HEADER IMMUNE SYSTEM 04-MAY-20 6YYE TITLE TREM2 EXTRACELLULAR DOMAIN (19-131) IN COMPLEX WITH SINGLE-CHAIN TITLE 2 VARIABLE FRAGMENT (SCFV-2) 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; COMPND 6 OTHER_DETAILS: COMPND 7 MHNTTVFQGVAGQSLQVSCPYDSMKHWGRRKAWCRQLGEKGPCQRVVSTHNLWLLSFLRRWNGSTAITD COMPND 8 DTLGGTLTITLRNLQPHDAGLYQCQSLHGSEADTLRKVLVEVLAD; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: TREM2 SINGLE CHAIN VARIABLE 2; COMPND 11 CHAIN: C, D; COMPND 12 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: HOMO SAPIENS; SOURCE 7 EXPRESSION_SYSTEM_COMMON: HUMAN; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 9 MOL_ID: 2; SOURCE 10 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 11 ORGANISM_COMMON: HUMAN; SOURCE 12 ORGANISM_TAXID: 9606; SOURCE 13 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 14 EXPRESSION_SYSTEM_COMMON: FALL ARMYWORM; SOURCE 15 EXPRESSION_SYSTEM_TAXID: 7108 KEYWDS SCFV, COMPLEX, RECEPTOR, ALZHEIMER'S, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR A.SZYKOWSKA,C.PREGER,T.KROJER,S.M.M.MUKHOPADHYAY,G.MCKINLEY, AUTHOR 2 S.GRASLUND,E.WIGREN,H.PERSSON,F.VON DELFT,C.H.ARROWSMITH,A.EDWARDS, AUTHOR 3 C.BOUNTRA,E.DI DANIEL,N.BURGESS-BROWN,A.BULLOCK REVDAT 6 23-OCT-24 6YYE 1 REMARK REVDAT 5 31-JAN-24 6YYE 1 REMARK REVDAT 4 21-DEC-22 6YYE 1 JRNL REMARK REVDAT 3 17-NOV-21 6YYE 1 JRNL REMARK REVDAT 2 21-JUL-21 6YYE 1 JRNL REVDAT 1 17-FEB-21 6YYE 0 JRNL AUTH A.SZYKOWSKA,Y.CHEN,T.B.SMITH,C.PREGER,J.YANG,D.QIAN, JRNL AUTH 2 S.M.MUKHOPADHYAY,E.WIGREN,S.J.NEAME,S.GRASLUND,H.PERSSON, JRNL AUTH 3 P.J.ATKINSON,E.DI DANIEL,E.MEAD,J.WANG,J.B.DAVIS, JRNL AUTH 4 N.A.BURGESS-BROWN,A.N.BULLOCK JRNL TITL SELECTION AND STRUCTURAL CHARACTERIZATION OF ANTI-TREM2 JRNL TITL 2 SCFVS THAT REDUCE LEVELS OF SHED ECTODOMAIN. JRNL REF STRUCTURE V. 29 1241 2021 JRNL REFN ISSN 0969-2126 JRNL PMID 34233201 JRNL DOI 10.1016/J.STR.2021.06.010 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH A.SZYKOWSKA,Y.CHEN,T.B.SMITH,C.PREGER,J.YANG,D.QIAN, REMARK 1 AUTH 2 S.MUKHOPADHYAY,E.WIGREN,S.J.NEAME,S.GRASLUND,H.PERSSON, REMARK 1 AUTH 3 P.J.ATKINSON,E.DI DANIEL,E.MEAD,J.WANG,J.B.DAVIS, REMARK 1 AUTH 4 N.A.BURGESS-BROWN,A.N.BULLOCK REMARK 1 TITL SELECTION AND STRUCTURAL CHARACTERISATION OF ANTI-TREM2 REMARK 1 TITL 2 SCFVS THAT REDUCE LEVELS OF SHED ECTODOMAIN REMARK 1 REF BIORXIV 2021 REMARK 1 REFN ISSN 2692-8205 REMARK 1 DOI 10.1101/2021.02.07.430123 REMARK 2 REMARK 2 RESOLUTION. 