HEADER VIRAL PROTEIN 30-NOV-20 7B3B TITLE STRUCTURE OF ELONGATING SARS-COV-2 RNA-DEPENDENT RNA POLYMERASE WITH TITLE 2 REMDESIVIR AT POSITION -3 (STRUCTURE 1) COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA-DIRECTED RNA POLYMERASE NSP12; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: POL,RDRP,NON-STRUCTURAL PROTEIN 12,NSP12; COMPND 5 EC: 2.7.7.48; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: NON-STRUCTURAL PROTEIN 8; COMPND 9 CHAIN: B; COMPND 10 SYNONYM: NSP8; COMPND 11 ENGINEERED: YES; COMPND 12 MOL_ID: 3; COMPND 13 MOLECULE: NON-STRUCTURAL PROTEIN 7; COMPND 14 CHAIN: C; COMPND 15 SYNONYM: NSP7; COMPND 16 ENGINEERED: YES; COMPND 17 MOL_ID: 4; COMPND 18 MOLECULE: DNA/RNA (5'-R(P*CP*UP*AP*CP*GP*CP*G)-D(P*(RMP))-R(P*UP*G)- COMPND 19 3'); COMPND 20 CHAIN: P; COMPND 21 ENGINEERED: YES; COMPND 22 MOL_ID: 5; COMPND 23 MOLECULE: RNA (5'-R(P*UP*GP*CP*AP*UP*CP*GP*CP*GP*UP*AP*G)-3'); COMPND 24 CHAIN: T; COMPND 25 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS SOURCE 3 2; SOURCE 4 ORGANISM_TAXID: 2697049; SOURCE 5 GENE: REP, 1A-1B; SOURCE 6 EXPRESSION_SYSTEM: TRICHOPLUSIA NI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 7111; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: SEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS SOURCE 10 2; SOURCE 11 ORGANISM_TAXID: 2697049; SOURCE 12 GENE: REP, 1A-1B; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 14 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 15 EXPRESSION_SYSTEM_VARIANT: RIL; SOURCE 16 MOL_ID: 3; SOURCE 17 ORGANISM_SCIENTIFIC: SEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS SOURCE 18 2; SOURCE 19 ORGANISM_TAXID: 2697049; SOURCE 20 GENE: REP, 1A-1B; SOURCE 21 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 22 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 23 EXPRESSION_SYSTEM_VARIANT: RIL; SOURCE 24 MOL_ID: 4; SOURCE 25 SYNTHETIC: YES; SOURCE 26 ORGANISM_SCIENTIFIC: SEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS SOURCE 27 2; SOURCE 28 ORGANISM_TAXID: 2697049; SOURCE 29 MOL_ID: 5; SOURCE 30 SYNTHETIC: YES; SOURCE 31 ORGANISM_SCIENTIFIC: SEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS SOURCE 32 2; SOURCE 33 ORGANISM_TAXID: 2697049 KEYWDS SARS-COV-2, POLYMERASE, TRANSCRIPTION, REPLICATION, RNA, REMDESIVIR, KEYWDS 2 INHIBITION, NUCLEOTIDE ANALOGUE, VIRAL PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR G.KOKIC,H.S.HILLEN,D.TEGUNOV,C.DIENEMANN,F.SEITZ,J.SCHMITZOVA, AUTHOR 2 L.FARNUNG,A.SIEWERT,C.HOEBARTNER,P.CRAMER REVDAT 4 27-JUL-22 7B3B 1 COMPND SOURCE REVDAT 3 03-FEB-21 7B3B 1 JRNL REVDAT 2 27-JAN-21 7B3B 1 JRNL REVDAT 1 23-DEC-20 7B3B 0 JRNL AUTH G.KOKIC,H.S.HILLEN,D.TEGUNOV,C.DIENEMANN,F.SEITZ, JRNL AUTH 2 J.SCHMITZOVA,L.FARNUNG,A.SIEWERT,C.HOBARTNER,P.CRAMER JRNL TITL MECHANISM OF SARS-COV-2 POLYMERASE STALLING BY REMDESIVIR. JRNL REF NAT COMMUN V. 12 279 2021 JRNL REFN ESSN 2041-1723 JRNL PMID 33436624 JRNL DOI 10.1038/S41467-020-20542-0 REMARK 2 REMARK 2 RESOLUTION. 3.