HEADER IMMUNE SYSTEM/VIRAL PROTEIN 25-AUG-22 8GON TITLE SARS-COV-2 SPECIFIC PRIVATE TCR RLQ7 IN COMPLEX WITH RLQ-T1006I-HLA-A2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: MHC CLASS I ANTIGEN; 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 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: SPIKE PROTEIN S2; COMPND 11 CHAIN: C; COMPND 12 FRAGMENT: RLQ MUTANT EPITOPE; COMPND 13 ENGINEERED: YES; COMPND 14 MUTATION: YES; COMPND 15 MOL_ID: 4; COMPND 16 MOLECULE: SARS-COV-2 SPECIFIC PRIVATE TCR RLQ7 ALPHA; COMPND 17 CHAIN: D; COMPND 18 ENGINEERED: YES; COMPND 19 MOL_ID: 5; COMPND 20 MOLECULE: SARS-COV-2 SPECIFIC PRIVATE TCR RLQ7 BETA; COMPND 21 CHAIN: E; COMPND 22 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; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; 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; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 15 MOL_ID: 3; SOURCE 16 ORGANISM_SCIENTIFIC: SEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS SOURCE 17 2; SOURCE 18 ORGANISM_COMMON: 2019-NCOV, SARS-COV-2; SOURCE 19 ORGANISM_TAXID: 2697049; SOURCE 20 GENE: S, 2; SOURCE 21 EXPRESSION_SYSTEM: SYNTHECIUM; SOURCE 22 EXPRESSION_SYSTEM_TAXID: 2480903; SOURCE 23 MOL_ID: 4; SOURCE 24 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 25 ORGANISM_TAXID: 9606; SOURCE 26 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 27 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 28 MOL_ID: 5; SOURCE 29 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 30 ORGANISM_TAXID: 9606; SOURCE 31 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 32 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS SARS-COV-2, PRIVATE TCR, TCR-P-HLA, IMMUNE SYSTEM, IMMUNE SYSTEM- KEYWDS 2 VIRAL PROTEIN COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR D.WU,R.A.MARIUZZA REVDAT 4 29-NOV-23 8GON 1 REMARK REVDAT 3 29-MAR-23 8GON 1 JRNL REVDAT 2 08-MAR-23 8GON 1 JRNL REVDAT 1 01-MAR-23 8GON 0 JRNL AUTH D.WU,G.A.EFIMOV,A.V.BOGOLYUBOVA,B.G.PIERCE,R.A.MARIUZZA JRNL TITL STRUCTURAL INSIGHTS INTO PROTECTION AGAINST A SARS-COV-2 JRNL TITL 2 SPIKE VARIANT BY T CELL RECEPTOR (TCR) DIVERSITY. JRNL REF J.BIOL.CHEM. V. 299 03035 2023 JRNL REFN ESSN 1083-351X JRNL PMID 36806685 JRNL DOI 10.1016/J.JBC.2023.103035 REMARK 2 REMARK 2 RESOLUTION. 2.60 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) : 2.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.24 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.390 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 35771 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.201 REMARK 3 R VALUE (WORKING SET) : 0.198 REMARK 3 FREE R VALUE : 0.253 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.970 REMARK 3 FREE R VALUE TEST SET COUNT : 1779 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 48.2370 - 6.1110 0.99 2826 140 0.1723 0.2125 REMARK 3 2 6.1110 - 4.8520 1.00 2692 146 0.1693 0.2322 REMARK 3 3 4.8520 - 4.2390 