3.36 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.17.1_3660 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.36 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 110.07 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 68.9 REMARK 3 NUMBER OF REFLECTIONS : 16272 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.300 REMARK 3 R VALUE (WORKING SET) : 0.299 REMARK 3 FREE R VALUE : 0.327 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.760 REMARK 3 FREE R VALUE TEST SET COUNT : 774 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1112.5000 - 6.1000 1.00 3910 183 0.2828 0.3111 REMARK 3 2 6.1000 - 4.8400 1.00 3747 196 0.2796 0.3240 REMARK 3 3 4.8400 - 4.2300 1.00 3708 188 0.2931 0.3128 REMARK 3 4 4.2300 - 3.8400 0.67 2497 123 0.3489 0.3606 REMARK 3 5 3.8400 - 3.5700 0.35 1283 69 0.3776 0.4053 REMARK 3 6 3.5700 - 3.3600 0.10 353 15 0.4010 0.4107 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL 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) : 0.593 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 36.828 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 79.88 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 91.39 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 : 0.003 5166 REMARK 3 ANGLE : 0.535 7037 REMARK 3 CHIRALITY : 0.041 785 REMARK 3 PLANARITY : 0.005 901 REMARK 3 DIHEDRAL : 12.840 1736 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): -26.1951 -30.8135 -57.1322 REMARK 3 T TENSOR REMARK 3 T11: 0.9478 T22: 0.5510 REMARK 3 T33: 0.6182 T12: -0.2143 REMARK 3 T13: -0.1930 T23: -0.0618 REMARK 3 L TENSOR REMARK 3 L11: 2.0342 L22: 1.4748 REMARK 3 L33: 3.8823 L12: -1.2204 REMARK 3 L13: -1.4149 L23: 1.8125 REMARK 3 S TENSOR REMARK 3 S11: 0.4206 S12: -0.1139 S13: 0.1935 REMARK 3 S21: 0.1008 S22: 0.1375 S23: -0.3548 REMARK 3 S31: 0.4107 S32: -0.0261 S33: -0.4901 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 6YYE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 04-MAY-20. REMARK 100 THE DEPOSITION ID IS D_1292107876. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-APR-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I24 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 : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX-300 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : STARANISO REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16278 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.356 REMARK 200 RESOLUTION RANGE LOW (A) : 110.070 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.0 REMARK 200 DATA REDUNDANCY : 13.40 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.36 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.68 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 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: PHENIX REMARK 200 STARTING MODEL: 6CY6 REMARK 200 REMARK 200 REMARK: LARGE CUBES REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 77.18 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 5.39 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.015M NICKEL CHLORIDE,0.1M TRIS PH REMARK 280 8.5,2.2M AMMONIUM ACETATE, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 