HEADER VIRAL PROTEIN/IMMUNE SYSTEM 03-AUG-20 7JMW TITLE CRYSTAL STRUCTURE OF SARS-COV-2 SPIKE PROTEIN RECEPTOR-BINDING DOMAIN TITLE 2 IN COMPLEX WITH CROSS-NEUTRALIZING ANTIBODY COVA1-16 FAB COMPND MOL_ID: 1; COMPND 2 MOLECULE: SPIKE PROTEIN S1; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: COVA1-16 HEAVY CHAIN; COMPND 7 CHAIN: H; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: COVA1-16 LIGHT CHAIN; COMPND 11 CHAIN: L; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS SOURCE 3 2; SOURCE 4 ORGANISM_COMMON: 2019-NCOV; SOURCE 5 ORGANISM_TAXID: 2697049; SOURCE 6 GENE: S, 2; SOURCE 7 EXPRESSION_SYSTEM: TRICHOPLUSIA NI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 7111; SOURCE 9 MOL_ID: 2; SOURCE 10 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 11 ORGANISM_TAXID: 9606; SOURCE 12 EXPRESSION_SYSTEM: MUS MUSCULUS; SOURCE 13 EXPRESSION_SYSTEM_TAXID: 10090; SOURCE 14 MOL_ID: 3; SOURCE 15 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 16 ORGANISM_TAXID: 9606; SOURCE 17 EXPRESSION_SYSTEM: MUS MUSCULUS; SOURCE 18 EXPRESSION_SYSTEM_TAXID: 10090 KEYWDS SARS-COV-2, ANTIBODY, SPIKE, CORONAVIRUS, COVID-19, IMMUNE SYSTEM, KEYWDS 2 VIRAL PROTEIN-IMMUNE SYSTEM COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR H.LIU,M.YUAN,X.ZHU,N.C.WU,I.A.WILSON REVDAT 5 18-OCT-23 7JMW 1 JRNL REVDAT 4 09-FEB-22 7JMW 1 JRNL REVDAT 3 30-DEC-20 7JMW 1 JRNL REVDAT 2 16-DEC-20 7JMW 1 JRNL REVDAT 1 14-OCT-20 7JMW 0 JRNL AUTH H.LIU,N.C.WU,M.YUAN,S.BANGARU,J.L.TORRES,T.G.CANIELS, JRNL AUTH 2 J.VAN SCHOOTEN,X.ZHU,C.D.LEE,P.J.M.BROUWER,M.J.VAN GILS, JRNL AUTH 3 R.W.SANDERS,A.B.WARD,I.A.WILSON JRNL TITL CROSS-NEUTRALIZATION OF A SARS-COV-2 ANTIBODY TO A JRNL TITL 2 FUNCTIONALLY CONSERVED SITE IS MEDIATED BY AVIDITY. JRNL REF IMMUNITY V. 53 1272 2020 JRNL REFN ISSN 1074-7613 JRNL PMID 33242394 JRNL DOI 10.1016/J.IMMUNI.2020.10.023 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH H.LIU,N.C.WU,M.YUAN,S.BANGARU,J.L.TORRES,T.G.CANIELS, REMARK 1 AUTH 2 J.VAN SCHOOTEN,X.ZHU,C.D.LEE,P.J.M.BROUWER,M.J.VAN GILS, REMARK 1 AUTH 3 R.W.SANDERS,A.B.WARD,I.A.WILSON REMARK 1 TITL CROSS-NEUTRALIZATION OF A SARS-COV-2 ANTIBODY TO A REMARK 1 TITL 2 FUNCTIONALLY CONSERVED SITE IS MEDIATED BY AVIDITY. REMARK 1 REF BIORXIV 2020 REMARK 1 REFN ISSN 2692-8205 REMARK 1 PMID 32793906 REMARK 1 DOI 10.1101/2020.08.02.233536 REMARK 1 REFERENCE 2 REMARK 1 AUTH H.LIU,N.C.WU,M.YUAN,S.BANGARU,J.L.TORRES,T.G.CANIELS, REMARK 1 AUTH 2 J.VAN SCHOOTEN,X.ZHU,C.D.LEE,P.J.M.BROUWER,M.J.VAN GILS, REMARK 1 AUTH 3 R.W.SANDERS,A.B.WARD,I.A.WILSON REMARK 1 TITL CROSS-NEUTRALIZATION OF A SARS-COV-2 ANTIBODY TO A REMARK 1 TITL 2 FUNCTIONALLY CONSERVED SITE IS MEDIATED BY AVIDITY. REMARK 1 REF IMMUNITY V. 53 1272 2020 REMARK 1 REFN ISSN 1074-7613 REMARK 1 PMID 33242394 REMARK 1 DOI 10.1016/J.IMMUNI.2020.10.023 REMARK 2 REMARK 2 RESOLUTION. 