1.00 2653 126 0.1563 0.1931 REMARK 3 4 4.2390 - 3.8516 1.00 2637 128 0.1802 0.2333 REMARK 3 5 3.8516 - 3.5757 1.00 2602 135 0.1974 0.2317 REMARK 3 6 3.5757 - 3.3649 1.00 2584 152 0.2253 0.2911 REMARK 3 7 3.3649 - 3.1964 1.00 2574 150 0.2305 0.3031 REMARK 3 8 3.1964 - 3.0573 1.00 2589 131 0.2481 0.3240 REMARK 3 9 3.0573 - 2.9396 1.00 2579 129 0.2518 0.2910 REMARK 3 10 2.9396 - 2.8382 1.00 2550 140 0.2560 0.3347 REMARK 3 11 2.8382 - 2.7495 1.00 2592 136 0.2625 0.3398 REMARK 3 12 2.7495 - 2.6709 1.00 2545 147 0.2550 0.3419 REMARK 3 13 2.6709 - 2.6010 1.00 2569 119 0.2523 0.2851 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) : 0.330 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.200 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 56.12 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 8GON COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 08-SEP-22. REMARK 100 THE DEPOSITION ID IS D_1300031837. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-OCT-21 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 : APS REMARK 200 BEAMLINE : 23-ID-B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9793 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 : 35792 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.600 REMARK 200 RESOLUTION RANGE LOW (A) : 48.240 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 25.10 REMARK 200 R MERGE (I) : 0.11300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 22.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.69 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: 8GOM REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.84 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.92 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M TRIS-HCL PH 8.5, 15% PEG 6000, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/6 REMARK 290 6555 X-Y,X,Z+5/6 REMARK 290 7555 Y,X,-Z+2/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+1/3 REMARK 290 10555 -Y,-X,-Z+1/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+5/6 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 119.21267 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 59.60633 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 89.40950 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 29.80317 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 149.01583 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 119.21267 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 59.60633 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 29.80317 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 89.40950 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 149.01583 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: PENTAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 11130 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 36500 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -46.0 KCAL/MOL 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 