HEADER IMMUNE SYSTEM 27-MAY-21 7N1E TITLE SARS-COV-2 RLQ PEPTIDE-SPECIFIC TCR PRLQ3 BINDS TO RLQ-HLA-A2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: MHC CLASS I ANTIGEN, A-2 ALPHA CHAIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: BETA-2-MICROGLOBULIN; COMPND 7 CHAIN: B; COMPND 8 FRAGMENT: UNP RESIDUES 21-119; COMPND 9 ENGINEERED: YES; COMPND 10 MOL_ID: 3; COMPND 11 MOLECULE: SPIKE PROTEIN S2; COMPND 12 CHAIN: C; COMPND 13 ENGINEERED: YES; COMPND 14 MOL_ID: 4; COMPND 15 MOLECULE: PRLQ3 T CELL RECEPTOR ALPHA CHAIN; COMPND 16 CHAIN: D; COMPND 17 ENGINEERED: YES; COMPND 18 MOL_ID: 5; COMPND 19 MOLECULE: PRLQ3 T CELL RECEPTOR BETA CHAIN; COMPND 20 CHAIN: E; COMPND 21 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: HLA-A; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 10 ORGANISM_COMMON: HUMAN; SOURCE 11 ORGANISM_TAXID: 9606; SOURCE 12 GENE: B2M, CDABP0092, HDCMA22P; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 14 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 15 MOL_ID: 3; SOURCE 16 SYNTHETIC: YES; SOURCE 17 ORGANISM_SCIENTIFIC: SEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS SOURCE 18 2; SOURCE 19 ORGANISM_COMMON: 2019-NCOV, SARS-COV-2; SOURCE 20 ORGANISM_TAXID: 2697049; SOURCE 21 MOL_ID: 4; SOURCE 22 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 23 ORGANISM_COMMON: HUMAN; SOURCE 24 ORGANISM_TAXID: 9606; SOURCE 25 GENE: TCR ALPHA; SOURCE 26 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 27 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 28 MOL_ID: 5; SOURCE 29 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 30 ORGANISM_COMMON: HUMAN; SOURCE 31 ORGANISM_TAXID: 9606; SOURCE 32 GENE: TCR BETA; SOURCE 33 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 34 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS TCR-PMHC, SARS-COV-2, SPIKE, RLQ, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR D.WU,R.A.MARIUZZA REVDAT 4 18-OCT-23 7N1E 1 JRNL REVDAT 3 02-FEB-22 7N1E 1 JRNL REVDAT 2 18-AUG-21 7N1E 1 JRNL REMARK REVDAT 1 28-JUL-21 7N1E 0 JRNL AUTH D.WU,A.KOLESNIKOV,R.YIN,J.D.GUEST,R.GOWTHAMAN,A.SHMELEV, JRNL AUTH 2 Y.SERDYUK,D.V.DIANOV,G.A.EFIMOV,B.G.PIERCE,R.A.MARIUZZA JRNL TITL STRUCTURAL ASSESSMENT OF HLA-A2-RESTRICTED SARS-COV-2 SPIKE JRNL TITL 2 EPITOPES RECOGNIZED BY PUBLIC AND PRIVATE T-CELL RECEPTORS. JRNL REF NAT COMMUN V. 13 19 2022 JRNL REFN ESSN 2041-1723 JRNL PMID 35013235 JRNL DOI 10.1038/S41467-021-27669-8 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH D.WU,A.KOLESNIKOV,R.YIN,J.D.GUEST,R.GOWTHAMAN,A.SHMELEV, REMARK 1 AUTH 2 Y.SERDYUK,G.A.EFIMOV,B.G.PIERCE,R.A.MARIUZZA REMARK 1 TITL STRUCTURAL BASIS FOR RECOGNITION