68 LEU A 75 1 8 HELIX 2 AA2 GLN A 101 ALA A 105 5 5 HELIX 3 AA3 GLN B 101 ALA B 105 5 5 SHEET 1 AA1 5 THR A 21 VAL A 27 0 SHEET 2 AA1 5 GLU A 117 LEU A 129 1 O GLU A 127 N GLY A 26 SHEET 3 AA1 5 GLY A 106 HIS A 114 -1 N GLY A 106 O VAL A 126 SHEET 4 AA1 5 LYS A 48 GLN A 53 -1 N ALA A 49 O GLN A 111 SHEET 5 AA1 5 CYS A 60 SER A 65 -1 O GLN A 61 N ARG A 52 SHEET 1 AA2 3 LEU A 32 PRO A 37 0 SHEET 2 AA2 3 THR A 92 LEU A 97 -1 O ILE A 95 N VAL A 34 SHEET 3 AA2 3 ALA A 83 ASP A 87 -1 N THR A 85 O THR A 94 SHEET 1 AA3 5 THR B 21 VAL B 27 0 SHEET 2 AA3 5 GLU B 117 LEU B 129 1 O LEU B 129 N GLY B 26 SHEET 3 AA3 5 GLY B 106 HIS B 114 -1 N CYS B 110 O LEU B 121 SHEET 4 AA3 5 HIS B 47 GLN B 53 -1 N HIS B 47 O LEU B 113 SHEET 5 AA3 5 CYS B 60 SER B 65 -1 O GLN B 61 N ARG B 52 SHEET 1 AA4 3 LEU B 32 PRO B 37 0 SHEET 2 AA4 3 THR B 92 LEU B 97 -1 O ILE B 95 N VAL B 34 SHEET 3 AA4 3 ALA B 83 ASP B 87 -1 N THR B 85 O THR B 94 SSBOND 1 CYS A 36 CYS A 110 1555 1555 2.04 SSBOND 2 CYS A 51 CYS A 60 1555 1555 2.04 SSBOND 3 CYS B 36 CYS B 110 1555 1555 2.03 SSBOND 4 CYS B 51 CYS B 60 1555 1555 2.05 CRYST1 23.790 62.530 125.270 90.00 90.00 90.00 P 2 21 21 8 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 0.042034 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015992 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007983 0.00000