MET A 0 REMARK 465 MET D 0 REMARK 465 SER D 181 REMARK 465 ASP D 182 REMARK 465 ILE D 193 REMARK 465 ILE D 194 REMARK 465 PRO D 195 REMARK 465 GLU D 196 REMARK 465 ASP D 197 REMARK 465 THR D 198 REMARK 465 PHE D 199 REMARK 465 PHE D 200 REMARK 465 PRO D 201 REMARK 465 SER D 202 REMARK 465 PRO D 203 REMARK 465 GLU D 204 REMARK 465 SER D 205 REMARK 465 SER D 206 REMARK 465 MET E 0 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 19 CG CD OE1 OE2 REMARK 470 GLU A 177 CG CD OE1 OE2 REMARK 470 LYS B 19 CD CE NZ REMARK 470 ARG B 45 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 48 CG CD CE NZ REMARK 470 LYS B 58 CG CD CE NZ REMARK 470 GLN D 57 CG CD OE1 NE2 REMARK 470 LYS D 104 CG CD CE NZ REMARK 470 LYS D 128 CG CD CE NZ REMARK 470 LYS D 180 CG CD CE NZ REMARK 470 ARG E 9 CG CD NE CZ NH1 NH2 REMARK 470 MET E 40 CG SD CE REMARK 470 LYS E 119 CG CD CE NZ 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 OG1 THR A 233 O HOH A 401 1.98 REMARK 500 O HOH D 329 O HOH D 330 1.98 REMARK 500 OG1 THR D 106 O HOH D 301 2.00 REMARK 500 O SER D 133 O HOH D 302 2.05 REMARK 500 OH TYR E 216 O HOH E 301 2.06 REMARK 500 O ASP D 153 OG SER D 178 2.15 REMARK 500 OG SER D 95 O PRO D 99 2.15 REMARK 500 N ASN B 17 O HOH B 101 2.15 REMARK 500 OD2 ASP A 77 O HOH A 402 2.17 REMARK 500 OH TYR A 85 OD2 ASP A 137 2.18 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 NH1 ARG D 125 NH1 ARG D 125 9554 1.73 REMARK 500 O LYS B 75 NH2 ARG E 206 8445 1.99 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 PRO B 72 N PRO B 72 CA 0.204 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES 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,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) 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 ATM2 ATM3 REMARK 500 ARG A 97 CG - CD - NE ANGL. DEV. = 14.8 DEGREES REMARK 500 PRO B 72 C - N - CA ANGL. DEV. = 18.5 DEGREES REMARK 500 PRO B 72 CA - N - CD ANGL. DEV. = -9.7 DEGREES 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 ASP A 29 -123.96 50.63 REMARK 500 ASP A 137 -157.65 -123.77 REMARK 500 VAL A 194 -62.91 -95.86 REMARK 500 SER A 195 -156.49 -100.90 REMARK 500 PRO A 210 -177.14 -66.93 REMARK 500 ASP B 34 109.56 -59.64 REMARK 500 ARG B 45 108.60 -57.12 REMARK 500 LEU B 54 126.25 -38.73 REMARK 500 ALA D 16 -13.25 81.12 REMARK 500 ARG D 43 -7.71 77.68 REMARK 500 ASN D 62 -119.20 46.22 REMARK 500 PHE D 75 64.47 -152.72 REMARK 500 ASP D 118 50.02 -156.29 REMARK 500 LYS D 128 -74.04 -96.76 REMARK 500 SER D 152 2.55 83.88 REMARK 500 SER D 178 -160.75 -165.55 REMARK 500 MET E 15 157.04 -49.38 REMARK 500 ASP E 63 -38.59 -138.97 REMARK 500 PRO E 153 -164.98 -72.30 REMARK 500 THR E 225 51.57 -140.71 REMARK 500 REMARK 500 REMARK: NULL DBREF 8GON A 1 275 UNP Q861F7 Q861F7_HUMAN 1 275 DBREF 8GON B 1 99 UNP P61769 B2MG_HUMAN 21 119 DBREF 8GON C 1 9 UNP P0DTC2 SPIKE_SARS2 1000 1008 DBREF 8GON D 0 206 PDB 8GON 8GON 0 206 DBREF 8GON E 0 245 