OF TWO HLA-A2-RESTRICTED REMARK 1 TITL 2 SARS-COV-2 SPIKE EPITOPES BY PUBLIC AND PRIVATE T CELL REMARK 1 TITL 3 RECEPTORS REMARK 1 REF BIORXIV 2021 REMARK 1 REFN ISSN 2692-8205 REMARK 1 DOI 10.1101/2021.07.28.454232 REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.16_3549 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.37 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 46620 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.215 REMARK 3 R VALUE (WORKING SET) : 0.212 REMARK 3 FREE R VALUE : 0.258 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.940 REMARK 3 FREE R VALUE TEST SET COUNT : 2302 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 49.3730 - 5.7933 1.00 2884 151 0.2037 0.2345 REMARK 3 2 5.7933 - 4.5994 1.00 2851 139 0.1680 0.2005 REMARK 3 3 4.5994 - 4.0183 1.00 2772 149 0.1707 0.1946 REMARK 3 4 4.0183 - 3.6511 1.00 2794 158 0.1917 0.2225 REMARK 3 5 3.6511 - 3.3894 1.00 2783 167 0.2079 0.2565 REMARK 3 6 3.3894 - 3.1896 1.00 2763 143 0.2225 0.2496 REMARK 3 7 3.1896 - 3.0299 1.00 2788 147 0.2326 0.2811 REMARK 3 8 3.0299 - 2.8980 1.00 2788 136 0.2442 0.3190 REMARK 3 9 2.8980 - 2.7865 1.00 2733 151 0.2369 0.2806 REMARK 3 10 2.7865 - 2.6903 1.00 2784 147 0.2472 0.2980 REMARK 3 11 2.6903 - 2.6062 0.99 2747 131 0.2502 0.3275 REMARK 3 12 2.6062 - 2.5317 1.00 2763 145 0.2465 0.3377 REMARK 3 13 2.5317 - 2.4651 1.00 2768 149 0.2469 0.3772 REMARK 3 14 2.4651 - 2.4049 1.00 2756 121 0.2539 0.3267 REMARK 3 15 2.4049 - 2.3503 1.00 2817 127 0.2639 0.3915 REMARK 3 16 2.3503 - 2.3003 0.92 2527 141 0.2847 0.3614 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) : 0.340 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 31.560 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 41.12 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL 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 7N1E COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-MAY-21. REMARK 100 THE DEPOSITION ID IS D_1000257159. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-MAR-21 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 23-ID-D 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 : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 S 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 159246 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 49.400 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : 3.400 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.38 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: 3TFK, 3FFC, 6VR5 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.11 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.80 