HEADER VIRAL PROTEIN 23-SEP-16 5GYQ TITLE PUTATIVE RECEPTOR-BINDING DOMAIN OF BAT-DERIVED CORONAVIRUS HKU9 SPIKE TITLE 2 PROTEIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: SPIKE GLYCOPROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 355-521; COMPND 5 SYNONYM: S GLYCOPROTEIN,E2,PEPLOMER PROTEIN; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BAT CORONAVIRUS HKU9; SOURCE 3 ORGANISM_COMMON: BTCOV; SOURCE 4 ORGANISM_TAXID: 694006; SOURCE 5 GENE: S, 2; SOURCE 6 EXPRESSION_SYSTEM: TRICHOPLUSIA NI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 7111; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: BACULOVIRUS KEYWDS BAT CORONAVIRUS HKU9, PUTATIVE RECEPTOR BINDING DOMAIN (RBD), SPIKE KEYWDS 2 (S), SUGAR BINDING PROTEIN, VIRAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR C.HUANG,J.QI,G.F.GAO REVDAT 4 16-OCT-24 5GYQ 1 HETSYN REVDAT 3 29-JUL-20 5GYQ 1 COMPND JRNL REMARK HETNAM REVDAT 3 2 1 LINK SITE ATOM REVDAT 2 16-NOV-16 5GYQ 1 JRNL REVDAT 1 26-OCT-16 5GYQ 0 JRNL AUTH C.HUANG,J.QI,G.LU,Q.WANG,Y.YUAN,Y.WU,Y.ZHANG,J.YAN,G.F.GAO JRNL TITL PUTATIVE RECEPTOR BINDING DOMAIN OF BAT-DERIVED CORONAVIRUS JRNL TITL 2 HKU9 SPIKE PROTEIN: EVOLUTION OF BETACORONAVIRUS RECEPTOR JRNL TITL 3 BINDING MOTIFS JRNL REF BIOCHEMISTRY V. 55 5977 2016 JRNL REFN ISSN 0006-2960 JRNL PMID 27696819 JRNL DOI 10.1021/ACS.BIOCHEM.6B00790 REMARK 2 REMARK 2 RESOLUTION. 2.10 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) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.70 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.0 REMARK 3 NUMBER OF REFLECTIONS : 10811 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.172 REMARK 3 R VALUE (WORKING SET) : 0.170 REMARK 3 FREE R VALUE : 0.201 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.810 REMARK 3 FREE R VALUE TEST SET COUNT : 520 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 41.7108 - 3.3339 1.00 2718 118 0.1536 0.1772 REMARK 3 2 3.3339 - 2.6463 1.00 2608 160 0.1775 0.2262 REMARK 3 3 2.6463 - 2.3118 1.00 2627 138 0.1848 0.1863 REMARK 3 4 2.3118 - 2.1005 0.89 2338 104 0.1975 0.2329 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) : 0.220 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.570 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL 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 : 0.003 1416 REMARK 3 ANGLE : 0.820 1942 REMARK 3 CHIRALITY : 0.033 219 REMARK 3 PLANARITY : 0.003 249 REMARK 3 DIHEDRAL : 12.313 499 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): -4.3169 -6.8610 -17.2583 REMARK 3 T TENSOR REMARK 3 T11: 0.0908 T22: 0.0964 REMARK 3 T33: 0.0932 T12: -0.0214 REMARK 3 T13: 0.0003 T23: 0.0147 REMARK 3 L TENSOR REMARK 3 L11: 0.7254 L22: 1.1041 REMARK 3 L33: 1.2171 L12: 0.0195 REMARK 3 L13: 0.4280 L23: -0.1729 REMARK 3 S TENSOR REMARK 3 S11: -0.0229 S12: -0.0096 S13: -0.0305 REMARK 3 S21: 0.1750 S22: -0.0566 S23: -0.0808 REMARK 3 S31: -0.1052 S32: 0.0872 S33: -0.1139 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 5GYQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 03-OCT-16. REMARK 100 THE DEPOSITION ID IS D_1300001675. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-MAY-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL17U REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.03906 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10822 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.1 REMARK 200 DATA REDUNDANCY : 9.400 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 34.0230 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.18 REMARK 200 COMPLETENESS FOR SHELL (%) : 80.7 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: SAD REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.22 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.38 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M