PDB 8GON 8GON 0 245 SEQADV 8GON MET A 0 UNP Q861F7 INITIATING METHIONINE SEQADV 8GON MET B 0 UNP P61769 EXPRESSION TAG SEQADV 8GON ILE C 7 UNP P0DTC2 THR 1006 ENGINEERED MUTATION SEQRES 1 A 276 MET GLY SER HIS SER MET ARG TYR PHE PHE THR SER VAL SEQRES 2 A 276 SER ARG PRO GLY ARG GLY GLU PRO ARG PHE ILE ALA VAL SEQRES 3 A 276 GLY TYR VAL ASP ASP THR GLN PHE VAL ARG PHE ASP SER SEQRES 4 A 276 ASP ALA ALA SER GLN ARG MET GLU PRO ARG ALA PRO TRP SEQRES 5 A 276 ILE GLU GLN GLU GLY PRO GLU TYR TRP ASP GLY GLU THR SEQRES 6 A 276 ARG LYS VAL LYS ALA HIS SER GLN THR HIS ARG VAL ASP SEQRES 7 A 276 LEU GLY THR LEU ARG GLY TYR TYR ASN GLN SER GLU ALA SEQRES 8 A 276 GLY SER HIS THR VAL GLN ARG MET TYR GLY CYS ASP VAL SEQRES 9 A 276 GLY SER ASP TRP ARG PHE LEU ARG GLY TYR HIS GLN TYR SEQRES 10 A 276 ALA TYR ASP GLY LYS ASP TYR ILE ALA LEU LYS GLU ASP SEQRES 11 A 276 LEU ARG SER TRP THR ALA ALA ASP MET ALA ALA GLN THR SEQRES 12 A 276 THR LYS HIS LYS TRP GLU ALA ALA HIS VAL ALA GLU GLN SEQRES 13 A 276 LEU ARG ALA TYR LEU GLU GLY THR CYS VAL GLU TRP LEU SEQRES 14 A 276 ARG ARG TYR LEU GLU ASN GLY LYS GLU THR LEU GLN ARG SEQRES 15 A 276 THR ASP ALA PRO LYS THR HIS MET THR HIS HIS ALA VAL SEQRES 16 A 276 SER ASP HIS GLU ALA THR LEU ARG CYS TRP ALA LEU SER SEQRES 17 A 276 PHE TYR PRO ALA GLU ILE THR LEU THR TRP GLN ARG ASP SEQRES 18 A 276 GLY GLU ASP GLN THR GLN ASP THR GLU LEU VAL GLU THR SEQRES 19 A 276 ARG PRO ALA GLY ASP GLY THR PHE GLN LYS TRP ALA ALA SEQRES 20 A 276 VAL VAL VAL PRO SER GLY GLN GLU GLN ARG TYR THR CYS SEQRES 21 A 276 HIS VAL GLN HIS GLU GLY LEU PRO LYS PRO LEU THR LEU SEQRES 22 A 276 ARG 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 ILE TYR VAL SEQRES 1 D 207 MET ALA GLN THR VAL THR GLN SER GLN PRO GLU MET SER SEQRES 2 D 207 VAL GLN GLU ALA GLU THR VAL THR LEU SER CYS THR TYR SEQRES 3 D 207 ASP THR SER GLU SER ASP TYR TYR LEU PHE TRP TYR LYS SEQRES 4 D 207 GLN PRO PRO SER ARG GLN MET ILE LEU VAL ILE ARG GLN SEQRES 5 D 207 GLU ALA TYR LYS GLN GLN ASN ALA THR GLU ASN ARG PHE SEQRES 6 D 207 SER VAL ASN PHE GLN LYS ALA ALA LYS SER PHE SER LEU SEQRES 7 D 207 LYS ILE SER ASP SER GLN LEU GLY ASP ALA ALA MET TYR SEQRES 8 D 207 PHE CYS ALA SER SER GLY ASN THR PRO LEU VAL PHE GLY SEQRES 9 D 207 LYS GLY THR ARG LEU SER VAL ILE PRO ASN ILE GLN ASN SEQRES 10 D 207 PRO ASP PRO ALA VAL TYR GLN LEU ARG ASP SER LYS SER SEQRES 11 D 207 SER ASP LYS SER VAL CYS LEU PHE THR ASP PHE ASP SER SEQRES 12 D 207 GLN THR ASN VAL SER GLN SER LYS ASP SER ASP VAL TYR SEQRES 13 D 207 ILE THR ASP LYS CYS VAL LEU ASP MET ARG SER MET ASP SEQRES 14 D 207 PHE LYS SER ASN SER ALA VAL ALA TRP SER ASN LYS SER SEQRES 15 D 207 ASP PHE ALA CYS ALA ASN ALA PHE ASN ASN SER ILE ILE SEQRES 16 D 207 PRO GLU ASP THR PHE PHE PRO SER PRO GLU SER SER SEQRES 1 E 246 MET ASP ALA GLY VAL ILE GLN SER PRO ARG HIS GLU VAL SEQRES 2 E 246 THR GLU MET GLY GLN GLU VAL THR LEU ARG CYS LYS PRO SEQRES 3 E 246 ILE SER GLY HIS ASN SER LEU PHE TRP