2 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,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-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 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 56.97100 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 63.10050 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 112.50350 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 56.97100 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 63.10050 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 112.50350 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 56.97100 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 63.10050 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 112.50350 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 56.97100 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 63.10050 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 112.50350 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1650 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15380 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -6.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1260 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15450 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -8.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, 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 GLU A 16 REMARK 465 THR A 17 REMARK 465 GLY A 18 REMARK 465 HIS A 19 REMARK 465 GLU B 16 REMARK 465 THR B 17 REMARK 465 LEU B 69 REMARK 465 TRP B 70 REMARK 465 LEU B 71 REMARK 465 LEU B 72 REMARK 465 SER B 73 REMARK 465 SER C 1 REMARK 465 MET C 2 REMARK 465 GLY C 125 REMARK 465 GLY C 126 REMARK 465 GLY C 127 REMARK 465 GLY C 128 REMARK 465 SER C 129 REMARK 465 GLY C 130 REMARK 465 GLY C 131 REMARK 465 GLY C 132 REMARK 465 GLY C 133 REMARK 465 SER C 134 REMARK 465 GLY C 135 REMARK 465 GLY C 136 REMARK 465 GLY C 137 REMARK 465 GLY C 138 REMARK 465 SER D 1 REMARK 465 GLY D 125 REMARK 465 GLY D 126 REMARK 465 GLY D 127 REMARK 465 GLY D 128 REMARK 465 SER D 129 REMARK 465 GLY D 130 REMARK 465 GLY D 131 REMARK 465 GLY D 132 REMARK 465 GLY D 133 REMARK 465 SER D 134 REMARK 465 GLY D 135 REMARK 465 GLY D 136 REMARK 465 GLY D 137 REMARK 465 GLY D 138 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 42 CE NZ REMARK 470 TRP A 44 CG CD1 CD2 NE1 CE2 CE3 CZ2 REMARK 470 TRP A 44 CZ3 CH2 REMARK 470 ARG A 46 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 48 CG CD CE NZ REMARK 470 GLU A 56 CD OE1 OE2 REMARK 470 LYS A 57 CG CD CE NZ REMARK 470 ARG A 62 CG CD NE CZ NH1 NH2 REMARK 470 LEU A 71 CG CD1 CD2 REMARK 470 SER A 73 OG REMARK 470 ARG A 76 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 77 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 98 CZ NH1 NH2 REMARK 470 LEU A 100 CG