2.89 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0258 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN 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) : 2.89 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.77 REMARK 3 DATA CUTOFF (SIGMA(F)) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.4 REMARK 3 NUMBER OF REFLECTIONS : 17632 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) : 0.241 REMARK 3 R VALUE (WORKING SET) : 0.238 REMARK 3 FREE R VALUE : 0.291 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.380 REMARK 3 FREE R VALUE TEST SET COUNT : 948 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) : 2.89 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.04 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2303 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 93.84 REMARK 3 BIN R VALUE (WORKING SET) : 0.3439 REMARK 3 BIN FREE R VALUE SET COUNT : 134 REMARK 3 BIN FREE R VALUE : 0.4069 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4845 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 28 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 42.71 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 47.36 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): 0.432 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): 32.6080 -24.9838 36.0594 REMARK 3 T TENSOR REMARK 3 T11: 0.2148 T22: 0.2497 REMARK 3 T33: 0.1909 T12: -0.0136 REMARK 3 T13: 0.0452 T23: -0.0150 REMARK 3 L TENSOR REMARK 3 L11: 1.1838 L22: 2.0972 REMARK 3 L33: 0.7462 L12: -0.8918 REMARK 3 L13: 0.7994 L23: -0.8559 REMARK 3 S TENSOR REMARK 3 S11: -0.0618 S12: -0.0060 S13: -0.0211 REMARK 3 S21: 0.2381 S22: 0.0516 S23: -0.1364 REMARK 3 S31: -0.0736 S32: -0.0087 S33: 0.0335 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 7JMW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-AUG-20. REMARK 100 THE DEPOSITION ID IS D_1000251082. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-JUN-20 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.9 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL12-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9795 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17656 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.890 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.9 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.15300 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) : 2.89 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.95 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) : 0.69100 REMARK 200 FOR SHELL : 1.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.8.3 REMARK 200 STARTING MODEL: 6XC4,4IMK,2Q20 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.82 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.72 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG 3350, 0.2 M NA-IODIDE, PH 6.9, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 62.45250 REMARK 290 SMTRY3 2 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3820 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 30240 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -17.0 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 350 APPLY THE FOLLOWING TO CHAINS: H, L REMARK 350 BIOMT1 2 1.000000 0.000000 0.000000 57.40300 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 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 319 REMARK 465 VAL A 320 REMARK 465 GLN A 321 REMARK 465 PRO A 322 REMARK 465 THR A 323 REMARK 465 GLU A 324 REMARK 465 SER A 325 REMARK 465 ILE A 326 REMARK 465 VAL A 327 REMARK 465 ARG A 328 REMARK 465 PHE A 329 REMARK 465 PRO A 330 REMARK 465 ASN A 331 REMARK 465 ILE A 332 REMARK 465 THR A 333 REMARK 465 LYS A 529 REMARK 465 SER A 530 REMARK 465 THR A 531 REMARK 465 ASN A 532 REMARK 465 LEU A 533 REMARK 465 VAL A 534 REMARK 465 LYS A 535 REMARK 465 ASN A 536 REMARK 465 LYS A 537 REMARK 465 CYS A 538 REMARK 465 VAL A 539 REMARK 465 ASN A 540 REMARK 465 PHE A 541 REMARK 465 SER A 542 REMARK 465 GLY A 543 REMARK 465 HIS A 544 REMARK 465 HIS A 545 REMARK 465 HIS A 546 REMARK 465 HIS A 547 REMARK 465 HIS A 548 REMARK 465 HIS A 549 REMARK 465 SER H 128 REMARK 465 LYS H 129 REMARK 465 SER H 130 REMARK 465 THR H 131 REMARK 465 SER H 132 REMARK 465 GLY H 133 REMARK 465 HIS H 221 REMARK 465 HIS H 222 REMARK 465 CYS L 214 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 ASN A 334 CG OD1 ND2 REMARK 470 LEU A 335 CG CD1 CD2 REMARK 470 ARG A 346 CG CD NE CZ NH1 NH2 REMARK 470 VAL A 362 CG1 CG2 REMARK 470 ASP A 364 CG OD1 OD2 REMARK 470 LYS A 386 CD CE NZ REMARK 470 ASN A 394 CG OD1 ND2 REMARK 470 LYS A 444 CG CD CE NZ REMARK 470 VAL A 445 CG1 CG2 REMARK 470 LYS A 458 CG CD CE NZ REMARK 470 