HEADER VIRAL PROTEIN 31-MAR-20 6YHU TITLE CRYSTAL STRUCTURE OF THE NSP7-NSP8 COMPLEX OF SARS-COV-2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: REPLICASE POLYPROTEIN 1A; COMPND 3 CHAIN: A, C; COMPND 4 SYNONYM: PP1A,ORF1A POLYPROTEIN; COMPND 5 EC: 3.4.19.12,3.4.22.-,3.4.22.69; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: REPLICASE POLYPROTEIN 1A; COMPND 9 CHAIN: B, D; COMPND 10 SYNONYM: PP1A,ORF1A POLYPROTEIN; COMPND 11 EC: 3.4.19.12,3.4.22.-,3.4.22.69; 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 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: SEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS SOURCE 10 2; SOURCE 11 ORGANISM_COMMON: 2019-NCOV; SOURCE 12 ORGANISM_TAXID: 2697049; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 14 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS NSP7, NSP8, SARS-COV-2, NCOV-2019, COVID-19, VIRAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR E.KONKOLOVA,M.KLIMA,E.BOURA REVDAT 4 24-JAN-24 6YHU 1 REMARK REVDAT 3 11-NOV-20 6YHU 1 JRNL REVDAT 2 06-MAY-20 6YHU 1 COMPND SOURCE DBREF REVDAT 1 29-APR-20 6YHU 0 JRNL AUTH E.KONKOLOVA,M.KLIMA,R.NENCKA,E.BOURA JRNL TITL STRUCTURAL ANALYSIS OF THE PUTATIVE SARS-COV-2 PRIMASE JRNL TITL 2 COMPLEX. JRNL REF J.STRUCT.BIOL. V. 211 07548 2020 JRNL REFN ESSN 1095-8657 JRNL PMID 32535228 JRNL DOI 10.1016/J.JSB.2020.107548 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.9_1692 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.79 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.353 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 23317 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.216 REMARK 3 R VALUE (WORKING SET) : 0.214 REMARK 3 FREE R VALUE : 0.239 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.001 REMARK 3 FREE R VALUE TEST SET COUNT : 1166 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 38.7868 - 3.9988 1.00 2854 150 0.1766 0.1971 REMARK 3 2 3.9988 - 3.1744 1.00 2803 148 0.2014 0.1935 REMARK 3 3 3.1744 - 2.7733 1.00 2789 146 0.2383 0.2832 REMARK 3 4 2.7733 - 2.5198 1.00 2754 145 0.2366 0.2730 REMARK 3 5 2.5198 - 2.3392 1.00 2781 147 0.2419 0.2514 REMARK 3 6 2.3392 - 2.2013 1.00 2746 145 0.2344 0.3316 REMARK 3 7 2.2013 - 2.0910 1.00 2741 144 0.2378 0.2763 REMARK 3 8 2.0910 - 2.0000 0.96 2683 141 0.2666 0.2837 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.242 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.206 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 25.54 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 30.32 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.002 2923 REMARK 3 ANGLE : 0.603 3967 REMARK 3 CHIRALITY : 0.021 503 REMARK 3 PLANARITY : 0.002 492 REMARK 3 DIHEDRAL : 12.058 1081 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 6YHU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 31-MAR-20. REMARK 100 THE DEPOSITION ID IS D_1292107631. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-MAR-20 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU MICROMAX-007 HF REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.541870 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 200K REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS MAR 15, 2019 REMARK 200 DATA SCALING SOFTWARE : XDS MAR 15, 2019 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 23341 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 38.790 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 6.400 REMARK 200 R MERGE (I) : 0.07411 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.07 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.52170 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.880 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.5.6 REMARK 200 STARTING MODEL: 2AHM REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.14 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.09 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M MAGNESIUM CHLORID HEXAHYDRATE, REMARK 280 0.1 M TRIS PH 8.5, 30% PEG 4000, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 291K 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 24.83000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2730 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9930 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -22.0 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 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2620 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9880 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -26.