CD1 CD2 REMARK 470 SER A 116 OG REMARK 470 ASN B 20 CG OD1 ND2 REMARK 470 GLN B 25 CG CD OE1 NE2 REMARK 470 GLN B 30 CG CD OE1 NE2 REMARK 470 GLN B 33 CG CD OE1 NE2 REMARK 470 HIS B 43 CG ND1 CD2 CE1 NE2 REMARK 470 TRP B 44 CG CD1 CD2 NE1 CE2 CE3 CZ2 REMARK 470 TRP B 44 CZ3 CH2 REMARK 470 ARG B 46 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 48 CG CD CE NZ REMARK 470 GLU B 56 CG CD OE1 OE2 REMARK 470 LYS B 57 CG CD CE NZ REMARK 470 GLN B 61 CD OE1 NE2 REMARK 470 ARG B 62 CG CD NE CZ NH1 NH2 REMARK 470 HIS B 67 CG ND1 CD2 CE1 NE2 REMARK 470 ARG B 76 CG CD NE CZ NH1 NH2 REMARK 470 ARG B 77 CG CD NE CZ NH1 NH2 REMARK 470 ASP B 86 CG OD1 OD2 REMARK 470 LEU B 89 CG CD1 CD2 REMARK 470 LEU B 93 CG CD1 CD2 REMARK 470 ARG B 98 CG CD NE CZ NH1 NH2 REMARK 470 LEU B 113 CG CD1 CD2 REMARK 470 SER B 116 OG REMARK 470 ASP B 119 CG OD1 OD2 REMARK 470 LYS B 123 CG CD CE NZ REMARK 470 LEU B 125 CG CD1 CD2 REMARK 470 GLN C 15 OE1 NE2 REMARK 470 GLU C 48 CG CD OE1 OE2 REMARK 470 SER C 58 OG REMARK 470 LYS C 67 CG CD CE NZ REMARK 470 ARG C 89 NH1 NH2 REMARK 470 GLN C 116 CD OE1 NE2 REMARK 470 LEU C 150 CG CD1 CD2 REMARK 470 SER C 169 OG REMARK 470 LYS C 178 CG CD CE NZ REMARK 470 LYS C 181 CD CE NZ REMARK 470 LYS C 184 CG CD CE NZ REMARK 470 LYS C 243 CG CD CE NZ REMARK 470 LYS C 247 NZ REMARK 470 VAL D 14 CG1 CG2 REMARK 470 GLN D 15 CG CD OE1 NE2 REMARK 470 LYS D 45 CE NZ REMARK 470 LYS D 67 CG CD CE NZ REMARK 470 ILE D 141 CG1 CG2 CD1 REMARK 470 GLN D 142 CG CD OE1 NE2 REMARK 470 ARG D 163 NH1 NH2 REMARK 470 GLN D 166 CG CD OE1 NE2 REMARK 470 ILE D 168 CG1 CG2 CD1 REMARK 470 LYS D 181 CG CD CE NZ REMARK 470 LYS D 184 CG CD CE NZ REMARK 470 LYS D 243 CG CD CE NZ REMARK 470 LYS D 247 NZ 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 ASP B 39 99.01 -59.65 REMARK 500 SER B 81 35.02 -90.49 REMARK 500 ASP B 87 94.05 -66.94 REMARK 500 ASN B 99 76.55 52.35 REMARK 500 GLU C 48 119.76 -162.37 REMARK 500 VAL C 50 -61.46 -101.51 REMARK 500 SER C 58 37.46 -91.37 REMARK 500 SER C 59 105.10 -163.31 REMARK 500 TYR C 104 91.04 -56.85 REMARK 500 SER C 169 -108.64 60.04 REMARK 500 TYR C 171 57.90 -104.27 REMARK 500 LEU C 186 -63.67 -99.49 REMARK 500 ALA C 190 -44.57 63.67 REMARK 500 SER C 216 82.17 54.54 REMARK 500 ALA C 223 -171.06 -174.29 REMARK 500 VAL C 232 -62.92 -93.52 REMARK 500 PRO C 235 76.76 -65.28 REMARK 500 PHE C 236 66.62 -69.27 REMARK 500 VAL D 50 -63.38 -91.94 REMARK 500 TYR D 104 92.08 -55.44 REMARK 500 ILE D 111 106.33 -59.41 REMARK 500 SER D 169 -107.29 51.53 REMARK 500 LEU D 186 -76.85 -97.13 REMARK 500 ALA D 190 -48.65 63.73 REMARK 500 SER D 216 70.76 52.22 REMARK 500 VAL D 232 -85.06 -93.06 REMARK 500 PRO D 235 75.98 -64.88 REMARK 500 PHE D 236 74.07 -68.90 REMARK 500 REMARK 500 REMARK: NULL DBREF 6YYE A 19 131 UNP Q9NZC2 TREM2_HUMAN 19 131 DBREF 