LYS A 462 CG CD CE NZ REMARK 470 GLU A 471 CG CD OE1 OE2 REMARK 470 SER A 477 OG REMARK 470 THR A 478 OG1 CG2 REMARK 470 ASN A 481 CG OD1 ND2 REMARK 470 VAL A 483 CG1 CG2 REMARK 470 PHE A 486 CG CD1 CD2 CE1 CE2 CZ REMARK 470 LEU A 517 CG CD1 CD2 REMARK 470 LEU A 518 CG CD1 CD2 REMARK 470 HIS A 519 CG ND1 CD2 CE1 NE2 REMARK 470 LYS A 528 CG CD CE NZ REMARK 470 GLN H 61 CG CD OE1 NE2 REMARK 470 SER H 188 OG REMARK 470 LEU H 189 CG CD1 CD2 REMARK 470 THR H 191 OG1 CG2 REMARK 470 GLN H 192 CG CD OE1 NE2 REMARK 470 ARG H 210 CD NE CZ NH1 NH2 REMARK 470 GLU H 212 CG CD OE1 OE2 REMARK 470 PRO H 213 CG CD REMARK 470 LYS H 214 CG CD CE NZ REMARK 470 SER H 215 OG REMARK 470 LYS L 107 CE NZ REMARK 470 ASP L 122 CG OD1 OD2 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 ASN A 343 31.34 -87.91 REMARK 500 ALA A 352 55.12 -115.08 REMARK 500 ASN A 360 72.18 54.07 REMARK 500 TYR A 369 34.38 -83.22 REMARK 500 PHE A 377 94.53 -162.87 REMARK 500 ASN A 422 -70.34 -136.69 REMARK 500 ALA H 16 -158.15 -96.30 REMARK 500 SER H 53 -62.93 -106.29 REMARK 500 PRO H 96 -169.23 -73.30 REMARK 500 ASP H 144 103.09 28.65 REMARK 500 THR H 160 -42.14 -133.53 REMARK 500 SER L 30 -125.53 59.24 REMARK 500 ALA L 51 -44.51 74.83 REMARK 500 SER L 76 -70.22 -52.86 REMARK 500 ALA L 84 -178.26 -172.36 REMARK 500 ASN L 138 75.79 51.36 REMARK 500 REMARK 500 REMARK: NULL DBREF 7JMW A 319 541 UNP P0DTC2 SPIKE_SARS2 319 541 DBREF 7JMW H 1 222 PDB 7JMW 7JMW 1 222 DBREF 7JMW L 1 214 PDB 7JMW 7JMW 1 214 SEQADV 7JMW SER A 542 UNP P0DTC2 EXPRESSION TAG SEQADV 7JMW GLY A 543 UNP P0DTC2 EXPRESSION TAG SEQADV 7JMW HIS A 544 UNP P0DTC2 EXPRESSION TAG SEQADV 7JMW HIS A 545 UNP P0DTC2 EXPRESSION TAG SEQADV 7JMW HIS A 546 UNP P0DTC2 EXPRESSION TAG SEQADV 7JMW HIS A 547 UNP P0DTC2 EXPRESSION TAG SEQADV 7JMW HIS A 548 UNP P0DTC2 EXPRESSION TAG SEQADV 7JMW HIS A 549 UNP P0DTC2 EXPRESSION TAG SEQRES 1 A 231 ARG VAL GLN PRO THR GLU SER ILE VAL ARG PHE PRO ASN SEQRES 2 A 231 ILE THR ASN LEU CYS PRO PHE GLY GLU VAL PHE ASN ALA SEQRES 3 A 231 THR ARG PHE ALA SER VAL TYR ALA TRP ASN ARG LYS ARG SEQRES 4 A 231 ILE SER ASN CYS VAL ALA ASP TYR SER VAL LEU TYR ASN SEQRES 5 A 231 SER ALA SER PHE SER THR PHE LYS CYS TYR GLY VAL SER SEQRES 6 A 231 PRO THR LYS LEU ASN ASP LEU CYS PHE THR ASN VAL TYR SEQRES 7 A 231 ALA ASP SER PHE VAL ILE ARG GLY ASP GLU VAL ARG GLN SEQRES 8 A 231 ILE ALA PRO GLY GLN THR GLY LYS ILE ALA ASP TYR ASN SEQRES 9 A 231 TYR LYS LEU PRO ASP ASP PHE THR GLY CYS VAL ILE ALA SEQRES 10 A 231 TRP ASN SER ASN ASN LEU ASP