SODIUM CITRATE TRIBASIC DIHYDRATE REMARK 280 PH 7.0, 12% PEG 20000, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 277K 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 17.99500 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 550 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9040 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 6.0 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 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 A 172 REMARK 465 HIS A 173 REMARK 465 HIS A 174 REMARK 465 HIS A 175 REMARK 465 HIS A 176 REMARK 465 HIS A 177 REMARK 465 HIS A 178 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 17 77.61 -150.56 REMARK 500 VAL A 40 -83.20 -125.12 REMARK 500 ASN A 93 -62.08 -132.21 REMARK 500 PHE A 121 84.58 65.69 REMARK 500 ALA A 162 73.16 -150.24 REMARK 500 LYS A 165 79.53 55.88 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A1027 DISTANCE = 6.00 ANGSTROMS REMARK 525 HOH A1028 DISTANCE = 6.27 ANGSTROMS DBREF 5GYQ A 6 172 UNP A3EXG6 SPIKE_BCHK9 355 521 SEQADV 5GYQ GLY A 3 UNP A3EXG6 EXPRESSION TAG SEQADV 5GYQ ILE A 4 UNP A3EXG6 EXPRESSION TAG SEQADV 5GYQ GLN A 5 UNP A3EXG6 EXPRESSION TAG SEQADV 5GYQ HIS A 173 UNP A3EXG6 EXPRESSION TAG SEQADV 5GYQ HIS A 174 UNP A3EXG6 EXPRESSION TAG SEQADV 5GYQ HIS A 175 UNP A3EXG6 EXPRESSION TAG SEQADV 5GYQ HIS A 176 UNP A3EXG6 EXPRESSION TAG SEQADV 5GYQ HIS A 177 UNP A3EXG6 EXPRESSION TAG SEQADV 5GYQ HIS A 178 UNP A3EXG6 EXPRESSION TAG SEQRES 1 A 176 GLY ILE GLN SER TYR CYS THR PRO PRO TYR SER VAL LEU SEQRES 2 A 176 GLN ASP PRO PRO GLN PRO VAL VAL TRP ARG ARG TYR MET SEQRES 3 A 176 LEU TYR ASP CYS VAL PHE ASP PHE THR VAL VAL VAL ASP SEQRES 4 A 176 SER LEU PRO THR HIS GLN LEU GLN CYS TYR GLY VAL SER SEQRES 5 A 176 PRO ARG ARG LEU ALA SER MET CYS TYR GLY SER VAL THR SEQRES 6 A 176 LEU ASP VAL MET ARG ILE ASN GLU THR HIS LEU ASN ASN SEQRES 7 A 176 LEU PHE ASN ARG VAL PRO ASP THR PHE SER LEU TYR ASN SEQRES 8 A 176 TYR ALA LEU PRO ASP ASN PHE TYR GLY CYS LEU HIS ALA SEQRES 9 A 176 PHE TYR LEU ASN SER THR ALA PRO TYR ALA VAL ALA ASN SEQRES 10 A 176 ARG PHE PRO ILE LYS PRO GLY GLY ARG GLN SER ASN SER SEQRES 11 A 176 ALA PHE ILE ASP THR VAL ILE ASN ALA ALA HIS TYR SER SEQRES 12 A 176 PRO PHE SER TYR VAL TYR GLY LEU ALA VAL ILE THR LEU SEQRES 13 A 176 LYS PRO ALA ALA GLY SER LYS LEU VAL CYS PRO VAL ALA SEQRES 14 A 176 ASN HIS HIS HIS HIS HIS HIS HET NAG B 1 14 HET NAG B 2 14 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETSYN NAG N-ACETYL-BETA-D-GLUCOSAMINE; 2-ACETAMIDO-2-DEOXY-BETA- HETSYN 2 NAG D-GLUCOSE; 2-ACETAMIDO-2-DEOXY-D-GLUCOSE; 2-ACETAMIDO- HETSYN 3 NAG 2-DEOXY-GLUCOSE; N-ACETYL-D-GLUCOSAMINE FORMUL 2 NAG 2(C8 H15 N O6) FORMUL 3 HOH *128(H2 O) HELIX 1 AA1 PRO A 11 ASP A 17 1 7 HELIX 2 AA2 GLN A 20 TRP A 24 5 5 HELIX 3 AA3 ASP A 35 VAL A 40 5 6 HELIX 4 AA4 SER A 54 ALA A 59 1 6 HELIX 5 AA5 ASN A 74 ARG A 84 1 11 HELIX 6 AA6 ASP A 87 ASN A 93 1 7 HELIX 7 AA7 ASN A 131 ALA A 142 1 12 HELIX 8 AA8 HIS A 143 SER A 145 5 3 SHEET 1 AA1 3 SER A 6 TYR A 7 0 SHEET 2 AA1 3 CYS A 32 PHE A 34 1 O VAL A 33 N SER A 6 SHEET 3 AA1 3 VAL A 167 PRO A 169 1 O CYS A 168 N PHE A 34 SHEET 1 AA2 5 ARG A 25 LEU A 29 0 SHEET 2 AA2 5 SER A 65 ILE A 73 -1 O VAL A 66 N LEU A 29 SHEET 3 AA2 5 SER A 148 LYS A 159 -1 O TYR A 151 N ILE A 73 SHEET 4 AA2 5 GLY A 102 ALA A 113 -1 N CYS A 103 O ILE A 156 SHEET 5 AA2 5 THR A 45 TYR A 51 -1 N HIS A 46 O ALA A 106 SSBOND 1 CYS A 8 CYS A 32 1555 1555 2.04 SSBOND 2 CYS A 50 CYS A 103 1555 1555 2.03 SSBOND 3 CYS A 62 CYS A 168 1555 1555 2.04 LINK ND2 ASN A 74 C1 NAG B 1 1555 1555 1.44 LINK O4 NAG B 1 C1 NAG B 2 1555 1555 1.44 CRYST1 42.752 35.990 62.886 90.00 102.72 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 0.023391 0.000000 0.005280 0.00000 SCALE2 0.000000 0.027785 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016302 0.00000