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : WARP, SERIALEM, WARP, COOT, PHENIX, REMARK 3 CRYOSPARC REMARK 3 RECONSTRUCTION SCHEMA : BACK PROJECTION REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : 6YYT REMARK 3 REFINEMENT SPACE : REAL REMARK 3 REFINEMENT PROTOCOL : OTHER REMARK 3 REFINEMENT TARGET : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE : NULL REMARK 3 REMARK 3 FITTING PROCEDURE : NULL REMARK 3 REMARK 3 EM IMAGE RECONSTRUCTION STATISTICS REMARK 3 NOMINAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 ACTUAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 EFFECTIVE RESOLUTION (ANGSTROMS) : 3.100 REMARK 3 NUMBER OF PARTICLES : 653972 REMARK 3 CTF CORRECTION METHOD : PHASE FLIPPING AND AMPLITUDE REMARK 3 CORRECTION REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL REMARK 3 REMARK 3 OTHER DETAILS: M WAS USED REMARK 4 REMARK 4 7B3B COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 30-NOV-20. REMARK 100 THE DEPOSITION ID IS D_1292112531. REMARK 245 REMARK 245 EXPERIMENTAL DETAILS REMARK 245 RECONSTRUCTION METHOD : SINGLE PARTICLE REMARK 245 SPECIMEN TYPE : NULL REMARK 245 REMARK 245 ELECTRON MICROSCOPE SAMPLE REMARK 245 SAMPLE TYPE : PARTICLE REMARK 245 PARTICLE TYPE : POINT REMARK 245 NAME OF SAMPLE : SARS-COV-2 RNA-DEPENDENT RNA REMARK 245 POLYMERASE COMPLEX (NSP12, NSP7, REMARK 245 NSP8) WITH ELONGATION SCAFFOLD REMARK 245 CONTAINING REMDESIVIR AT REMARK 245 POSITION -3.; SARS-COV-2 RNA- REMARK 245 DEPENDENT RNA POLYMERASE (NSP12) REMARK 245 ; SARS-COV-2 NSP7 AND NSP8; DNA REMARK 245 AND RNA REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 2.00 REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : NULL REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 7.40 REMARK 245 SAMPLE DETAILS : NULL REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : NULL REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : NULL REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : FEI TITAN KRIOS REMARK 245 DETECTOR TYPE : GATAN K3 BIOQUANTUM (6K X REMARK 245 4K) REMARK 245 MINIMUM DEFOCUS (NM) : NULL REMARK 245 MAXIMUM DEFOCUS (NM) : NULL REMARK 245 MINIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 NOMINAL CS : 2.70 REMARK 245 IMAGING MODE : OTHER REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 6000.00 REMARK 245 ILLUMINATION MODE : OTHER REMARK 245 NOMINAL MAGNIFICATION : 105000 REMARK 245 CALIBRATED MAGNIFICATION : NULL REMARK 245 SOURCE : FIELD EMISSION GUN REMARK 245 ACCELERATION VOLTAGE (KV) : 300 REMARK 245 IMAGING DETAILS : 30 DEG TILT. REMARK 247 REMARK 247 ELECTRON MICROSCOPY REMARK 247 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM ELECTRON REMARK 247 MICROSCOPY DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE REMARK 247 THAT CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES REMARK 247 ON THESE RECORDS ARE MEANINGLESS EXCEPT FOR THE CALCULATION REMARK 247 OF THE STRUCTURE FACTORS. 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: 11200 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 40880 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -93.