HEADER VIRAL PROTEIN 03-SEP-18 6HJC TITLE CRYSTAL STRUCTURE OF LOEI RIVER VIRUS GP1 GLYCOPROTEIN AT PH 8.0 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PRE-GLYCOPROTEIN POLYPROTEIN GP COMPLEX; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PRE-GP-C; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: LOEI RIVER MAMMARENAVIRUS; SOURCE 3 ORGANISM_COMMON: LOIE RIVER VIRUS; SOURCE 4 ORGANISM_TAXID: 1437126; SOURCE 5 GENE: GPC; SOURCE 6 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 8 EXPRESSION_SYSTEM_CELL: HEK293T KEYWDS ATTACHMENT, GLYCOPROTEIN, VIRAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR R.PRYCE,W.M.NG,A.ZELTINA,Y.WATANABE,K.EL OMARI,A.WAGNER,T.A.BOWDEN REVDAT 5 17-JAN-24 6HJC 1 HETSYN REVDAT 4 29-JUL-20 6HJC 1 COMPND REMARK HETNAM LINK REVDAT 4 2 1 SITE REVDAT 3 19-DEC-18 6HJC 1 JRNL REVDAT 2 24-OCT-18 6HJC 1 JRNL REVDAT 1 10-OCT-18 6HJC 0 JRNL AUTH R.PRYCE,W.M.NG,A.ZELTINA,Y.WATANABE,K.EL OMARI,A.WAGNER, JRNL AUTH 2 T.A.BOWDEN JRNL TITL STRUCTURE-BASED CLASSIFICATION DEFINES THE DISCRETE JRNL TITL 2 CONFORMATIONAL CLASSES ADOPTED BY THE ARENAVIRAL GP1. JRNL REF J. VIROL. V. 93 2019 JRNL REFN ESSN 1098-5514 JRNL PMID 30305351 JRNL DOI 10.1128/JVI.01048-18 REMARK 2 REMARK 2 RESOLUTION. 2.51 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.12_2829: ???) 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) : 2.51 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.13 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 3 NUMBER OF REFLECTIONS : 6480 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.209 REMARK 3 R VALUE (WORKING SET) : 0.208 REMARK 3 FREE R VALUE : 0.238 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.380 REMARK 3 FREE R VALUE TEST SET COUNT : 284 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 39.1302 - 3.1623 1.00 3223 145 0.1895 0.2053 REMARK 3 2 3.1623 - 2.5101 0.97 2973 139 0.2823 0.3634 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) : 0.270 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.440 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 : 0.002 1362 REMARK 3 ANGLE : 0.420 1857 REMARK 3 CHIRALITY : 0.035 210 REMARK 3 PLANARITY : 0.003 237 REMARK 3 DIHEDRAL : 9.505 785 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): 40.5414 38.8599 35.0600 REMARK 3 T TENSOR REMARK 3 T11: 0.3926 T22: 0.4797 REMARK 3 T33: 0.3846 T12: -0.0712 REMARK 3 T13: 0.0219 T23: -0.0232 REMARK 3 L TENSOR REMARK 3 L11: 7.0324 L22: 8.2887 REMARK 3 L33: 3.0605 L12: -2.3938 REMARK 3 L13: 0.3642 L23: 0.2202 REMARK 3 S TENSOR REMARK 3 S11: -0.0118 S12: 0.2317 S13: -0.5141 REMARK 3 S21: -0.1346 S22: -0.0444 S23: 0.2689 REMARK 3 S31: 0.3963 S32: 0.0527 S33: 0.0531 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 6HJC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 03-SEP-18. REMARK 100 THE DEPOSITION ID IS D_1200011759. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-APR-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I03 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97625 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XIA2 REMARK 200 DATA SCALING SOFTWARE : XIA2 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 6515 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.510 REMARK 200 RESOLUTION RANGE LOW (A) : 39.125 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : 11.80 REMARK 200 R MERGE (I) : 0.11200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.51 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.55 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: PHASER REMARK 200 STARTING MODEL: 4ZJF REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.98 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.28 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 5.3 MG/ML PROTEIN, 10% W/V ETHANOL, REMARK 280 AND 1.5 M NACL, PH 8.0, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 48.21000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 30.27000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 30.27000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 24.10500 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 