6YYE B 19 131 UNP Q9NZC2 TREM2_HUMAN 19 131 DBREF 6YYE C 1 247 PDB 6YYE 6YYE 1 247 DBREF 6YYE D 1 247 PDB 6YYE 6YYE 1 247 SEQADV 6YYE GLU A 16 UNP Q9NZC2 EXPRESSION TAG SEQADV 6YYE THR A 17 UNP Q9NZC2 EXPRESSION TAG SEQADV 6YYE GLY A 18 UNP Q9NZC2 EXPRESSION TAG SEQADV 6YYE GLU B 16 UNP Q9NZC2 EXPRESSION TAG SEQADV 6YYE THR B 17 UNP Q9NZC2 EXPRESSION TAG SEQADV 6YYE GLY B 18 UNP Q9NZC2 EXPRESSION TAG SEQRES 1 A 116 GLU THR GLY HIS ASN THR THR VAL PHE GLN GLY VAL ALA SEQRES 2 A 116 GLY GLN SER LEU GLN VAL SER CYS PRO TYR ASP SER MET SEQRES 3 A 116 LYS HIS TRP GLY ARG ARG LYS ALA TRP CYS ARG GLN LEU SEQRES 4 A 116 GLY GLU LYS GLY PRO CYS GLN ARG VAL VAL SER THR HIS SEQRES 5 A 116 ASN LEU TRP LEU LEU SER PHE LEU ARG ARG TRP ASN GLY SEQRES 6 A 116 SER THR ALA ILE THR ASP ASP THR LEU GLY GLY THR LEU SEQRES 7 A 116 THR ILE THR LEU ARG ASN LEU GLN PRO HIS ASP ALA GLY SEQRES 8 A 116 LEU TYR GLN CYS GLN SER LEU HIS GLY SER GLU ALA ASP SEQRES 9 A 116 THR LEU ARG LYS VAL LEU VAL GLU VAL LEU ALA ASP SEQRES 1 B 116 GLU THR GLY HIS ASN THR THR VAL PHE GLN GLY VAL ALA SEQRES 2 B 116 GLY GLN SER LEU GLN VAL SER CYS PRO TYR ASP SER MET SEQRES 3 B 116 LYS HIS TRP GLY ARG ARG LYS ALA TRP CYS ARG GLN LEU SEQRES 4 B 116 GLY GLU LYS GLY PRO CYS GLN ARG VAL VAL SER THR HIS SEQRES 5 B 116 ASN LEU TRP LEU LEU SER PHE LEU ARG ARG TRP ASN GLY SEQRES 6 B 116 SER THR ALA ILE THR ASP ASP THR LEU GLY GLY THR LEU SEQRES 7 B 116 THR ILE THR LEU ARG ASN LEU GLN PRO HIS ASP ALA GLY SEQRES 8 B 116 LEU TYR GLN CYS GLN SER LEU HIS GLY SER GLU ALA ASP SEQRES 9 B 116 THR LEU ARG LYS VAL LEU VAL GLU VAL LEU ALA ASP SEQRES 1 C 247 SER MET GLU VAL GLN LEU LEU GLU SER GLY GLY GLY LEU SEQRES 2 C 247 VAL GLN PRO GLY GLY SER LEU ARG LEU SER CYS ALA ALA SEQRES 3 C 247 SER GLY PHE THR PHE TYR SER SER TYR MET GLY TRP VAL SEQRES 4 C 247 ARG GLN ALA PRO GLY LYS GLY LEU GLU TRP VAL SER TYR SEQRES 5 C 247 ILE SER SER SER GLY SER SER THR TYR TYR ALA ASP SER SEQRES 6 C 247 VAL LYS GLY ARG PHE THR ILE SER ARG ASP ASN SER LYS SEQRES 7 C 247 ASN THR LEU TYR LEU GLN MET ASN SER LEU ARG ALA GLU SEQRES 8 C 247 ASP THR ALA VAL TYR TYR CYS ALA ARG VAL GLY GLY TYR SEQRES 9 C 247 TYR SER TRP GLY ASN GLY ILE ASP TYR TRP GLY GLN GLY SEQRES 10 C 247 THR LEU VAL THR VAL SER SER GLY GLY GLY GLY SER GLY SEQRES 11 C 247 GLY GLY GLY SER GLY GLY GLY GLY SER ASP ILE GLN MET SEQRES 12 C 247 THR GLN SER PRO SER SER LEU SER ALA SER VAL GLY ASP SEQRES 13 C 247 ARG VAL THR ILE THR CYS ARG ALA SER GLN SER ILE SER SEQRES 14 C 247 SER TYR LEU ASN TRP TYR GLN GLN LYS PRO GLY LYS ALA SEQRES 15 C 247 PRO LYS LEU LEU ILE TYR ALA ALA SER SER LEU GLN SER SEQRES 16 C 247 GLY VAL PRO SER ARG PHE SER GLY SER GLY SER GLY THR SEQRES 17 C 247 ASP PHE THR LEU THR ILE SER SER LEU GLN PRO GLU ASP SEQRES 18 C 247 PHE ALA THR TYR TYR CYS GLN GLN TYR