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, P, T 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 SER A -2 REMARK 465 ASN A -1 REMARK 465 ALA A 0 REMARK 465 SER A 1 REMARK 465 ALA A 2 REMARK 465 ASP A 3 REMARK 465 ALA A 4 REMARK 465 GLN A 5 REMARK 465 SER A 6 REMARK 465 PHE A 7 REMARK 465 LEU A 8 REMARK 465 ASN A 9 REMARK 465 ARG A 10 REMARK 465 VAL A 11 REMARK 465 CYS A 12 REMARK 465 GLY A 13 REMARK 465 VAL A 14 REMARK 465 SER A 15 REMARK 465 ALA A 16 REMARK 465 ALA A 17 REMARK 465 ARG A 18 REMARK 465 LEU A 19 REMARK 465 THR A 20 REMARK 465 PRO A 21 REMARK 465 CYS A 22 REMARK 465 GLY A 23 REMARK 465 THR A 24 REMARK 465 GLY A 25 REMARK 465 THR A 26 REMARK 465 SER A 27 REMARK 465 THR A 28 REMARK 465 ASP A 29 REMARK 465 VAL A 30 REMARK 465 THR A 51 REMARK 465 ASN A 52 REMARK 465 CYS A 53 REMARK 465 CYS A 54 REMARK 465 ARG A 55 REMARK 465 PHE A 56 REMARK 465 GLN A 57 REMARK 465 GLU A 58 REMARK 465 LYS A 59 REMARK 465 ASP A 60 REMARK 465 GLU A 61 REMARK 465 ASP A 62 REMARK 465 ASP A 63 REMARK 465 ASN A 64 REMARK 465 LEU A 65 REMARK 465 ILE A 66 REMARK 465 ASP A 67 REMARK 465 SER A 68 REMARK 465 TYR A 69 REMARK 465 PHE A 70 REMARK 465 VAL A 71 REMARK 465 VAL A 72 REMARK 465 LYS A 73 REMARK 465 ARG A 74 REMARK 465 HIS A 75 REMARK 465 THR A 76 REMARK 465 PHE A 77 REMARK 465 SER A 78 REMARK 465 ASN A 79 REMARK 465 TYR A 80 REMARK 465 GLN A 81 REMARK 465 HIS A 82 REMARK 465 GLU A 83 REMARK 465 GLU A 84 REMARK 465 THR A 85 REMARK 465 ILE A 86 REMARK 465 TYR A 87 REMARK 465 ASN A 88 REMARK 465 LEU A 89 REMARK 465 LEU A 90 REMARK 465 LYS A 91 REMARK 465 ASP A 92 REMARK 465 CYS A 93 REMARK 465 PRO A 94 REMARK 465 ALA A 95 REMARK 465 VAL A 96 REMARK 465 ALA A 97 REMARK 465 LYS A 98 REMARK 465 HIS A 99 REMARK 465 ASP A 100 REMARK 465 PHE A 101 REMARK 465 PHE A 102 REMARK 465 LYS A 103 REMARK 465 PHE A 104 REMARK 465 ARG A 105 REMARK 465 ILE A 106 REMARK 465 ASP A 107 REMARK 465 GLY A 108 REMARK 465 ASP A 109 REMARK 465 MET A 110 REMARK 465 VAL A 111 REMARK 465 PRO A 112 REMARK 465 HIS A 113 REMARK 465 ILE A 114 REMARK 465 SER A 115 REMARK 465 ARG A 116 REMARK 465 GLN A 117 REMARK 465 HIS A 362 REMARK 465 SER A 363 REMARK 465 SER A 364 REMARK 465 ARG A 365 REMARK 465 LEU A 366 REMARK 465 GLY A 897 REMARK 465 HIS A 898 REMARK 465 MET A 899 REMARK 465 LEU A 900 REMARK 465 ASP A 901 REMARK 465 MET A 902 REMARK 465 TYR A 903 REMARK 465 SER A 904 REMARK 465 VAL A 905 REMARK 465 MET A 906 REMARK 465 LEU A 907 REMARK 465 THR A 908 REMARK 465 ASN A 909 REMARK 465 VAL A 930 REMARK 465 LEU A 931 REMARK 465 GLN A 932 REMARK 465 SER B -2 REMARK 465 ASN B -1 REMARK 465 ALA B 0 REMARK 465 ALA B 1 REMARK 465 ILE B 2 REMARK 465 ALA B 3 REMARK 465 SER B 4 REMARK 465 GLU B 5 REMARK 465 PHE B 6 REMARK 465 SER B 7 REMARK 465 SER B 8 REMARK 465 LEU B 9 REMARK 465 PRO B 10 REMARK 465 SER B 11 REMARK 465 TYR B 12 REMARK 465 ALA B 13 REMARK 465 ALA B 14 REMARK 465 PHE B 15 REMARK 465 ALA B 16 REMARK 465 THR B 17 REMARK 465 ALA