SER LYS VAL GLY GLY ASN SEQRES 11 A 231 TYR ASN TYR LEU TYR ARG LEU PHE ARG LYS SER ASN LEU SEQRES 12 A 231 LYS PRO PHE GLU ARG ASP ILE SER THR GLU ILE TYR GLN SEQRES 13 A 231 ALA GLY SER THR PRO CYS ASN GLY VAL GLU GLY PHE ASN SEQRES 14 A 231 CYS TYR PHE PRO LEU GLN SER TYR GLY PHE GLN PRO THR SEQRES 15 A 231 ASN GLY VAL GLY TYR GLN PRO TYR ARG VAL VAL VAL LEU SEQRES 16 A 231 SER PHE GLU LEU LEU HIS ALA PRO ALA THR VAL CYS GLY SEQRES 17 A 231 PRO LYS LYS SER THR ASN LEU VAL LYS ASN LYS CYS VAL SEQRES 18 A 231 ASN PHE SER GLY HIS HIS HIS HIS HIS HIS SEQRES 1 H 238 GLN VAL GLN LEU VAL GLN SER GLY ALA GLU VAL LYS LYS SEQRES 2 H 238 PRO GLY ALA SER VAL LYS VAL SER CYS LYS ALA SER GLY SEQRES 3 H 238 TYR THR PHE THR SER TYR TYR MET HIS TRP VAL ARG GLN SEQRES 4 H 238 ALA PRO GLY GLN GLY LEU GLU TRP MET GLY ILE ILE ASN SEQRES 5 H 238 SER SER GLY GLY SER THR SER TYR ALA GLN LYS PHE GLN SEQRES 6 H 238 GLY ARG VAL THR MET THR ARG ASP THR SER THR SER THR SEQRES 7 H 238 VAL TYR MET GLU LEU SER SER LEU ARG SER GLU ASP THR SEQRES 8 H 238 ALA VAL TYR TYR CYS ALA ARG PRO PRO ARG ASN TYR TYR SEQRES 9 H 238 ASP ARG SER GLY TYR TYR GLN ARG ALA GLU TYR PHE GLN SEQRES 10 H 238 HIS TRP GLY GLN GLY THR LEU VAL THR VAL SER SER ALA SEQRES 11 H 238 SER THR LYS GLY PRO SER VAL PHE PRO LEU ALA PRO SER SEQRES 12 H 238 SER LYS SER THR SER GLY GLY THR ALA ALA LEU GLY CYS SEQRES 13 H 238 LEU VAL LYS ASP TYR PHE PRO GLU PRO VAL THR VAL SER SEQRES 14 H 238 TRP ASN SER GLY ALA LEU THR SER GLY VAL HIS THR PHE SEQRES 15 H 238 PRO ALA VAL LEU GLN SER SER GLY LEU TYR SER LEU SER SEQRES 16 H 238 SER VAL VAL THR VAL PRO SER SER SER LEU GLY THR GLN SEQRES 17 H 238 THR TYR ILE CYS ASN VAL ASN HIS LYS PRO SER ASN THR SEQRES 18 H 238 LYS VAL ASP LYS ARG VAL GLU PRO LYS SER CYS HIS HIS SEQRES 19 H 238 HIS HIS HIS HIS SEQRES 1 L 214 ASP ILE GLN LEU THR GLN SER PRO SER SER LEU SER ALA SEQRES 2 L 214 SER VAL GLY ASP ARG VAL THR ILE THR CYS GLN ALA SER SEQRES 3 L 214 GLN ASP ILE SER ASN TYR LEU ASN TRP TYR GLN GLN ARG SEQRES 4 L 214 PRO GLY LYS ALA PRO LYS LEU LEU ILE TYR ASP ALA SER SEQRES 5 L 214 ASN LEU GLU THR GLY VAL PRO SER ARG PHE SER GLY SER SEQRES 6 L 214 GLY SER GLY THR ASP PHE THR PHE THR ILE SER SER LEU SEQRES 7 L 214 GLN PRO GLU ASP ILE ALA THR TYR TYR CYS GLN GLN TYR SEQRES 8 L 214 ASP ASN PRO PRO LEU THR PHE GLY GLY GLY THR LYS LEU SEQRES 9 L 214 GLU ILE LYS ARG THR VAL ALA ALA PRO SER VAL PHE ILE SEQRES 10 L 214 PHE PRO PRO SER ASP GLU GLN LEU LYS SER GLY THR ALA SEQRES 11 L 214 SER VAL VAL CYS LEU