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M AMMONIUM SULFATE, 0.1M MES (PH REMARK 280 6.0), 12% (W/V) PEG 4000, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 295K 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 34.07500 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: PENTAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D, E 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 275 REMARK 465 PRO D 201 REMARK 465 GLU D 202 REMARK 465 SER D 203 REMARK 465 SER D 204 REMARK 465 ASP E 244 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 GLU A 173 CG CD OE1 OE2 REMARK 470 LYS A 176 CG CD CE NZ REMARK 470 LYS B 48 CG CD CE NZ REMARK 470 LYS B 75 CG CD CE NZ REMARK 470 PHE D 198 CG CD1 CD2 CE1 CE2 CZ REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 ASP E 61 CG REMARK 480 GLU E 66 CD REMARK 480 GLU E 83 CD REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O VAL E 53 O HOH E 301 1.83 REMARK 500 O HOH A 329 O HOH A 377 1.93 REMARK 500 O HOH A 351 O HOH A 374 1.93 REMARK 500 ND2 ASN D 189 O HOH D 301 1.94 REMARK 500 O SER B 20 O HOH B 101 2.00 REMARK 500 OE1 GLU E 134 O HOH E 302 2.01 REMARK 500 O HOH E 320 O HOH E 375 2.04 REMARK 500 O TYR D 26 O HOH D 302 2.05 REMARK 500 O HOH B 113 O HOH B 133 2.05 REMARK 500 OXT MET B 99 O HOH B 102 2.06 REMARK 500 OD2 ASP E 55 O HOH E 303 2.06 REMARK 500 O PRO B 14 O HOH B 103 2.08 REMARK 500 O HOH A 372 O HOH C 102 2.08 REMARK 500 OE2 GLU D 53 O HOH D 303 2.09 REMARK 500 O HOH B 111 O HOH B 114 2.09 REMARK 500 OD1 ASP D 139 O HOH D 304 2.10 REMARK 500 O HOH A 307 O HOH A 354 2.12 REMARK 500 OD1 ASP D 116 O HOH D 305 2.12 REMARK 500 O HOH D 326 O HOH D 328 2.13 REMARK 500 OG1 THR C 7 O HOH C 101 2.16 REMARK 500 OE2 GLU B 77 O HOH B 104 2.18 REMARK 500 O HOH B 102 O HOH B 108 2.18 REMARK 500 O HOH E 307 O HOH E 358 2.18 REMARK 500 OD1 ASP A 220 O HOH A 301 2.19 REMARK 500 NZ LYS B 19 O HOH B 103 2.19 REMARK 500 REMARK 500 REMARK: NULL 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 O HOH A 339 O HOH B 135 2546 2.00 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 GLU D 31 CD GLU D 31 OE1 -0.067 REMARK 500 GLU D 31 CD GLU D 31 OE2 -0.083 REMARK 500 REMARK 500 REMARK: NULL 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 ARG A 17 35.17 -143.04 REMARK 500 ASP A 29 -122.60 55.36 REMARK 500 ASP A 30 41.54 -107.66 REMARK 500 HIS A 114 110.71 -163.63 REMARK 500 ASP A 119 53.98 38.83 REMARK 500 ALA A 136 -73.42 -84.00 REMARK 500 VAL A 194 -63.66 -102.54 REMARK 500 SER A 195 -151.48 -107.04 REMARK 500 HIS A 197 10.37 -144.88 REMARK 500 PRO A 210 -175.81 -68.59 REMARK 500 THR A 225 42.98 -97.06 REMARK 500 GLN A 226 -75.76 -100.25 REMARK 500 ASP A 227 