HEADER VIRAL PROTEIN 18-MAY-21 7MX9 TITLE CRYSTAL STRUCTURE OF THE SARS-COV-2 ORF8 ACCESSORY PROTEIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: ORF8 PROTEIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: ORF8,NON-STRUCTURAL PROTEIN 8,NS8; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS SOURCE 3 2; SOURCE 4 ORGANISM_COMMON: 2019-NCOV, SARS-COV-2; SOURCE 5 ORGANISM_TAXID: 2697049; SOURCE 6 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 8 EXPRESSION_SYSTEM_CELL_LINE: HEK293 KEYWDS SARS-COV-2, COVID19, ORF8, IMMUNOGLOBULIN FOLD, VIRAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR B.A.BAILEY-ELKIN,J.STETEFELD REVDAT 3 23-OCT-24 7MX9 1 REMARK REVDAT 2 25-OCT-23 7MX9 1 REMARK REVDAT 1 25-JAN-23 7MX9 0 JRNL AUTH M.HAMDORF,T.IMHOF,S.J.THEOBALD,A.SIMONIS,V.DI CRISTANZIANO, JRNL AUTH 2 L.GIESELMANN,F.DEWALD,C.LEHMANN,M.AUGUSTIN,F.KLEIN, JRNL AUTH 3 M.A.ALEJANDRE ALCAZAR,R.RONGISCH,M.FABRI,C.CURSIEFEN, JRNL AUTH 4 J.RYBNIKER,B.A.BAILEY-ELKIN,J.STETEFELD,M.KOCH,F.BOCK JRNL TITL THE UNIQUE ORF8 PROTEIN OF SARS-COV-2 BINDS TO HUMAN JRNL TITL 2 DENDRITIC CELLS AND INDUCES A CYTOKINE STORM JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.18.2-3874_3874: ???) 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) : 30.04 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 3353 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.249 REMARK 3 R VALUE (WORKING SET) : 0.243 REMARK 3 FREE R VALUE : 0.297 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.020 REMARK 3 FREE R VALUE TEST SET COUNT : 336 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 30.0400 - 3.2800 1.00 1561 175 0.2240 0.2710 REMARK 3 2 3.2800 - 2.6000 1.00 1456 161 0.2982 0.3725 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) : 0.280 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 31.620 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 48.13 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : 0.004 759 REMARK 3 ANGLE : 0.748 1037 REMARK 3 CHIRALITY : 0.050 114 REMARK 3 PLANARITY : 0.005 133 REMARK 3 DIHEDRAL : 6.864 101 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 7MX9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-MAY-21. REMARK 100 THE DEPOSITION ID IS D_1000254891. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-FEB-21 REMARK 200 TEMPERATURE (KELVIN) : 93.15 REMARK 200 PH : 6.8 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 : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV++ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 3379 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.600 REMARK 200 RESOLUTION RANGE LOW (A) : 42.200 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 13.00 REMARK 200 R MERGE (I) : 0.16600 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 11.8000 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) : 2.72 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.79600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> 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: PHASER REMARK 200 STARTING MODEL: 7JTL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 34.99 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.89 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M LITHIUM CHLORIDE, 20% (W/V) REMARK 280 POLYETHYLENE GLYCOL 3350, PH 6.8, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 42 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -Y+1/2,X+1/2,Z+1/2 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/2 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/2 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 25.67450 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 25.67450 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 