TYR ARG GLN THR SEQRES 4 E 246 MET MET ARG GLY LEU GLU LEU LEU ILE TYR PHE ASN ASN SEQRES 5 E 246 ASN VAL PRO ILE ASP ASP SER GLY MET PRO GLU ASP ARG SEQRES 6 E 246 PHE SER ALA LYS MET PRO ASN ALA SER PHE SER THR LEU SEQRES 7 E 246 LYS ILE GLN PRO SER GLU PRO ARG ASP SER ALA VAL TYR SEQRES 8 E 246 PHE CYS ALA SER THR TRP GLY ARG ALA SER THR ASP THR SEQRES 9 E 246 GLN TYR PHE GLY PRO GLY THR ARG LEU THR VAL LEU GLU SEQRES 10 E 246 ASP LEU LYS ASN VAL PHE PRO PRO GLU VAL ALA VAL PHE SEQRES 11 E 246 GLU PRO SER GLU ALA GLU ILE SER HIS THR GLN LYS ALA SEQRES 12 E 246 THR LEU VAL CYS LEU ALA THR GLY PHE TYR PRO ASP HIS SEQRES 13 E 246 VAL GLU LEU SER TRP TRP VAL ASN GLY LYS GLU VAL HIS SEQRES 14 E 246 SER GLY VAL CYS THR ASP PRO GLN PRO LEU LYS GLU GLN SEQRES 15 E 246 PRO ALA LEU ASN ASP SER ARG TYR ALA LEU SER SER ARG SEQRES 16 E 246 LEU ARG VAL SER ALA THR PHE TRP GLN ASN PRO ARG ASN SEQRES 17 E 246 HIS PHE ARG CYS GLN VAL GLN PHE TYR GLY LEU SER GLU SEQRES 18 E 246 ASN ASP GLU TRP THR GLN ASP ARG ALA LYS PRO VAL THR SEQRES 19 E 246 GLN ILE VAL SER ALA GLU ALA TRP GLY ARG ALA ASP HET PG4 A 301 13 HETNAM PG4 TETRAETHYLENE GLYCOL FORMUL 6 PG4 C8 H18 O5 FORMUL 7 HOH *117(H2 O) HELIX 1 AA1 GLY A 56 ASN A 86 1 31 HELIX 2 AA2 MET A 138 HIS A 151 1 14 HELIX 3 AA3 HIS A 151 GLU A 161 1 11 HELIX 4 AA4 GLY A 162 GLY A 175 1 14 HELIX 5 AA5 GLY A 175 GLN A 180 1 6 HELIX 6 AA6 GLN A 253 GLN A 255 5 3 HELIX 7 AA7 GLN D 83 ALA D 87 5 5 HELIX 8 AA8 ARG D 165 ASP D 168 5 4 HELIX 9 AA9 GLU E 83 SER E 87 5 5 HELIX 10 AB1 ASP E 117 VAL E 121 5 5 HELIX 11 AB2 SER E 132 GLN E 140 1 9 HELIX 12 AB3 ALA E 199 GLN E 203 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 GLY A 26 O PHE A 33 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 ARG A 111 N ASP A 102 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 GLU A 198 PHE A 208 -1 O TRP A 204 N HIS A 188 SHEET 3 AA2 4 PHE A 241 PRO A 250 -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 GLU A 198 PHE A 208 -1 O TRP A 204 N HIS A 188 SHEET 3 AA3 4 PHE A 241 PRO A 250 -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 GLN A 224 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 HIS A 260 N THR A 216 SHEET 4 AA4 4 LEU A 270 ARG A 273 -1 O LEU A 272 N CYS A 259 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 THR B 68 N LEU B 23 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 THR B 68 N LEU B 23 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 ASN B 83 N GLU B 36 SHEET 4 AA7 4 LYS B 91 LYS B 94 -1 O LYS B 91 N VAL B 82 SHEET 1 AA8 2 GLN D 2 THR D 5 0 SHEET 2 AA8 2 THR D 24 THR D 27 -1 O THR D 24 N THR D 5 SHEET 1 AA9 5 GLU D 10 GLN D 14 0 SHEET 2 AA9 5 THR D 106 ILE D 111 1 O SER D 109 N MET D 11 SHEET 3 AA9 5 ALA D 88 SER D 95 -1 N TYR D 90 O THR D 106 SHEET 4 AA9 5 TYR D 33 GLN D 39 -1 N TYR D 37 O PHE D 91 SHEET 5 AA9 5 ILE D 46 GLU D 52 -1 O GLN D 51 N LEU D 34 SHEET 1 AB1 4 GLU D 10 GLN D 14 0 SHEET 2 AB1 4 THR D 106 ILE D 111 