40.03 -92.20 REMARK 500 PRO B 32 -163.38 -79.40 REMARK 500 TRP B 60 -5.49 80.43 REMARK 500 PHE D 69 57.06 -153.97 REMARK 500 ASP D 116 67.16 -151.70 REMARK 500 LYS D 126 -88.50 -126.41 REMARK 500 ASP D 129 19.06 51.46 REMARK 500 ASN D 185 53.80 -110.85 REMARK 500 PHE D 187 50.24 -107.37 REMARK 500 ASN D 189 -169.51 -115.13 REMARK 500 ASN E 49 -130.58 49.81 REMARK 500 GLN E 57 44.59 -86.50 REMARK 500 VAL E 71 -102.71 -120.11 REMARK 500 ALA E 97 31.17 -143.61 REMARK 500 ASP E 185 35.91 -91.49 REMARK 500 REMARK 500 REMARK: NULL DBREF1 7N1E A 1 275 UNP A0A5B8RNS7_HUMAN DBREF2 7N1E A A0A5B8RNS7 25 299 DBREF 7N1E B 1 99 UNP P61769 B2MG_HUMAN 21 119 DBREF 7N1E C 1 9 UNP P0DTC2 SPIKE_SARS2 1000 1008 DBREF 7N1E D 1 204 PDB 7N1E 7N1E 1 204 DBREF 7N1E E 1 244 PDB 7N1E 7N1E 1 244 SEQADV 7N1E MET B 0 UNP P61769 INITIATING METHIONINE SEQRES 1 A 275 GLY SER HIS SER MET ARG TYR PHE PHE THR SER VAL SER SEQRES 2 A 275 ARG PRO GLY ARG GLY GLU PRO ARG PHE ILE ALA VAL GLY SEQRES 3 A 275 TYR VAL ASP ASP THR GLN PHE VAL ARG PHE ASP SER ASP SEQRES 4 A 275 ALA ALA SER GLN ARG MET GLU PRO ARG ALA PRO TRP ILE SEQRES 5 A 275 GLU GLN GLU GLY PRO GLU TYR TRP ASP GLY GLU THR ARG SEQRES 6 A 275 LYS VAL LYS ALA HIS SER GLN THR HIS ARG VAL ASP LEU SEQRES 7 A 275 GLY THR LEU ARG GLY TYR TYR ASN GLN SER GLU ALA GLY SEQRES 8 A 275 SER HIS THR VAL GLN ARG MET TYR GLY CYS ASP VAL GLY SEQRES 9 A 275 SER ASP TRP ARG PHE LEU ARG GLY TYR HIS GLN TYR ALA SEQRES 10 A 275 TYR ASP GLY LYS ASP TYR ILE ALA LEU LYS GLU ASP LEU SEQRES 11 A 275 ARG SER TRP THR ALA ALA ASP MET ALA ALA GLN THR THR SEQRES 12 A 275 LYS HIS LYS TRP GLU ALA ALA HIS VAL ALA GLU GLN LEU SEQRES 13 A 275 ARG ALA TYR LEU GLU GLY THR CYS VAL GLU TRP LEU ARG SEQRES 14 A 275 ARG TYR LEU GLU ASN GLY LYS GLU THR LEU GLN ARG THR SEQRES 15 A 275 ASP ALA PRO LYS THR HIS MET THR HIS HIS ALA VAL SER SEQRES 16 A 275 ASP HIS GLU ALA THR LEU ARG CYS TRP ALA LEU SER PHE SEQRES 17 A 275 TYR PRO ALA GLU ILE THR LEU THR TRP GLN ARG ASP GLY SEQRES 18 A 275 GLU ASP GLN THR GLN ASP THR GLU LEU VAL GLU THR ARG SEQRES 19 A 275 PRO ALA GLY ASP GLY THR PHE GLN LYS TRP ALA ALA VAL SEQRES 20 A 275 VAL VAL PRO SER GLY GLN GLU GLN ARG TYR THR CYS HIS SEQRES 21 A 275 VAL GLN HIS GLU GLY LEU PRO LYS PRO LEU THR LEU ARG SEQRES 22 A 275 TRP GLU SEQRES 1 B 100 MET ILE GLN ARG THR PRO LYS ILE GLN VAL TYR SER ARG SEQRES 2 B 100 HIS PRO ALA GLU ASN GLY LYS SER ASN PHE LEU ASN CYS SEQRES 3 B 100 TYR VAL SER GLY PHE HIS PRO SER ASP ILE GLU VAL ASP SEQRES 4 B 100 LEU LEU LYS ASN GLY GLU ARG ILE GLU LYS VAL GLU HIS SEQRES 5 B 100 SER ASP LEU SER PHE SER LYS ASP TRP SER PHE TYR LEU SEQRES 6 B 100 LEU TYR TYR THR GLU PHE THR