B 18 REMARK 465 GLN B 19 REMARK 465 GLU B 20 REMARK 465 ALA B 21 REMARK 465 TYR B 22 REMARK 465 GLU B 23 REMARK 465 GLN B 24 REMARK 465 ALA B 25 REMARK 465 VAL B 26 REMARK 465 ALA B 27 REMARK 465 ASN B 28 REMARK 465 GLY B 29 REMARK 465 ASP B 30 REMARK 465 SER B 31 REMARK 465 GLU B 32 REMARK 465 VAL B 33 REMARK 465 VAL B 34 REMARK 465 LEU B 35 REMARK 465 LYS B 36 REMARK 465 LYS B 37 REMARK 465 LEU B 38 REMARK 465 LYS B 39 REMARK 465 LYS B 40 REMARK 465 SER B 41 REMARK 465 LEU B 42 REMARK 465 ASN B 43 REMARK 465 VAL B 44 REMARK 465 ALA B 45 REMARK 465 LYS B 46 REMARK 465 SER B 47 REMARK 465 GLU B 48 REMARK 465 PHE B 49 REMARK 465 ASP B 50 REMARK 465 ARG B 51 REMARK 465 ASP B 52 REMARK 465 ALA B 53 REMARK 465 ALA B 54 REMARK 465 MET B 55 REMARK 465 GLN B 56 REMARK 465 ARG B 57 REMARK 465 LYS B 58 REMARK 465 LEU B 59 REMARK 465 GLU B 60 REMARK 465 LYS B 61 REMARK 465 MET B 62 REMARK 465 ALA B 63 REMARK 465 ASP B 64 REMARK 465 GLN B 65 REMARK 465 ALA B 66 REMARK 465 MET B 67 REMARK 465 THR B 68 REMARK 465 GLN B 69 REMARK 465 MET B 70 REMARK 465 TYR B 71 REMARK 465 LYS B 72 REMARK 465 GLN B 73 REMARK 465 ALA B 74 REMARK 465 ARG B 75 REMARK 465 SER B 76 REMARK 465 ASN B 192 REMARK 465 SER B 193 REMARK 465 ALA B 194 REMARK 465 VAL B 195 REMARK 465 LYS B 196 REMARK 465 LEU B 197 REMARK 465 GLN B 198 REMARK 465 SER C -2 REMARK 465 ASN C -1 REMARK 465 ALA C 0 REMARK 465 GLN C 63 REMARK 465 GLY C 64 REMARK 465 ALA C 65 REMARK 465 VAL C 66 REMARK 465 ASP C 67 REMARK 465 ILE C 68 REMARK 465 ASN C 69 REMARK 465 LYS C 70 REMARK 465 LEU C 71 REMARK 465 CYS C 72 REMARK 465 GLU C 73 REMARK 465 GLU C 74 REMARK 465 MET C 75 REMARK 465 LEU C 76 REMARK 465 ASP C 77 REMARK 465 ASN C 78 REMARK 465 ARG C 79 REMARK 465 ALA C 80 REMARK 465 THR C 81 REMARK 465 LEU C 82 REMARK 465 GLN C 83 REMARK 465 U P 1 REMARK 465 G P 2 REMARK 465 A P 3 REMARK 465 G P 4 REMARK 465 C P 5 REMARK 465 U T 1 REMARK 465 U T 2 REMARK 465 U T 3 REMARK 465 U T 4 REMARK 465 C T 5 REMARK 465 A T 6 REMARK 465 G T 19 REMARK 465 C T 20 REMARK 465 U T 21 REMARK 465 C T 22 REMARK 465 A T 23 REMARK 465 U T 24 REMARK 465 A T 25 REMARK 465 C T 26 REMARK 465 C T 27 REMARK 465 G T 28 REMARK 465 U T 29 REMARK 465 A T 30 REMARK 465 U T 31 REMARK 465 U T 32 REMARK 465 G T 33 REMARK 465 A T 34 REMARK 465 G T 35 REMARK 465 A T 36 REMARK 465 C T 37 REMARK 465 C T 38 REMARK 465 U T 39 REMARK 465 U T 40 REMARK 465 U T 41 REMARK 465 U T 42 REMARK 465 G T 43 REMARK 465 G T 44 REMARK 465 U T 45 REMARK 465 C T 46 REMARK 465 U T 47 REMARK 465 C T 48 REMARK 465 A T 49 REMARK 465 A T 50 REMARK 465 U T 51 REMARK 465 A T 52 REMARK 465 C T 53 REMARK 465 G T 54 REMARK 465 G T 55 REMARK 465 U T 56 REMARK 465 A T 57 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 PHE A 287 66.38 -108.08 REMARK 500 VAL A 398 -71.35 -92.65 REMARK 500 VAL A 662 -59.06 -144.18 REMARK 500 THR A 686 43.95 -103.51 REMARK 500 PHE A 753 66.09 -158.50 REMARK 500 GLN A 789 -63.18 -101.83 REMARK 500 ASP A 824 -4.02 75.10 REMARK 500 THR B 141 -78.84 -96.47 