1 O SER D 109 N MET D 11 SHEET 3 AB1 4 ALA D 88 SER D 95 -1 N TYR D 90 O THR D 106 SHEET 4 AB1 4 VAL D 101 PHE D 102 -1 O VAL D 101 N SER D 94 SHEET 1 AB2 4 VAL D 19 LEU D 21 0 SHEET 2 AB2 4 SER D 74 ILE D 79 -1 O ILE D 79 N VAL D 19 SHEET 3 AB2 4 PHE D 64 GLN D 69 -1 N SER D 65 O LYS D 78 SHEET 4 AB2 4 THR D 60 GLU D 61 -1 N GLU D 61 O PHE D 64 SHEET 1 AB3 4 ALA D 120 ARG D 125 0 SHEET 2 AB3 4 SER D 133 THR D 138 -1 O LEU D 136 N TYR D 122 SHEET 3 AB3 4 PHE D 169 TRP D 177 -1 O ALA D 174 N PHE D 137 SHEET 4 AB3 4 TYR D 155 ILE D 156 -1 N TYR D 155 O TRP D 177 SHEET 1 AB4 4 ALA D 120 ARG D 125 0 SHEET 2 AB4 4 SER D 133 THR D 138 -1 O LEU D 136 N TYR D 122 SHEET 3 AB4 4 PHE D 169 TRP D 177 -1 O ALA D 174 N PHE D 137 SHEET 4 AB4 4 CYS D 160 MET D 164 -1 N MET D 164 O PHE D 169 SHEET 1 AB5 4 ILE E 5 SER E 7 0 SHEET 2 AB5 4 VAL E 19 LYS E 24 -1 O LYS E 24 N ILE E 5 SHEET 3 AB5 4 PHE E 74 ILE E 79 -1 O ILE E 79 N VAL E 19 SHEET 4 AB5 4 PHE E 65 ASN E 71 -1 N SER E 66 O LYS E 78 SHEET 1 AB6 6 HIS E 10 GLU E 14 0 SHEET 2 AB6 6 THR E 110 LEU E 115 1 O LEU E 115 N THR E 13 SHEET 3 AB6 6 ALA E 88 THR E 95 -1 N ALA E 88 O LEU E 112 SHEET 4 AB6 6 SER E 31 THR E 38 -1 N PHE E 33 O ALA E 93 SHEET 5 AB6 6 GLY E 42 ASN E 50 -1 O LEU E 46 N TRP E 34 SHEET 6 AB6 6 VAL E 53 ASP E 56 -1 O VAL E 53 N ASN E 50 SHEET 1 AB7 4 HIS E 10 GLU E 14 0 SHEET 2 AB7 4 THR E 110 LEU E 115 1 O LEU E 115 N THR E 13 SHEET 3 AB7 4 ALA E 88 THR E 95 -1 N ALA E 88 O LEU E 112 SHEET 4 AB7 4 TYR E 105 PHE E 106 -1 O TYR E 105 N SER E 94 SHEET 1 AB8 4 GLU E 125 PHE E 129 0 SHEET 2 AB8 4 LYS E 141 PHE E 151 -1 O VAL E 145 N PHE E 129 SHEET 3 AB8 4 TYR E 189 SER E 198 -1 O LEU E 191 N ALA E 148 SHEET 4 AB8 4 VAL E 171 THR E 173 -1 N CYS E 172 O ARG E 194 SHEET 1 AB9 4 GLU E 125 PHE E 129 0 SHEET 2 AB9 4 LYS E 141 PHE E 151 -1 O VAL E 145 N PHE E 129 SHEET 3 AB9 4 TYR E 189 SER E 198 -1 O LEU E 191 N ALA E 148 SHEET 4 AB9 4 LEU E 178 LYS E 179 -1 N LEU E 178 O ALA E 190 SHEET 1 AC1 4 LYS E 165 VAL E 167 0 SHEET 2 AC1 4 VAL E 156 VAL E 162 -1 N TRP E 160 O VAL E 167 SHEET 3 AC1 4 HIS E 208 PHE E 215 -1 O ARG E 210 N TRP E 161 SHEET 4 AC1 4 GLN E 234 TRP E 241 -1 O GLN E 234 N PHE E 215 SSBOND 1 CYS A 101 CYS A 164 1555 1555 1.99 SSBOND 2 CYS A 203 CYS A 259 1555 1555 2.04 SSBOND 3 CYS B 25 CYS B 80 1555 1555 2.02 SSBOND 4 CYS D 23 CYS D 92 1555 1555 2.05 SSBOND 5 CYS D 135 CYS D 185 1555 1555 2.05 SSBOND 6 CYS D 160 CYS E 172 1555 1555 2.05 SSBOND 7 CYS E 23 CYS E 92 1555 1555 2.03 SSBOND 8 CYS E 146 CYS E 211 1555 1555 2.06 CISPEP 1 TYR A 209 PRO A 210 0 -1.63 CISPEP 2 HIS B 31 PRO B 32 0 3.70 CISPEP 3 SER E 7 PRO E 8 0 -9.11 CISPEP 4 GLN E 80 PRO E 81 0 -7.34 CISPEP 5 TYR E 152 PRO E 153 0 -8.27 CRYST1 147.366 147.366 178.819 90.00 90.00 120.00 P 65 2 2 12 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 0.006786 0.003918 0.000000 0.00000 SCALE2 0.000000 0.007836 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005592 0.00000