PRO THR GLU LYS ASP GLU SEQRES 7 B 100 TYR ALA CYS ARG VAL ASN HIS VAL THR LEU SER GLN PRO SEQRES 8 B 100 LYS ILE VAL LYS TRP ASP ARG ASP MET SEQRES 1 C 9 ARG LEU GLN SER LEU GLN THR TYR VAL SEQRES 1 D 204 GLN ARG VAL THR GLN PRO GLU LYS LEU LEU SER VAL PHE SEQRES 2 D 204 LYS GLY ALA PRO VAL GLU LEU LYS CYS ASN TYR SER TYR SEQRES 3 D 204 SER GLY SER PRO GLU LEU PHE TRP TYR VAL GLN TYR SER SEQRES 4 D 204 ARG GLN ARG LEU GLN LEU LEU LEU ARG HIS ILE SER ARG SEQRES 5 D 204 GLU SER ILE LYS GLY PHE THR ALA ASP LEU ASN LYS GLY SEQRES 6 D 204 GLU THR SER PHE HIS LEU LYS LYS PRO PHE ALA GLN GLU SEQRES 7 D 204 GLU ASP SER ALA MET TYR TYR CYS ALA LEU SER GLY PHE SEQRES 8 D 204 ASN ASN ALA GLY ASN MET LEU THR PHE GLY GLY GLY THR SEQRES 9 D 204 ARG LEU MET VAL LYS PRO ASN ILE GLN ASN PRO ASP PRO SEQRES 10 D 204 ALA VAL TYR GLN LEU ARG ASP SER LYS SER SER ASP LYS SEQRES 11 D 204 SER VAL CYS LEU PHE THR ASP PHE ASP SER GLN THR ASN SEQRES 12 D 204 VAL SER GLN SER LYS ASP SER ASP VAL TYR ILE THR ASP SEQRES 13 D 204 LYS CYS VAL LEU ASP MET ARG SER MET ASP PHE LYS SER SEQRES 14 D 204 ASN SER ALA VAL ALA TRP SER ASN LYS SER ASP PHE ALA SEQRES 15 D 204 CYS ALA ASN ALA PHE ASN ASN SER ILE ILE PRO GLU ASP SEQRES 16 D 204 THR PHE PHE PRO SER PRO GLU SER SER SEQRES 1 E 244 GLY VAL ALA GLN SER PRO ARG TYR LYS ILE ILE GLU LYS SEQRES 2 E 244 ARG GLN SER VAL ALA PHE TRP CYS ASN PRO ILE SER GLY SEQRES 3 E 244 HIS ALA THR LEU TYR TRP TYR GLN GLN ILE LEU GLY GLN SEQRES 4 E 244 GLY PRO LYS LEU LEU ILE GLN PHE GLN ASN ASN GLY VAL SEQRES 5 E 244 VAL ASP ASP SER GLN LEU PRO LYS ASP ARG PHE SER ALA SEQRES 6 E 244 GLU ARG LEU LYS GLY VAL ASP SER THR LEU LYS ILE GLN SEQRES 7 E 244 PRO ALA LYS LEU GLU ASP SER ALA VAL TYR LEU CYS ALA SEQRES 8 E 244 SER SER LEU GLY GLY ALA GLY GLY ALA ASP THR GLN TYR SEQRES 9 E 244 PHE GLY PRO GLY THR ARG LEU THR VAL LEU GLU ASP LEU SEQRES 10 E 244 LYS ASN VAL PHE PRO PRO GLU VAL ALA VAL PHE GLU PRO SEQRES 11 E 244 SER GLU ALA GLU ILE SER HIS THR GLN LYS ALA THR LEU SEQRES 12 E 244 VAL CYS LEU ALA THR GLY PHE TYR PRO ASP HIS VAL GLU SEQRES 13 E 244 LEU SER TRP TRP VAL ASN GLY LYS GLU VAL HIS SER GLY SEQRES 14 E 244 VAL CYS THR ASP PRO GLN PRO LEU LYS GLU GLN PRO ALA SEQRES 15 E 244 LEU ASN ASP SER ARG TYR ALA LEU SER SER ARG LEU ARG SEQRES 16 E 244 VAL SER ALA THR PHE TRP GLN ASN PRO ARG ASN HIS PHE SEQRES 17 E 244 ARG CYS GLN VAL GLN PHE TYR GLY LEU SER GLU ASN ASP SEQRES 18 E 244 GLU TRP THR GLN ASP ARG ALA LYS PRO VAL THR GLN ILE SEQRES 19 E 244 VAL SER ALA GLU ALA TRP GLY ARG ALA ASP FORMUL 6 HOH *253(H2 O) HELIX 1 AA1 ALA A 49 GLU A 55 5 7 HELIX 2 AA2 GLY A 56 TYR A 85 1 30 HELIX 3 AA3 ASP A 137 HIS A 151 1 15 