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A2000 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 295 ND1 REMARK 620 2 CYS A 301 SG 109.6 REMARK 620 3 CYS A 306 SG 108.4 115.4 REMARK 620 4 CYS A 310 SG 120.5 91.8 110.7 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A2001 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 487 SG REMARK 620 2 HIS A 642 ND1 78.7 REMARK 620 3 CYS A 645 SG 125.5 101.8 REMARK 620 4 CYS A 646 SG 89.8 101.9 140.6 REMARK 620 N 1 2 3 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-11993 RELATED DB: EMDB REMARK 900 STRUCTURE OF ELONGATING SARS-COV-2 RNA-DEPENDENT RNA POLYMERASE REMARK 900 WITH REMDESIVIR AT POSITION -3 (STRUCTURE 1) REMARK 900 RELATED ID: EMD-11995 RELATED DB: EMDB REMARK 900 RELATED ID: EMD-11994 RELATED DB: EMDB DBREF 7B3B A 1 932 UNP P0DTD1 R1AB_SARS2 4393 5324 DBREF 7B3B B 1 198 UNP P0DTD1 R1AB_SARS2 3943 4140 DBREF 7B3B C 1 83 UNP P0DTD1 R1AB_SARS2 3860 3942 DBREF 7B3B P 1 15 PDB 7B3B 7B3B 1 15 DBREF 7B3B T 1 57 PDB 7B3B 7B3B 1 57 SEQADV 7B3B SER A -2 UNP P0DTD1 EXPRESSION TAG SEQADV 7B3B ASN A -1 UNP P0DTD1 EXPRESSION TAG SEQADV 7B3B ALA A 0 UNP P0DTD1 EXPRESSION TAG SEQADV 7B3B SER B -2 UNP P0DTD1 EXPRESSION TAG SEQADV 7B3B ASN B -1 UNP P0DTD1 EXPRESSION TAG SEQADV 7B3B ALA B 0 UNP P0DTD1 EXPRESSION TAG SEQADV 7B3B SER C -2 UNP P0DTD1 EXPRESSION TAG SEQADV 7B3B ASN C -1 UNP P0DTD1 EXPRESSION TAG SEQADV 7B3B ALA C 0 UNP P0DTD1 EXPRESSION TAG SEQRES 1 A 935 SER ASN ALA SER ALA ASP ALA GLN SER PHE LEU ASN ARG SEQRES 2 A 935 VAL CYS GLY VAL SER ALA ALA ARG LEU THR PRO CYS GLY SEQRES 3 A 935 THR GLY THR SER THR ASP VAL VAL TYR ARG ALA PHE ASP SEQRES 4 A 935 ILE TYR ASN ASP LYS VAL ALA GLY PHE ALA LYS PHE LEU SEQRES 5 A 935 LYS THR ASN CYS CYS ARG PHE GLN GLU LYS ASP GLU ASP SEQRES 6 A 935 ASP ASN LEU ILE ASP SER TYR PHE VAL VAL LYS ARG HIS SEQRES 7 A 935 THR PHE SER ASN TYR GLN HIS GLU GLU THR ILE TYR ASN SEQRES 8 A 935 LEU LEU LYS ASP CYS PRO ALA VAL ALA LYS HIS ASP PHE SEQRES 9 A 935 PHE LYS PHE ARG ILE ASP GLY ASP MET VAL PRO HIS ILE SEQRES 10 A 935 SER ARG GLN ARG LEU THR LYS TYR THR MET ALA ASP LEU SEQRES 11 A 935 VAL TYR ALA LEU ARG HIS PHE ASP GLU GLY ASN CYS ASP SEQRES 12 A 935 THR LEU LYS GLU ILE LEU VAL THR TYR ASN CYS CYS ASP SEQRES 13 A 935 ASP ASP TYR PHE ASN LYS LYS ASP TRP TYR ASP PHE VAL SEQRES 14 A 935 GLU ASN PRO ASP ILE LEU ARG VAL TYR ALA ASN LEU GLY SEQRES 15 A 935 GLU ARG VAL ARG GLN ALA LEU LEU LYS THR VAL GLN PHE SEQRES 16 A 935 CYS ASP ALA MET ARG ASN ALA GLY ILE VAL GLY VAL LEU SEQRES 17 A 935 THR LEU ASP ASN GLN ASP LEU ASN GLY ASN TRP TYR ASP SEQRES 18 A 935 PHE GLY ASP PHE ILE GLN THR THR PRO GLY SER GLY VAL SEQRES 19 A 935 PRO VAL VAL ASP SER TYR TYR SER LEU LEU MET PRO ILE SEQRES 20 A 935 LEU THR LEU THR ARG ALA LEU THR ALA GLU SER HIS VAL SEQRES 21 A 935 ASP THR ASP LEU THR LYS PRO TYR ILE LYS TRP ASP LEU SEQRES 22 A 935 LEU LYS TYR ASP PHE THR GLU GLU ARG LEU LYS LEU PHE SEQRES 23 A 935 ASP ARG TYR PHE LYS TYR TRP ASP GLN THR TYR HIS PRO SEQRES 24 A 935 ASN CYS VAL ASN