HEADER VIRAL PROTEIN 07-SEP-20 7CZ6 TITLE PROTRUSION STRUCTURE OF OMONO RIVER VIRUS COMPND MOL_ID: 1; COMPND 2 MOLECULE: CAPSID PROTEIN; COMPND 3 CHAIN: C SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: OMONO RIVER VIRUS; SOURCE 3 ORGANISM_TAXID: 753758; SOURCE 4 STRAIN: LZ; SOURCE 5 CELL_LINE: C6/36; SOURCE 6 ATCC: CRL-1660 KEYWDS PROTRUSION, PENTAMER, FIVE-FOLD VERTEX, VIRAL PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR Q.SHAO,X.JIA,Y.GAO,Z.LIU REVDAT 3 27-MAR-24 7CZ6 1 REMARK REVDAT 2 31-MAR-21 7CZ6 1 JRNL REVDAT 1 03-MAR-21 7CZ6 0 JRNL AUTH Q.SHAO,X.JIA,Y.GAO,Z.LIU,H.ZHANG,Q.TAN,X.ZHANG,H.ZHOU,Y.LI, JRNL AUTH 2 Q.ZHANG JRNL TITL CRYO-EM REVEALS A PREVIOUSLY UNRECOGNIZED STRUCTURAL PROTEIN JRNL TITL 2 OF A DSRNA VIRUS IMPLICATED IN ITS EXTRACELLULAR JRNL TITL 3 TRANSMISSION. JRNL REF PLOS PATHOG. V. 17 09396 2021 JRNL REFN ESSN 1553-7374 JRNL PMID 33730056 JRNL DOI 10.1371/JOURNAL.PPAT.1009396 REMARK 2 REMARK 2 RESOLUTION. 4.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : ETHAN, EPU, GCTF, PHENIX, RELION, JSPR, REMARK 3 RELION, RELION REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : NULL REMARK 3 REFINEMENT SPACE : REAL REMARK 3 REFINEMENT PROTOCOL : AB INITIO MODEL 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) : 4.100 REMARK 3 NUMBER OF PARTICLES : 38935 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: NULL REMARK 4 REMARK 4 7CZ6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 09-SEP-20. REMARK 100 THE DEPOSITION ID IS D_1300017814. 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 : OMONO RIVER VIRUS REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : NULL 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 : PROTRUSION STRUCTURE LOCATED REMARK 245 UPON THE FIVE-FOLD VERTEX OF THE MAJOR CAPSID. 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 : FEI FALCON III (4K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 1000.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2500.00 REMARK 245 MINIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 NOMINAL CS : NULL REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 3900.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : 75000 REMARK 245 CALIBRATED MAGNIFICATION : NULL REMARK 245 SOURCE : FIELD EMISSION GUN REMARK 245 ACCELERATION VOLTAGE (KV) : 300 REMARK 245 IMAGING DETAILS : NULL 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 300 THE ASSEMBLY REPRESENTED IN THIS ENTRY HAS REGULAR REMARK 300 CYCLIC POINT SYMMETRY (SCHOENFLIES SYMBOL = C5). 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 APPLY THE FOLLOWING TO CHAINS: C 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 0.309017 -0.951056 -0.000213 -0.00163 REMARK 350 BIOMT2 2 0.951057 0.309017 0.000041 0.00508 REMARK 350 BIOMT3 2 0.000027 -0.000216 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.809017 -0.587785 -0.000319 -0.00696 REMARK 350 BIOMT2 3 0.587785 -0.809017 -0.000149 0.00510 REMARK 350 BIOMT3 3 -0.000170 -0.000308 1.000000 0.00000 REMARK 350 BIOMT1 4 -0.809017 0.587785 -0.000170 -0.00863 REMARK 350 BIOMT2 4 -0.587785 -0.809017 -0.000308 0.00004 REMARK 350 BIOMT3 4 -0.000319 -0.000149 1.000000 0.00000 REMARK 350 BIOMT1 5 0.309017 0.951057 0.000027 -0.00433 REMARK 350 BIOMT2 5 -0.951056 0.309017 -0.000216 -0.00312 REMARK 350 BIOMT3 5 -0.000213 0.000041 1.000000 0.00000 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 ILE C 257 -71.55 -138.15 REMARK 500 PHE C 297 -78.01 -110.22 REMARK 500 TYR C 304 76.82 -154.82 REMARK 500 ASP C 308 -127.46 58.86 REMARK 500 PHE C 311 113.72 -163.16 REMARK 500 LEU C 339 79.69 -156.63 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-30507 RELATED DB: EMDB REMARK 900 OMRV-LZ PROTRUSION DBREF 7CZ6 C 244 369 PDB 7CZ6 7CZ6 244 369 SEQRES 1 C 126 ILE ASP CYS ASP SER SER VAL PHE GLY ASN ASN PHE ASN SEQRES 2 C 126 ILE THR THR SER PRO GLN THR LEU THR MET SER GLY PRO SEQRES 3 C 126 LEU ALA PRO GLY LYS TYR GLN THR THR LEU THR VAL GLN SEQRES 4 C 126 ALA LEU ILE GLY GLY THR GLY VAL VAL VAL GLY THR VAL SEQRES 5 C 126 THR PHE ALA GLY LYS THR VAL ALA TYR GLN VAL PHE ASP SEQRES 6 C 126 ASP SER PHE ALA SER PHE ASP LEU GLY THR VAL THR VAL SEQRES 7 C 126 SER ALA SER THR THR PRO SER VAL ILE TRP THR GLY SER SEQRES 8 C 126 THR GLY ALA THR LEU THR MET ALA VAL ASN ILE ILE CYS SEQRES 9 C 126 LYS PRO ILE THR PRO THR SER VAL ALA ILE SER GLY GLN SEQRES 10 C 126 PRO ILE TRP THR THR PRO TYR ALA PRO SHEET 1 AA1 4 SER C 248 ASN C 254 0 SHEET 2 AA1 4 MET C 341 PRO C 349 -1 O MET C 341 N ASN C 254 SHEET 3 AA1 4 TYR C 275 GLN C 282 -1 N THR C 280 O ASN C 344 SHEET 4 AA1 4 ALA C 312 VAL C 319 -1 O ALA C 312 N VAL C 281 SHEET 1 AA2 4 GLN C 262 LEU C 264 0 SHEET 2 AA2 4 SER C 328 GLY C 333 -1 O VAL C 329 N THR C 263 SHEET 3 AA2 4 GLY C 293 THR C 296 -1 N THR C 294 O THR C 332 SHEET 4 AA2 4 THR C 301 ALA C 303 -1 O VAL C 302 N VAL C 295 CISPEP 1 GLN C 360 PRO C 361 0 -1.84 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