HELIX 4 AA4 HIS A 151 GLY A 162 1 12 HELIX 5 AA5 GLY A 162 GLY A 175 1 14 HELIX 6 AA6 GLY A 175 GLN A 180 1 6 HELIX 7 AA7 GLN A 253 GLN A 255 5 3 HELIX 8 AA8 ILE D 50 ARG D 52 5 3 HELIX 9 AA9 GLN D 77 SER D 81 5 5 HELIX 10 AB1 ASN D 93 ASN D 96 5 4 HELIX 11 AB2 LYS E 81 SER E 85 5 5 HELIX 12 AB3 ASP E 116 VAL E 120 5 5 HELIX 13 AB4 SER E 131 GLN E 139 1 9 HELIX 14 AB5 ALA E 198 GLN E 202 1 5 SHEET 1 AA1 8 GLU A 46 PRO A 47 0 SHEET 2 AA1 8 THR A 31 ASP A 37 -1 N ARG A 35 O GLU A 46 SHEET 3 AA1 8 ARG A 21 VAL A 28 -1 N VAL A 28 O THR A 31 SHEET 4 AA1 8 HIS A 3 VAL A 12 -1 N ARG A 6 O TYR A 27 SHEET 5 AA1 8 THR A 94 VAL A 103 -1 O VAL A 103 N HIS A 3 SHEET 6 AA1 8 PHE A 109 TYR A 118 -1 O GLN A 115 N MET A 98 SHEET 7 AA1 8 LYS A 121 LEU A 126 -1 O ILE A 124 N TYR A 116 SHEET 8 AA1 8 TRP A 133 ALA A 135 -1 O THR A 134 N ALA A 125 SHEET 1 AA2 4 LYS A 186 ALA A 193 0 SHEET 2 AA2 4 ALA A 199 PHE A 208 -1 O LEU A 206 N LYS A 186 SHEET 3 AA2 4 PHE A 241 VAL A 249 -1 O VAL A 249 N ALA A 199 SHEET 4 AA2 4 THR A 228 LEU A 230 -1 N GLU A 229 O ALA A 246 SHEET 1 AA3 4 LYS A 186 ALA A 193 0 SHEET 2 AA3 4 ALA A 199 PHE A 208 -1 O LEU A 206 N LYS A 186 SHEET 3 AA3 4 PHE A 241 VAL A 249 -1 O VAL A 249 N ALA A 199 SHEET 4 AA3 4 ARG A 234 PRO A 235 -1 N ARG A 234 O GLN A 242 SHEET 1 AA4 4 GLU A 222 ASP A 223 0 SHEET 2 AA4 4 THR A 214 ARG A 219 -1 N ARG A 219 O GLU A 222 SHEET 3 AA4 4 TYR A 257 GLN A 262 -1 O THR A 258 N GLN A 218 SHEET 4 AA4 4 LEU A 270 LEU A 272 -1 O LEU A 270 N VAL A 261 SHEET 1 AA5 4 LYS B 6 SER B 11 0 SHEET 2 AA5 4 ASN B 21 PHE B 30 -1 O ASN B 24 N TYR B 10 SHEET 3 AA5 4 PHE B 62 PHE B 70 -1 O PHE B 70 N ASN B 21 SHEET 4 AA5 4 GLU B 50 HIS B 51 -1 N GLU B 50 O TYR B 67 SHEET 1 AA6 4 LYS B 6 SER B 11 0 SHEET 2 AA6 4 ASN B 21 PHE B 30 -1 O ASN B 24 N TYR B 10 SHEET 3 AA6 4 PHE B 62 PHE B 70 -1 O PHE B 70 N ASN B 21 SHEET 4 AA6 4 SER B 55 PHE B 56 -1 N SER B 55 O TYR B 63 SHEET 1 AA7 4 GLU B 44 ARG B 45 0 SHEET 2 AA7 4 GLU B 36 LYS B 41 -1 N LYS B 41 O GLU B 44 SHEET 3 AA7 4 TYR B 78 ASN B 83 -1 O ARG B 81 N ASP B 38 SHEET 4 AA7 4 LYS B 91 LYS B 94 -1 O LYS B 91 N VAL B 82 SHEET 1 AA8 2 ARG D 2 THR D 4 0 SHEET 2 AA8 2 ASN D 23 SER D 25 -1 O ASN D 23 N THR D 4 SHEET 1 AA9 5 LEU D 9 PHE D 13 0 SHEET 2 AA9 5 THR D 104 LYS D 109 1 O LYS D 109 N VAL D 12 SHEET 3 AA9 5 ALA D 82 GLY D 90 -1 N ALA D 82 O LEU D 106 SHEET 4 AA9 5 PRO D 30 GLN D 37 -1 N TYR D 35 O TYR D 85 SHEET 5 AA9 5 GLN D 44 ARG D 48 -1 O GLN D 44 N VAL D 36 SHEET 1 AB1 4 LEU D 9 PHE D 13 0 SHEET 2 AB1 4 THR D 104 LYS D 109 1 O LYS D 109 N VAL D 12 SHEET 3 AB1 4 ALA D 82 GLY D 90 -1 N ALA D 82 O LEU D 106 SHEET 4 AB1 4 LEU D 98 PHE D 100 -1 O THR D 99 