CYS LEU ASP ASP ARG CYS ILE LEU HIS SEQRES 25 A 935 CYS ALA ASN PHE ASN VAL LEU PHE SER THR VAL PHE PRO SEQRES 26 A 935 PRO THR SER PHE GLY PRO LEU VAL ARG LYS ILE PHE VAL SEQRES 27 A 935 ASP GLY VAL PRO PHE VAL VAL SER THR GLY TYR HIS PHE SEQRES 28 A 935 ARG GLU LEU GLY VAL VAL HIS ASN GLN ASP VAL ASN LEU SEQRES 29 A 935 HIS SER SER ARG LEU SER PHE LYS GLU LEU LEU VAL TYR SEQRES 30 A 935 ALA ALA ASP PRO ALA MET HIS ALA ALA SER GLY ASN LEU SEQRES 31 A 935 LEU LEU ASP LYS ARG THR THR CYS PHE SER VAL ALA ALA SEQRES 32 A 935 LEU THR ASN ASN VAL ALA PHE GLN THR VAL LYS PRO GLY SEQRES 33 A 935 ASN PHE ASN LYS ASP PHE TYR ASP PHE ALA VAL SER LYS SEQRES 34 A 935 GLY PHE PHE LYS GLU GLY SER SER VAL GLU LEU LYS HIS SEQRES 35 A 935 PHE PHE PHE ALA GLN ASP GLY ASN ALA ALA ILE SER ASP SEQRES 36 A 935 TYR ASP TYR TYR ARG TYR ASN LEU PRO THR MET CYS ASP SEQRES 37 A 935 ILE ARG GLN LEU LEU PHE VAL VAL GLU VAL VAL ASP LYS SEQRES 38 A 935 TYR PHE ASP CYS TYR ASP GLY GLY CYS ILE ASN ALA ASN SEQRES 39 A 935 GLN VAL ILE VAL ASN ASN LEU ASP LYS SER ALA GLY PHE SEQRES 40 A 935 PRO PHE ASN LYS TRP GLY LYS ALA ARG LEU TYR TYR ASP SEQRES 41 A 935 SER MET SER TYR GLU ASP GLN ASP ALA LEU PHE ALA TYR SEQRES 42 A 935 THR LYS ARG ASN VAL ILE PRO THR ILE THR GLN MET ASN SEQRES 43 A 935 LEU LYS TYR ALA ILE SER ALA LYS ASN ARG ALA ARG THR SEQRES 44 A 935 VAL ALA GLY VAL SER ILE CYS SER THR MET THR ASN ARG SEQRES 45 A 935 GLN PHE HIS GLN LYS LEU LEU LYS SER ILE ALA ALA THR SEQRES 46 A 935 ARG GLY ALA THR VAL VAL ILE GLY THR SER LYS PHE TYR SEQRES 47 A 935 GLY GLY TRP HIS ASN MET LEU LYS THR VAL TYR SER ASP SEQRES 48 A 935 VAL GLU ASN PRO HIS LEU MET GLY TRP ASP TYR PRO LYS SEQRES 49 A 935 CYS ASP ARG ALA MET PRO ASN MET LEU ARG ILE MET ALA SEQRES 50 A 935 SER LEU VAL LEU ALA ARG LYS HIS THR THR CYS CYS SER SEQRES 51 A 935 LEU SER HIS ARG PHE TYR ARG LEU ALA ASN GLU CYS ALA SEQRES 52 A 935 GLN VAL LEU SER GLU MET VAL MET CYS GLY GLY SER LEU SEQRES 53 A 935 TYR VAL LYS PRO GLY GLY THR SER SER GLY ASP ALA THR SEQRES 54 A 935 THR ALA TYR ALA ASN SER VAL PHE ASN ILE CYS GLN ALA SEQRES 55 A 935 VAL THR ALA ASN VAL ASN ALA LEU LEU SER THR ASP GLY SEQRES 56 A 935 ASN LYS ILE ALA ASP LYS TYR VAL ARG ASN LEU GLN HIS SEQRES 57 A 935 ARG LEU TYR GLU CYS LEU TYR ARG ASN ARG ASP VAL ASP SEQRES 58 A 935 THR ASP PHE VAL ASN GLU PHE TYR ALA TYR LEU ARG LYS SEQRES 59 A 935 HIS PHE SER MET MET ILE LEU SER ASP ASP ALA VAL VAL SEQRES 60 A 935 CYS PHE ASN SER THR TYR ALA SER GLN GLY LEU VAL ALA SEQRES 61 A 935 SER ILE LYS ASN PHE LYS SER VAL LEU TYR TYR GLN ASN SEQRES 62 A 935 ASN VAL PHE MET SER GLU ALA LYS CYS TRP THR GLU THR SEQRES 63 A 935 ASP LEU THR LYS GLY PRO HIS GLU PHE CYS SER GLN HIS SEQRES 64 A 935 THR MET LEU VAL LYS GLN GLY ASP ASP TYR VAL TYR LEU SEQRES 65 A 935 PRO TYR PRO ASP PRO SER ARG ILE LEU GLY ALA GLY CYS SEQRES 66 A 935 PHE VAL ASP ASP ILE VAL LYS THR ASP GLY THR LEU MET SEQRES 67 A 935 ILE GLU ARG PHE VAL SER LEU ALA ILE ASP ALA TYR PRO SEQRES 68 A 935 LEU THR LYS HIS PRO ASN GLN GLU TYR ALA