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, D REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 ASN D 192 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 ALA D 125 -1.16 72.63 REMARK 500 REMARK 500 REMARK: NULL DBREF 6YHU A 1 71 UNP P0DTC1 R1A_SARS2 3860 3930 DBREF 6YHU B 76 192 UNP P0DTC1 R1A_SARS2 4018 4134 DBREF 6YHU C 1 71 UNP P0DTC1 R1A_SARS2 3860 3930 DBREF 6YHU D 76 192 UNP P0DTC1 R1A_SARS2 4018 4134 SEQRES 1 A 71 SER LYS MET SER ASP VAL LYS CYS THR SER VAL VAL LEU SEQRES 2 A 71 LEU SER VAL LEU GLN GLN LEU ARG VAL GLU SER SER SER SEQRES 3 A 71 LYS LEU TRP ALA GLN CYS VAL GLN LEU HIS ASN ASP ILE SEQRES 4 A 71 LEU LEU ALA LYS ASP THR THR GLU ALA PHE GLU LYS MET SEQRES 5 A 71 VAL SER LEU LEU SER VAL LEU LEU SER MET GLN GLY ALA SEQRES 6 A 71 VAL ASP ILE ASN LYS LEU SEQRES 1 B 117 SER GLU ASP LYS ARG ALA LYS VAL THR SER ALA MET GLN SEQRES 2 B 117 THR MET LEU PHE THR MET LEU ARG LYS LEU ASP ASN ASP SEQRES 3 B 117 ALA LEU ASN ASN ILE ILE ASN ASN ALA ARG ASP GLY CYS SEQRES 4 B 117 VAL PRO LEU ASN ILE ILE PRO LEU THR THR ALA ALA LYS SEQRES 5 B 117 LEU MET VAL VAL ILE PRO ASP TYR ASN THR TYR LYS ASN SEQRES 6 B 117 THR CYS ASP GLY THR THR PHE THR TYR ALA SER ALA LEU SEQRES 7 B 117 TRP GLU ILE GLN GLN VAL VAL ASP ALA ASP SER LYS ILE SEQRES 8 B 117 VAL GLN LEU SER GLU ILE SER MET ASP ASN SER PRO ASN SEQRES 9 B 117 LEU ALA TRP PRO LEU ILE VAL THR ALA LEU ARG ALA ASN SEQRES 1 C 71 SER LYS MET SER ASP VAL LYS CYS THR SER VAL VAL LEU SEQRES 2 C 71 LEU SER VAL LEU GLN GLN LEU ARG VAL GLU SER SER SER SEQRES 3 C 71 LYS LEU TRP ALA GLN CYS VAL GLN LEU HIS ASN ASP ILE SEQRES 4 C 71 LEU LEU ALA LYS ASP THR THR GLU ALA PHE GLU LYS MET SEQRES 5 C 71 VAL SER LEU LEU SER VAL LEU LEU SER MET GLN GLY ALA SEQRES 6 C 71 VAL ASP ILE ASN LYS LEU SEQRES 1 D 117 SER GLU ASP LYS ARG ALA LYS VAL THR SER ALA MET GLN SEQRES 2 D 117 THR MET LEU PHE THR MET LEU ARG LYS LEU ASP ASN ASP SEQRES 3 D 117 ALA LEU ASN ASN ILE ILE ASN ASN ALA ARG ASP GLY CYS SEQRES 4 D 117 VAL PRO LEU ASN ILE ILE PRO LEU THR THR ALA ALA LYS SEQRES 5 D 117 LEU MET VAL VAL ILE PRO ASP TYR ASN THR TYR LYS ASN SEQRES 6 D 117 THR CYS ASP GLY THR THR PHE THR TYR ALA SER ALA LEU SEQRES 7 D 117 TRP GLU ILE GLN GLN VAL VAL ASP ALA ASP SER LYS ILE SEQRES 8 D 117 VAL GLN LEU SER GLU ILE SER MET ASP ASN SER PRO ASN SEQRES 9 D 117 LEU ALA TRP PRO LEU ILE VAL THR ALA LEU ARG ALA ASN FORMUL 5 HOH *131(H2 O) HELIX 1 AA1 SER A 1 LEU A 20 1 20 HELIX 2 AA2 ARG A 21 SER A 24 5 4 HELIX 3 AA3 SER A 25 LEU A 41 1 17 HELIX 4 AA4 ASP A 44 SER A 61 1 18 HELIX 5 AA5 ASP A 67 LEU A 71 5 5 HELIX 6 AA6 GLU B 77 ASP B 99 1 23 HELIX 7 AA7 ASN B 100 ASP B 112 1 13 HELIX 8 AA8 ASP B 134 THR B 141 1 8 HELIX 9 AA9 GLN B 168 ILE B 172 5 5 HELIX 10 AB1 ASN B 176 LEU B 180 5 5 HELIX 11 AB2 LYS C 2 LEU C 20 1 19 HELIX 12 AB3 ARG C 21 SER C 24 5 4 HELIX 13 AB4 SER C 25 LEU C 41 1 17 HELIX 14 AB5 ASP C 44 MET C 62 1 19 HELIX 15 AB6 ASP C 67 LEU C 71 5 5 HELIX 16 AB7 ASP D 78 ASP D 99 1 22 HELIX 17 AB8 ASN D 100 ASP D 112 1 13 HELIX 18 AB9 ASP D 134 THR D 141 1 8 HELIX 19 AC1 GLN D 168 ILE D 172 5 5 HELIX 20 AC2 ASN D 176 LEU D 180 5 5 SHEET 1 AA1 6 VAL B 115 PRO B 116 0 SHEET 2 AA1 6 LEU B 128 ILE B 132 -1 O VAL B 131 N VAL B 115 SHEET 3 AA1 6 LEU B 184 ARG B 190 -1 O LEU B 184 N ILE B 132 SHEET 4 AA1 6 ALA B 152 VAL B 160 -1 N GLN B 158 O THR B 187 SHEET 5 AA1 6 THR B 146 TYR B 149 -1 N PHE B 147 O TRP B 154 SHEET 6 AA1 6 CYS B 142 ASP B 143 -1 N ASP B 143 O THR B 146 SHEET 1 AA2 5 LYS D 127 ILE D 132 0 SHEET 2 AA2 5 LEU D 184 ARG D 190 -1 O LEU D 184 N ILE D 132 SHEET 3 AA2 5 ALA D 152 VAL D 160 -1 N GLU D 155 O LEU D 189 SHEET 4 AA2 5 THR D 146 TYR D 149 -1 N PHE D 147 O TRP D 154 SHEET 5 AA2 5 CYS D 142 ASP D 143 -1 N ASP D 143 O THR D 146 SSBOND 1 CYS A 8 CYS C 8 1555 1555 2.03 CISPEP 1 TRP B 182 PRO B 183 0 -0.64 CISPEP 2 TRP D 182 PRO D 183 0 -1.47 CRYST1 56.420 49.660 64.750 90.00 106.41 90.00 P 1 21 1 4 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 0.017724 0.000000 0.005221 0.00000 SCALE2 0.000000 0.020137 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016100 0.00000