LEU ASN ASN PHE TYR PRO ARG GLU SEQRES 12 L 214 ALA LYS VAL GLN TRP LYS VAL ASP ASN ALA LEU GLN SER SEQRES 13 L 214 GLY ASN SER GLN GLU SER VAL THR GLU GLN ASP SER LYS SEQRES 14 L 214 ASP SER THR TYR SER LEU SER SER THR LEU THR LEU SER SEQRES 15 L 214 LYS ALA ASP TYR GLU LYS HIS LYS VAL TYR ALA CYS GLU SEQRES 16 L 214 VAL THR HIS GLN GLY LEU SER SER PRO VAL THR LYS SER SEQRES 17 L 214 PHE ASN ARG GLY GLU CYS HET NAG B 1 14 HET NAG B 2 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 4 NAG 2(C8 H15 N O6) HELIX 1 AA1 PRO A 337 ASN A 343 1 7 HELIX 2 AA2 SER A 383 ASP A 389 5 7 HELIX 3 AA3 ASP A 405 ILE A 410 5 6 HELIX 4 AA4 GLY A 416 ASN A 422 1 7 HELIX 5 AA5 SER A 438 SER A 443 1 6 HELIX 6 AA6 GLY A 502 TYR A 505 5 4 HELIX 7 AA7 THR H 28 SER H 31 5 4 HELIX 8 AA8 ARG H 83 THR H 87 5 5 HELIX 9 AA9 SER H 187 GLN H 192 1 6 HELIX 10 AB1 GLN L 79 ILE L 83 5 5 HELIX 11 AB2 SER L 121 LYS L 126 1 6 HELIX 12 AB3 LYS L 183 GLU L 187 1 5 SHEET 1 AA1 5 ASN A 354 ILE A 358 0 SHEET 2 AA1 5 ASN A 394 ARG A 403 -1 O ALA A 397 N LYS A 356 SHEET 3 AA1 5 PRO A 507 GLU A 516 -1 O TYR A 508 N ILE A 402 SHEET 4 AA1 5 GLY A 431 ASN A 437 -1 N CYS A 432 O LEU A 513 SHEET 5 AA1 5 THR A 376 TYR A 380 -1 N LYS A 378 O VAL A 433 SHEET 1 AA2 3 CYS A 361 VAL A 362 0 SHEET 2 AA2 3 VAL A 524 CYS A 525 1 O CYS A 525 N CYS A 361 SHEET 3 AA2 3 CYS A 391 PHE A 392 -1 N PHE A 392 O VAL A 524 SHEET 1 AA3 2 LEU A 452 ARG A 454 0 SHEET 2 AA3 2 LEU A 492 SER A 494 -1 O GLN A 493 N TYR A 453 SHEET 1 AA4 2 TYR A 473 GLN A 474 0 SHEET 2 AA4 2 CYS A 488 TYR A 489 -1 O TYR A 489 N TYR A 473 SHEET 1 AA5 4 GLN H 3 GLN H 6 0 SHEET 2 AA5 4 VAL H 18 SER H 25 -1 O LYS H 23 N VAL H 5 SHEET 3 AA5 4 THR H 77 LEU H 82 -1 O MET H 80 N VAL H 20 SHEET 4 AA5 4 VAL H 67 ASP H 72 -1 N THR H 68 O GLU H 81 SHEET 1 AA6 6 GLU H 10 LYS H 12 0 SHEET 2 AA6 6 THR H 107 VAL H 111 1 O LEU H 108 N GLU H 10 SHEET 3 AA6 6 ALA H 88 ARG H 94 -1 N TYR H 90 O THR H 107 SHEET 4 AA6 6 TYR H 33 GLN H 39 -1 N VAL H 37 O TYR H 91 SHEET 5 AA6 6 LEU H 45 ASN H 52 -1 O GLU H 46 N ARG H 38 SHEET 6 AA6 6 THR H 57 TYR H 59 -1 O SER H 58 N ILE H 50 SHEET 1 AA7 4 GLU H 10 LYS H 12 0 SHEET 2 AA7 4 THR H 107 VAL H 111 1 O LEU H 108 N GLU H 10 SHEET 3 AA7 4 ALA H 88 ARG H 94 -1 N TYR H 90 O THR H 107 SHEET 4 AA7 4 HIS H 102 TRP H 103 -1 O HIS H 102 N ARG H 94 SHEET 1 AA8 2 TYR H 99 TYR H 100 0 SHEET 2 AA8 2 TYR H 100F GLN H 100G-1 O GLN H 100G N TYR H 99 SHEET 1 AA9 4 SER H 120 LEU H 124 0 SHEET 2 AA9 4 THR H 135 TYR H 145 -1 O LEU H 141 N PHE H 122 SHEET 3 