30.27000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 30.27000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 72.31500 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 30.27000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 30.27000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 24.10500 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 30.27000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 30.27000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 72.31500 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 48.21000 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: 1670 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8710 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 18.0 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 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 GLU A 77 REMARK 465 THR A 78 REMARK 465 THR A 238 REMARK 465 GLY A 239 REMARK 465 THR A 240 REMARK 465 LYS A 241 REMARK 465 HIS A 242 REMARK 465 HIS A 243 REMARK 465 HIS A 244 REMARK 465 HIS A 245 REMARK 465 HIS A 246 REMARK 465 HIS A 247 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 ASN A 117 -70.66 -49.48 REMARK 500 SER A 167 62.49 -111.04 REMARK 500 REMARK 500 REMARK: NULL DBREF1 6HJC A 80 238 UNP A0A023J4Z7_9VIRU DBREF2 6HJC A A0A023J4Z7 80 238 SEQADV 6HJC GLU A 77 UNP A0A023J4Z EXPRESSION TAG SEQADV 6HJC THR A 78 UNP A0A023J4Z EXPRESSION TAG SEQADV 6HJC GLY A 79 UNP A0A023J4Z EXPRESSION TAG SEQADV 6HJC GLY A 239 UNP A0A023J4Z EXPRESSION TAG SEQADV 6HJC THR A 240 UNP A0A023J4Z EXPRESSION TAG SEQADV 6HJC LYS A 241 UNP A0A023J4Z EXPRESSION TAG SEQADV 6HJC HIS A 242 UNP A0A023J4Z EXPRESSION TAG SEQADV 6HJC HIS A 243 UNP A0A023J4Z EXPRESSION TAG SEQADV 6HJC HIS A 244 UNP A0A023J4Z EXPRESSION TAG SEQADV 6HJC HIS A 245 UNP A0A023J4Z EXPRESSION TAG SEQADV 6HJC HIS A 246 UNP A0A023J4Z EXPRESSION TAG SEQADV 6HJC HIS A 247 UNP A0A023J4Z EXPRESSION TAG SEQRES 1 A 171 GLU THR GLY MET PRO LEU SER CYS SER LYS ASN ASN SER SEQRES 2 A 171 HIS HIS TYR ILE PHE VAL GLY ASN ASN SER GLY LEU GLU SEQRES 3 A 171 LEU THR LEU THR ASN THR SER LEU LEU ASN HIS LYS PHE SEQRES 4 A 171 CYS ASN LEU SER ASP ALA HIS LYS ARG ALA GLN TYR ASP SEQRES 5 A 171 MET ALA LEU MET SER ILE VAL SER THR PHE HIS LEU SER SEQRES 6 A 171 ILE PRO ASN PHE ASN GLN TYR GLU ALA MET SER CYS ASP SEQRES 7 A 171 PHE ASN GLY ASP ASN ILE THR VAL GLN TYR ASN LEU SER SEQRES 8 A 171 HIS ALA SER ALA VAL ASP ALA ALA ASN HIS CYS GLY THR SEQRES 9 A 171 VAL ALA ASN GLY ILE LEU GLU THR PHE HIS LYS PHE PHE SEQRES 10 A 171 TRP SER ASN ASN ILE LYS ASP ALA TYR GLN LEU PRO ASN SEQRES 11 A 171 GLN GLY LYS LEU ALA HIS CYS TYR SER THR SER TYR GLN SEQRES 12 A 171 PHE LEU ILE ILE GLN ASN THR THR TRP GLU ASP HIS CYS SEQRES 13 A 171 THR PHE SER ARG PRO THR GLY THR LYS HIS HIS HIS HIS SEQRES 14 A 171 HIS HIS HET GOL A 301 6 HET NAG A 302 14 HET NAG A 303 14 HET NAG A 304 14 HET NAG A 305 14 HETNAM GOL GLYCEROL HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL 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 GOL C3 H8 O3 FORMUL 3 NAG 4(C8 H15 N O6) FORMUL 7 HOH *14(H2 O) HELIX 1 AA1 ASP A 120 HIS A 139 1 20 HELIX 2 AA2 SER A 170 ASN A 176 1 7 HELIX 3 AA3 THR A 180 PHE A 192 1 13 SHEET 1 AA1 5 SER A 89 GLY A 96 0 SHEET 2 AA1 5 SER A 99 THR A 106 -1 O LEU A 105 N SER A 89 SHEET 3 AA1 5 PHE A 220 THR A 226 -1 O ILE A 222 N THR A 104 SHEET 4 AA1 5 ASN A 159 ASN A 165 -1 N VAL A 162 O ILE A 223 SHEET 5 AA1 5 MET A 151 ASN A 156 -1 N ASP A 154 O THR A 161 SHEET 1 AA2 2 LYS A 199 LEU A 204 0 SHEET 2 AA2 2 ALA A 211 SER A 215 -1 O CYS A 213 N TYR A 202 SSBOND 1 CYS A 84 CYS A 232 1555 1555 2.04 SSBOND 2 CYS A 116 CYS A 153 1555 1555 2.02 SSBOND 3 CYS A 178 CYS A 213 1555 1555 2.03 LINK ND2 ASN A 107 C1 NAG A 302 1555 1555 1.44 LINK ND2 ASN A 159 C1 NAG A 304 1555 1555 1.44 LINK ND2 ASN A 165 C1 NAG A 305 1555 1555 1.44 LINK ND2 ASN A 225 C1 NAG A 303 1555 1555 1.44 CRYST1 60.540 60.540 96.420 90.00 90.00 90.00 P 41 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 0.016518 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016518 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010371 0.00000