37.04650 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 25.67450 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 25.67450 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 37.04650 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 25.67450 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 25.67450 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 37.04650 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 25.67450 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 25.67450 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 37.04650 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1340 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10390 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -8.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 BIOMT1 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 74.09300 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 GLY A 9 REMARK 465 VAL A 10 REMARK 465 ARG A 11 REMARK 465 LEU A 12 REMARK 465 ALA A 13 REMARK 465 SER A 14 REMARK 465 ALA A 15 REMARK 465 PHE A 16 REMARK 465 HIS A 17 REMARK 465 GLN A 18 REMARK 465 ASP A 63 REMARK 465 GLU A 64 REMARK 465 ALA A 65 REMARK 465 GLY A 66 REMARK 465 SER A 67 REMARK 465 LYS A 68 REMARK 465 SER A 69 REMARK 465 PRO A 70 REMARK 465 ILE A 71 REMARK 465 GLN A 72 REMARK 465 TYR A 73 REMARK 465 ILE A 74 REMARK 465 ASP A 75 REMARK 465 ILE A 76 REMARK 465 GLY A 77 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 LYS A 94 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 OE1 GLU A 110 NE2 HIS A 112 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 SG CYS A 20 HG CYS A 20 7556 1.58 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 HIS A 40 -23.56 80.11 REMARK 500 ALA A 51 32.31 -91.25 REMARK 500 CYS A 90 81.41 -68.75 REMARK 500 REMARK 500 REMARK: NULL DBREF 7MX9 A 15 121 UNP P0DTC8 NS8_SARS2 15 121 SEQADV 7MX9 GLY A 9 UNP P0DTC8 EXPRESSION TAG SEQADV 7MX9 VAL A 10 UNP P0DTC8 EXPRESSION TAG SEQADV 7MX9 ARG A 11 UNP P0DTC8 EXPRESSION TAG SEQADV 7MX9 LEU A 12 UNP P0DTC8 EXPRESSION TAG SEQADV 7MX9 ALA A 13 UNP P0DTC8 EXPRESSION TAG SEQADV 7MX9 SER A 14 UNP P0DTC8 EXPRESSION TAG SEQADV 7MX9 GLN A 78 UNP P0DTC8 ASN 78 CONFLICT SEQRES 1 A 113 GLY VAL ARG LEU ALA SER ALA PHE HIS GLN GLU CYS SER SEQRES 2 A 113 LEU GLN SER CYS THR GLN HIS GLN PRO TYR VAL VAL ASP SEQRES 3 A 113 ASP PRO CYS PRO ILE HIS PHE TYR SER LYS TRP TYR ILE SEQRES 4 A 113 ARG VAL GLY ALA ARG LYS SER ALA PRO LEU ILE GLU LEU SEQRES 5 A 113 CYS VAL ASP GLU ALA GLY SER LYS SER PRO ILE GLN TYR SEQRES 6 A 113 ILE ASP ILE GLY GLN TYR THR VAL SER CYS LEU PRO PHE SEQRES 7 A 113 THR ILE ASN CYS GLN GLU PRO LYS LEU GLY SER LEU VAL SEQRES 8 A 113 VAL ARG CYS SER PHE TYR GLU ASP PHE LEU GLU TYR HIS SEQRES 9 A 113 ASP VAL ARG VAL VAL LEU ASP PHE ILE FORMUL 2 HOH *11(H2 O) SHEET 1 AA1 5 CYS A 20 CYS A 25 0 SHEET 2 AA1 5 HIS A 112 PHE A 120 1 O VAL A 117 N SER A 21 SHEET 3 AA1 5 LEU A 98 SER A 103 -1 N CYS A 102 O HIS A 112 SHEET 4 AA1 5 TYR A 42 ARG A 48 -1 N LYS A 44 O ARG A 101 SHEET 5 AA1 5 LEU A 57 LEU A 60 -1 O LEU A 60 N TRP A 45 SHEET 1 AA2 3 PRO A 30 VAL A 32 0 SHEET 2 AA2 3 THR A 87 ASN A 89 -1 O ILE A 88 N TYR A 31 SHEET 3 AA2 3 THR A 80 SER A 82 -1 N SER A 82 O THR A 87 SSBOND 1 CYS A 20 CYS A 20 1555 7556 2.03 SSBOND 2 CYS A 25 CYS A 90 1555 1555 2.03 SSBOND 3 CYS A 37 CYS A 102 1555 1555 2.03 SSBOND 4 CYS A 61 CYS A 83 1555 1555 2.03 CISPEP 1 LEU A 84 PRO A 85 0 -5.73 CRYST1 51.349 51.349 74.093 90.00 90.00 90.00 P 42 21 2 8 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 0.019475 0.000000 0.000000 0.00000 SCALE2 0.000000 0.019475 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013497 0.00000