N LEU D 88 SHEET 1 AB2 3 VAL D 18 LEU D 20 0 SHEET 2 AB2 3 LEU D 71 LYS D 73 -1 O LYS D 73 N VAL D 18 SHEET 3 AB2 3 THR D 59 ALA D 60 -1 N THR D 59 O LYS D 72 SHEET 1 AB3 7 TYR D 153 ILE D 154 0 SHEET 2 AB3 7 PHE D 167 TRP D 175 -1 O TRP D 175 N TYR D 153 SHEET 3 AB3 7 CYS D 158 MET D 162 -1 N MET D 162 O PHE D 167 SHEET 4 AB3 7 PHE D 167 TRP D 175 -1 O PHE D 167 N MET D 162 SHEET 5 AB3 7 SER D 131 THR D 136 -1 N CYS D 133 O ALA D 174 SHEET 6 AB3 7 ALA D 118 ASP D 124 -1 N LEU D 122 O VAL D 132 SHEET 7 AB3 7 THR D 196 PHE D 197 1 O THR D 196 N VAL D 119 SHEET 1 AB4 7 ALA D 118 ASP D 124 0 SHEET 2 AB4 7 GLU E 124 GLU E 129 -1 O GLU E 129 N ARG D 123 SHEET 3 AB4 7 LYS E 140 PHE E 150 -1 O VAL E 144 N PHE E 128 SHEET 4 AB4 7 TYR E 188 SER E 197 -1 O VAL E 196 N ALA E 141 SHEET 5 AB4 7 LEU E 177 LYS E 178 -1 N LEU E 177 O ALA E 189 SHEET 6 AB4 7 TYR E 188 SER E 197 -1 O ALA E 189 N LEU E 177 SHEET 7 AB4 7 VAL E 170 THR E 172 -1 N CYS E 171 O ARG E 193 SHEET 1 AB5 4 ALA E 3 SER E 5 0 SHEET 2 AB5 4 VAL E 17 ASN E 22 -1 O TRP E 20 N SER E 5 SHEET 3 AB5 4 SER E 73 ILE E 77 -1 O LEU E 75 N PHE E 19 SHEET 4 AB5 4 PHE E 63 GLU E 66 -1 N SER E 64 O LYS E 76 SHEET 1 AB6 6 TYR E 8 GLU E 12 0 SHEET 2 AB6 6 THR E 109 LEU E 114 1 O THR E 112 N LYS E 9 SHEET 3 AB6 6 ALA E 86 SER E 93 -1 N ALA E 86 O LEU E 111 SHEET 4 AB6 6 THR E 29 GLN E 35 -1 N TYR E 33 O LEU E 89 SHEET 5 AB6 6 LYS E 42 GLN E 48 -1 O LEU E 44 N TRP E 32 SHEET 6 AB6 6 GLY E 51 ASP E 54 -1 O VAL E 53 N GLN E 46 SHEET 1 AB7 4 TYR E 8 GLU E 12 0 SHEET 2 AB7 4 THR E 109 LEU E 114 1 O THR E 112 N LYS E 9 SHEET 3 AB7 4 ALA E 86 SER E 93 -1 N ALA E 86 O LEU E 111 SHEET 4 AB7 4 TYR E 104 PHE E 105 -1 O TYR E 104 N SER E 92 SHEET 1 AB8 4 LYS E 164 VAL E 166 0 SHEET 2 AB8 4 VAL E 155 VAL E 161 -1 N VAL E 161 O LYS E 164 SHEET 3 AB8 4 HIS E 207 PHE E 214 -1 O GLN E 211 N SER E 158 SHEET 4 AB8 4 GLN E 233 TRP E 240 -1 O ALA E 237 N CYS E 210 SSBOND 1 CYS A 101 CYS A 164 1555 1555 2.04 SSBOND 2 CYS A 203 CYS A 259 1555 1555 2.03 SSBOND 3 CYS B 25 CYS B 80 1555 1555 2.06 SSBOND 4 CYS D 22 CYS D 86 1555 1555 2.03 SSBOND 5 CYS D 133 CYS D 183 1555 1555 2.03 SSBOND 6 CYS D 158 CYS E 171 1555 1555 2.04 SSBOND 7 CYS E 21 CYS E 90 1555 1555 2.08 SSBOND 8 CYS E 145 CYS E 210 1555 1555 2.03 CISPEP 1 TYR A 209 PRO A 210 0 -2.73 CISPEP 2 HIS B 31 PRO B 32 0 5.77 CISPEP 3 SER E 5 PRO E 6 0 -7.61 CISPEP 4 GLN E 78 PRO E 79 0 -4.18 CISPEP 5 TYR E 151 PRO E 152 0 -0.06 CRYST1 52.799 68.150 148.598 90.00 94.61 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 0.018940 0.000000 0.001527 0.00000 SCALE2 0.000000 0.014674 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006751 0.00000