GLY VAL TYR TYR SEQRES 19 C 247 PRO PHE THR PHE GLY GLN GLY THR LYS LEU GLU ILE LYS SEQRES 1 D 247 SER MET GLU VAL GLN LEU LEU GLU SER GLY GLY GLY LEU SEQRES 2 D 247 VAL GLN PRO GLY GLY SER LEU ARG LEU SER CYS ALA ALA SEQRES 3 D 247 SER GLY PHE THR PHE TYR SER SER TYR MET GLY TRP VAL SEQRES 4 D 247 ARG GLN ALA PRO GLY LYS GLY LEU GLU TRP VAL SER TYR SEQRES 5 D 247 ILE SER SER SER GLY SER SER THR TYR TYR ALA ASP SER SEQRES 6 D 247 VAL LYS GLY ARG PHE THR ILE SER ARG ASP ASN SER LYS SEQRES 7 D 247 ASN THR LEU TYR LEU GLN MET ASN SER LEU ARG ALA GLU SEQRES 8 D 247 ASP THR ALA VAL TYR TYR CYS ALA ARG VAL GLY GLY TYR SEQRES 9 D 247 TYR SER TRP GLY ASN GLY ILE ASP TYR TRP GLY GLN GLY SEQRES 10 D 247 THR LEU VAL THR VAL SER SER GLY GLY GLY GLY SER GLY SEQRES 11 D 247 GLY GLY GLY SER GLY GLY GLY GLY SER ASP ILE GLN MET SEQRES 12 D 247 THR GLN SER PRO SER SER LEU SER ALA SER VAL GLY ASP SEQRES 13 D 247 ARG VAL THR ILE THR CYS ARG ALA SER GLN SER ILE SER SEQRES 14 D 247 SER TYR LEU ASN TRP TYR GLN GLN LYS PRO GLY LYS ALA SEQRES 15 D 247 PRO LYS LEU LEU ILE TYR ALA ALA SER SER LEU GLN SER SEQRES 16 D 247 GLY VAL PRO SER ARG PHE SER GLY SER GLY SER GLY THR SEQRES 17 D 247 ASP PHE THR LEU THR ILE SER SER LEU GLN PRO GLU ASP SEQRES 18 D 247 PHE ALA THR TYR TYR CYS GLN GLN TYR GLY VAL TYR TYR SEQRES 19 D 247 PRO PHE THR PHE GLY GLN GLY THR LYS LEU GLU ILE LYS HET NAG A 201 14 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETSYN NAG N-ACETYL-BETA-D-GLUCOSAMINE; 2-ACETAMIDO-2-DEOXY-BETA- HETSYN 2 NAG D-GLUCOSE; 2-ACETAMIDO-2-DEOXY-D-GLUCOSE; 2-ACETAMIDO- HETSYN 3 NAG 2-DEOXY-GLUCOSE; N-ACETYL-D-GLUCOSAMINE FORMUL 5 NAG C8 H15 N O6 HELIX 1 AA1 TRP A 70 LEU A 75 5 6 HELIX 2 AA2 GLN A 101 ALA A 105 5 5 HELIX 3 AA3 GLN B 101 ALA B 105 5 5 HELIX 4 AA4 ARG C 89 THR C 93 5 5 HELIX 5 AA5 GLN C 218 PHE C 222 5 5 HELIX 6 AA6 ARG D 89 THR D 93 5 5 HELIX 7 AA7 GLN D 218 PHE D 222 5 5 SHEET 1 AA1 5 THR A 22 VAL A 27 0 SHEET 2 AA1 5 GLU A 117 LEU A 129 1 O LEU A 125 N PHE A 24 SHEET 3 AA1 5 GLY A 106 HIS A 114 -1 N GLY A 106 O VAL A 126 SHEET 4 AA1 5 ARG A 47 GLN A 53 -1 N ARG A 47 O LEU A 113 SHEET 5 AA1 5 CYS A 60 SER A 65 -1 O GLN A 61 N ARG A 52 SHEET 1 AA2 4 LEU A 32 PRO A 37 0 SHEET 2 AA2 4 THR A 92 LEU A 97 -1 O LEU A 93 N CYS A 36 SHEET 3 AA2 4 THR A 82 ASP A 87 -1 N THR A 85 O THR A 94 SHEET 4 AA2 4 ARG A 77 ASN A 79 -1 N ASN A 79 O THR A 82 SHEET 1 AA3 5 VAL B 23 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 TYR B 108 O VAL B 124 SHEET 4 AA3 5 LYS B 48 GLN B 53 -1 N ALA B 49 O GLN B 111 SHEET 5 AA3 5 CYS B 60 SER B 65 -1 O VAL B 64 N TRP B 50 SHEET 1 AA4 4 LEU B 32 PRO B 37 0 SHEET 2 AA4 4 THR B 92 LEU B 97 -1 O LEU B 93 N CYS B 36 SHEET 3 AA4 4 THR B 82 ASP B 87 -1 N ALA B 83 O THR B 96 SHEET 4 AA4 4 ARG B 77 TRP B 78 -1 N ARG B 77 O ILE B 84 SHEET 1 