ASP VAL PHE SEQRES 69 A 935 HIS LEU TYR LEU GLN TYR ILE ARG LYS LEU HIS ASP GLU SEQRES 70 A 935 LEU THR GLY HIS MET LEU ASP MET TYR SER VAL MET LEU SEQRES 71 A 935 THR ASN ASP ASN THR SER ARG TYR TRP GLU PRO GLU PHE SEQRES 72 A 935 TYR GLU ALA MET TYR THR PRO HIS THR VAL LEU GLN SEQRES 1 B 201 SER ASN ALA ALA ILE ALA SER GLU PHE SER SER LEU PRO SEQRES 2 B 201 SER TYR ALA ALA PHE ALA THR ALA GLN GLU ALA TYR GLU SEQRES 3 B 201 GLN ALA VAL ALA ASN GLY ASP SER GLU VAL VAL LEU LYS SEQRES 4 B 201 LYS LEU LYS LYS SER LEU ASN VAL ALA LYS SER GLU PHE SEQRES 5 B 201 ASP ARG ASP ALA ALA MET GLN ARG LYS LEU GLU LYS MET SEQRES 6 B 201 ALA ASP GLN ALA MET THR GLN MET TYR LYS GLN ALA ARG SEQRES 7 B 201 SER GLU ASP LYS ARG ALA LYS VAL THR SER ALA MET GLN SEQRES 8 B 201 THR MET LEU PHE THR MET LEU ARG LYS LEU ASP ASN ASP SEQRES 9 B 201 ALA LEU ASN ASN ILE ILE ASN ASN ALA ARG ASP GLY CYS SEQRES 10 B 201 VAL PRO LEU ASN ILE ILE PRO LEU THR THR ALA ALA LYS SEQRES 11 B 201 LEU MET VAL VAL ILE PRO ASP TYR ASN THR TYR LYS ASN SEQRES 12 B 201 THR CYS ASP GLY THR THR PHE THR TYR ALA SER ALA LEU SEQRES 13 B 201 TRP GLU ILE GLN GLN VAL VAL ASP ALA ASP SER LYS ILE SEQRES 14 B 201 VAL GLN LEU SER GLU ILE SER MET ASP ASN SER PRO ASN SEQRES 15 B 201 LEU ALA TRP PRO LEU ILE VAL THR ALA LEU ARG ALA ASN SEQRES 16 B 201 SER ALA VAL LYS LEU GLN SEQRES 1 C 86 SER ASN ALA SER LYS MET SER ASP VAL LYS CYS THR SER SEQRES 2 C 86 VAL VAL LEU LEU SER VAL LEU GLN GLN LEU ARG VAL GLU SEQRES 3 C 86 SER SER SER LYS LEU TRP ALA GLN CYS VAL GLN LEU HIS SEQRES 4 C 86 ASN ASP ILE LEU LEU ALA LYS ASP THR THR GLU ALA PHE SEQRES 5 C 86 GLU LYS MET VAL SER LEU LEU SER VAL LEU LEU SER MET SEQRES 6 C 86 GLN GLY ALA VAL ASP ILE ASN LYS LEU CYS GLU GLU MET SEQRES 7 C 86 LEU ASP ASN ARG ALA THR LEU GLN SEQRES 1 P 15 U G A G C C U A C G C G F86 SEQRES 2 P 15 U G SEQRES 1 T 57 U U U U C A U G C A U C G SEQRES 2 T 57 C G U A G G C U C A U A C SEQRES 3 T 57 C G U A U U G A G A C C U SEQRES 4 T 57 U U U G G U C U C A A U A SEQRES 5 T 57 C G G U A HET F86 P 13 24 HET ZN A2000 1 HET ZN A2001 1 HETNAM F86 [(2~{R},3~{S},4~{R},5~{R})-5-(4-AZANYLPYRROLO[2,1-F][1, HETNAM 2 F86 2,4]TRIAZIN-7-YL)-5-CYANO-3,4-BIS(OXIDANYL)OXOLAN-2- HETNAM 3 F86 YL]METHYL DIHYDROGEN PHOSPHATE HETNAM ZN ZINC ION HETSYN F86 REMDESIVIR, BOUND FORM FORMUL 4 F86 C12 H14 N5 O7 P FORMUL 6 ZN 2(ZN 2+) HELIX 1 AA1 THR A 123 HIS A 133 1 11 HELIX 2 AA2 CYS A 139 TYR A 149 1 11 HELIX 3 AA3 ASP A 153 LYS A 159 1 7 HELIX 4 AA4 ASP A 170 GLY A 200 1 31 HELIX 5 AA5 THR A 206 GLN A 210 5 5 HELIX 6 AA6 VAL A 234 THR A 248 1 15 HELIX 7 AA7 ARG A 249 ASP A 260 5 12 HELIX 8 AA8 PHE A 275 PHE A 287 1 13 HELIX 9 AA9 ASN A 297 CYS A 301 5 5 HELIX 10 AB1 ASP A 303 THR A 319 1 17 HELIX 11 AB2 PHE A 368 ASP A 377 1 10 HELIX 12 AB3 ASP A 377 SER A 384 1 8 HELIX 13 AB4 ASN A 416 LYS A 426 1 11 HELIX 14 AB5 ASN A 447 TYR A 455 1 9 HELIX 15 AB6 TYR A 456 ASN A 459 5 4 HELIX 16 AB7 ASP A 465 TYR A 479 1 15 HELIX 17 AB8 ASN A 489 VAL A 493 5 5 HELIX 18 AB9 PRO A 505 TRP A 509 5 5 HELIX 