AA9 4 TYR H 176 PRO H 185 -1 O TYR H 176 N TYR H 145 SHEET 4 AA9 4 VAL H 163 THR H 165 -1 N HIS H 164 O VAL H 181 SHEET 1 AB1 4 SER H 120 LEU H 124 0 SHEET 2 AB1 4 THR H 135 TYR H 145 -1 O LEU H 141 N PHE H 122 SHEET 3 AB1 4 TYR H 176 PRO H 185 -1 O TYR H 176 N TYR H 145 SHEET 4 AB1 4 VAL H 169 LEU H 170 -1 N VAL H 169 O SER H 177 SHEET 1 AB2 3 THR H 151 TRP H 154 0 SHEET 2 AB2 3 TYR H 194 HIS H 200 -1 O ASN H 197 N SER H 153 SHEET 3 AB2 3 THR H 205 VAL H 211 -1 O THR H 205 N HIS H 200 SHEET 1 AB3 4 LEU L 4 SER L 7 0 SHEET 2 AB3 4 VAL L 19 ALA L 25 -1 O THR L 22 N SER L 7 SHEET 3 AB3 4 ASP L 70 ILE L 75 -1 O PHE L 73 N ILE L 21 SHEET 4 AB3 4 PHE L 62 SER L 67 -1 N SER L 65 O THR L 72 SHEET 1 AB4 6 SER L 10 SER L 14 0 SHEET 2 AB4 6 THR L 102 LYS L 107 1 O LYS L 107 N ALA L 13 SHEET 3 AB4 6 THR L 85 GLN L 90 -1 N TYR L 86 O THR L 102 SHEET 4 AB4 6 LEU L 33 GLN L 38 -1 N GLN L 38 O THR L 85 SHEET 5 AB4 6 LYS L 45 TYR L 49 -1 O ILE L 48 N TRP L 35 SHEET 6 AB4 6 ASN L 53 LEU L 54 -1 O ASN L 53 N TYR L 49 SHEET 1 AB5 4 SER L 10 SER L 14 0 SHEET 2 AB5 4 THR L 102 LYS L 107 1 O LYS L 107 N ALA L 13 SHEET 3 AB5 4 THR L 85 GLN L 90 -1 N TYR L 86 O THR L 102 SHEET 4 AB5 4 THR L 97 PHE L 98 -1 O THR L 97 N GLN L 90 SHEET 1 AB6 4 SER L 114 PHE L 118 0 SHEET 2 AB6 4 THR L 129 PHE L 139 -1 O LEU L 135 N PHE L 116 SHEET 3 AB6 4 TYR L 173 SER L 182 -1 O LEU L 179 N VAL L 132 SHEET 4 AB6 4 SER L 159 VAL L 163 -1 N SER L 162 O SER L 176 SHEET 1 AB7 4 ALA L 153 LEU L 154 0 SHEET 2 AB7 4 LYS L 145 VAL L 150 -1 N VAL L 150 O ALA L 153 SHEET 3 AB7 4 VAL L 191 THR L 197 -1 O GLU L 195 N GLN L 147 SHEET 4 AB7 4 VAL L 205 ASN L 210 -1 O VAL L 205 N VAL L 196 SSBOND 1 CYS A 336 CYS A 361 1555 1555 2.00 SSBOND 2 CYS A 379 CYS A 432 1555 1555 2.03 SSBOND 3 CYS A 391 CYS A 525 1555 1555 2.02 SSBOND 4 CYS A 480 CYS A 488 1555 1555 2.02 SSBOND 5 CYS H 22 CYS H 92 1555 1555 2.03 SSBOND 6 CYS H 140 CYS H 196 1555 1555 2.03 SSBOND 7 CYS L 23 CYS L 88 1555 1555 2.04 SSBOND 8 CYS L 134 CYS L 194 1555 1555 2.03 LINK ND2 ASN A 343 C1 NAG B 1 1555 1555 1.45 LINK O4 NAG B 1 C1 NAG B 2 1555 1555 1.37 CISPEP 1 PHE H 146 PRO H 147 0 -3.34 CISPEP 2 GLU H 148 PRO H 149 0 -1.93 CISPEP 3 SER L 7 PRO L 8 0 2.02 CISPEP 4 PRO L 94 PRO L 95 0 -2.85 CISPEP 5 TYR L 140 PRO L 141 0 3.79 CRYST1 57.403 124.905 57.614 90.00 96.10 90.00 P 1 21 1 2 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 0.017421 0.000000 0.001862 0.00000 SCALE2 0.000000 0.008006 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017456 0.00000