AA5 4 GLN C 5 SER C 9 0 SHEET 2 AA5 4 LEU C 20 SER C 27 -1 O ALA C 25 N LEU C 7 SHEET 3 AA5 4 THR C 80 MET C 85 -1 O MET C 85 N LEU C 20 SHEET 4 AA5 4 PHE C 70 ASP C 75 -1 N THR C 71 O GLN C 84 SHEET 1 AA6 6 GLY C 12 LEU C 13 0 SHEET 2 AA6 6 THR C 118 THR C 121 1 O THR C 121 N GLY C 12 SHEET 3 AA6 6 ALA C 94 ARG C 100 -1 N TYR C 96 O THR C 118 SHEET 4 AA6 6 MET C 36 GLN C 41 -1 N GLN C 41 O VAL C 95 SHEET 5 AA6 6 LEU C 47 ILE C 53 -1 O GLU C 48 N ARG C 40 SHEET 6 AA6 6 THR C 60 TYR C 62 -1 O TYR C 61 N TYR C 52 SHEET 1 AA7 4 MET C 143 SER C 146 0 SHEET 2 AA7 4 VAL C 158 ALA C 164 -1 O THR C 161 N SER C 146 SHEET 3 AA7 4 ASP C 209 ILE C 214 -1 O ILE C 214 N VAL C 158 SHEET 4 AA7 4 PHE C 201 SER C 206 -1 N SER C 202 O THR C 213 SHEET 1 AA8 6 SER C 149 ALA C 152 0 SHEET 2 AA8 6 THR C 242 ILE C 246 1 O GLU C 245 N LEU C 150 SHEET 3 AA8 6 ALA C 223 GLN C 229 -1 N ALA C 223 O LEU C 244 SHEET 4 AA8 6 LEU C 172 GLN C 177 -1 N GLN C 177 O THR C 224 SHEET 5 AA8 6 LEU C 185 TYR C 188 -1 O LEU C 186 N TRP C 174 SHEET 6 AA8 6 SER C 192 LEU C 193 -1 O SER C 192 N TYR C 188 SHEET 1 AA9 4 GLN D 5 SER D 9 0 SHEET 2 AA9 4 LEU D 20 SER D 27 -1 O ALA D 25 N LEU D 7 SHEET 3 AA9 4 THR D 80 MET D 85 -1 O MET D 85 N LEU D 20 SHEET 4 AA9 4 PHE D 70 ASP D 75 -1 N THR D 71 O GLN D 84 SHEET 1 AB1 6 GLY D 12 VAL D 14 0 SHEET 2 AB1 6 THR D 118 VAL D 122 1 O THR D 121 N GLY D 12 SHEET 3 AB1 6 ALA D 94 ARG D 100 -1 N TYR D 96 O THR D 118 SHEET 4 AB1 6 MET D 36 GLN D 41 -1 N GLN D 41 O VAL D 95 SHEET 5 AB1 6 LEU D 47 ILE D 53 -1 O ILE D 53 N MET D 36 SHEET 6 AB1 6 THR D 60 TYR D 62 -1 O TYR D 61 N TYR D 52 SHEET 1 AB2 4 MET D 143 SER D 146 0 SHEET 2 AB2 4 VAL D 158 ALA D 164 -1 O THR D 161 N SER D 146 SHEET 3 AB2 4 ASP D 209 ILE D 214 -1 O LEU D 212 N ILE D 160 SHEET 4 AB2 4 PHE D 201 SER D 206 -1 N SER D 202 O THR D 213 SHEET 1 AB3 6 SER D 149 ALA D 152 0 SHEET 2 AB3 6 THR D 242 ILE D 246 1 O GLU D 245 N ALA D 152 SHEET 3 AB3 6 THR D 224 GLN D 229 -1 N TYR D 225 O THR D 242 SHEET 4 AB3 6 LEU D 172 GLN D 177 -1 N GLN D 177 O THR D 224 SHEET 5 AB3 6 PRO D 183 TYR D 188 -1 O LEU D 186 N TRP D 174 SHEET 6 AB3 6 SER D 192 LEU D 193 -1 O SER D 192 N TYR D 188 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 2.04 SSBOND 4 CYS B 51 CYS B 60 1555 1555 2.03 SSBOND 5 CYS C 24 CYS C 98 1555 1555 2.03 SSBOND 6 CYS C 162 CYS C 227 1555 1555 2.04 SSBOND 7 CYS D 24 CYS D 98 1555 1555 2.03 SSBOND 8 CYS D 162 CYS D 227 1555 1555 2.04 LINK ND2 ASN A 79 C1 NAG A 201 1555 1555 1.44 CISPEP 1 SER C 146 PRO C 147 0 -3.46 CISPEP 2 SER D 146 PRO D 147 0 -3.02 CRYST1 113.942 126.201 225.007 90.00 90.00 90.00 I 2 2 2 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 0.008776 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007924 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004444 0.00000