19 AC1 LYS A 511 MET A 519 1 9 HELIX 20 AC2 SER A 520 LYS A 532 1 13 HELIX 21 AC3 SER A 561 ALA A 581 1 21 HELIX 22 AC4 GLY A 596 TYR A 606 1 11 HELIX 23 AC5 LYS A 621 MET A 626 1 6 HELIX 24 AC6 PRO A 627 ARG A 640 1 14 HELIX 25 AC7 SER A 647 VAL A 662 1 16 HELIX 26 AC8 THR A 686 THR A 710 1 25 HELIX 27 AC9 ASP A 717 ARG A 733 1 17 HELIX 28 AD1 ASP A 738 HIS A 752 1 15 HELIX 29 AD2 SER A 768 GLN A 773 1 6 HELIX 30 AD3 SER A 778 GLN A 789 1 12 HELIX 31 AD4 SER A 795 CYS A 799 5 5 HELIX 32 AD5 ASP A 833 CYS A 842 1 10 HELIX 33 AD6 THR A 853 TYR A 867 1 15 HELIX 34 AD7 PRO A 868 HIS A 872 5 5 HELIX 35 AD8 ASN A 874 THR A 896 1 23 HELIX 36 AD9 THR A 912 GLU A 917 1 6 HELIX 37 AE1 PRO A 918 MET A 924 1 7 HELIX 38 AE2 ASP B 78 LYS B 97 1 20 HELIX 39 AE3 ASP B 99 ALA B 110 1 12 HELIX 40 AE4 ASN B 118 ALA B 125 1 8 HELIX 41 AE5 ASP B 134 CYS B 142 1 9 HELIX 42 AE6 ASN B 176 LEU B 180 5 5 HELIX 43 AE7 LYS C 2 LEU C 20 1 19 HELIX 44 AE8 ARG C 21 SER C 24 5 4 HELIX 45 AE9 SER C 25 LEU C 41 1 17 HELIX 46 AF1 ASP C 44 MET C 62 1 19 SHEET 1 AA1 2 TYR A 32 TYR A 38 0 SHEET 2 AA1 2 ALA A 43 LEU A 49 -1 O GLY A 44 N ILE A 37 SHEET 1 AA2 2 ILE A 201 VAL A 202 0 SHEET 2 AA2 2 ILE A 223 GLN A 224 -1 O ILE A 223 N VAL A 202 SHEET 1 AA3 4 GLY A 352 HIS A 355 0 SHEET 2 AA3 4 VAL A 338 PHE A 348 -1 N PHE A 348 O GLY A 352 SHEET 3 AA3 4 GLY A 327 VAL A 335 -1 N VAL A 335 O VAL A 338 SHEET 4 AA3 4 VAL B 115 PRO B 116 -1 O VAL B 115 N VAL A 330 SHEET 1 AA410 THR A 556 GLY A 559 0 SHEET 2 AA410 ILE A 539 LEU A 544 -1 N ASN A 543 O VAL A 557 SHEET 3 AA410 MET A 666 MET A 668 1 O MET A 666 N THR A 540 SHEET 4 AA410 SER A 672 VAL A 675 -1 O TYR A 674 N VAL A 667 SHEET 5 AA410 SER A 397 ALA A 400 -1 N ALA A 399 O LEU A 673 SHEET 6 AA410 ASN A 386 ASP A 390 -1 N ASN A 386 O ALA A 400 SHEET 7 AA410 LYS B 127 ILE B 132 1 O MET B 129 N LEU A 389 SHEET 8 AA410 LEU B 184 ARG B 190 -1 O VAL B 186 N VAL B 130 SHEET 9 AA410 ALA B 152 VAL B 160 -1 N GLN B 157 O THR B 187 SHEET 10 AA410 THR B 146 TYR B 149 -1 N PHE B 147 O TRP B 154 SHEET 1 AA5 2 ASN A 414 PHE A 415 0 SHEET 2 AA5 2 PHE A 843 VAL A 844 -1 O VAL A 844 N ASN A 414 SHEET 1 AA6 4 PHE A 753 ILE A 757 0 SHEET 2 AA6 4 ALA A 762 ASN A 767 -1 O CYS A 765 N SER A 754 SHEET 3 AA6 4 PRO A 612 GLY A 616 -1 N HIS A 613 O PHE A 766 SHEET 4 AA6 4 TRP A 800 GLU A 802 -1 O GLU A 802 N LEU A 614 SHEET 1 AA7 2 GLN A 815 GLN A 822 0 SHEET 2 AA7 2 ASP A 825 PRO A 832 -1 O ASP A 825 N GLN A 822 LINK O3' G P 12 P1 F86 P 13 1555 1555 1.59 LINK O3 F86 P 13 P U P 14 1555 1555 1.59 LINK ND1 HIS A 295 ZN ZN A2000 1555 1555 2.08 LINK SG CYS A 301 ZN ZN A2000 1555 1555 2.33 LINK SG CYS A 306 ZN ZN A2000 1555 1555 2.34 LINK SG CYS A 310 ZN ZN A2000 1555 1555 2.33 LINK SG CYS A 487 ZN ZN A2001 1555 1555 2.31 LINK ND1 HIS A 642 ZN ZN A2001 1555 1555 2.32 LINK SG CYS A 645 ZN ZN A2001 1555 1555 2.33 LINK SG CYS A 646 ZN ZN A2001 1555 1555 2.32 CISPEP 1 PHE A 504 PRO A 505 0 -1.27 CISPEP 2 TRP B 182 PRO B 183 0 4.53 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000