HEADER VIRAL PROTEIN 20-JUL-22 7YJL TITLE MELBOURNEVIRUS MAJOR CAPSID PROTEIN BUILT FROM 4.4A RECONSTRUCTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: MAJOR CAPSID PROTEIN; COMPND 3 CHAIN: A SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MELBOURNEVIRUS; SOURCE 3 ORGANISM_TAXID: 1560514 KEYWDS MCP, MELBOURNEVIRUS, GIANT VIRUS, MAJOR CAPSID PROTEIN, VIRAL PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR R.N.BURTON-SMITH,K.OKAMOTO,K.MURATA REVDAT 1 02-AUG-23 7YJL 0 JRNL AUTH R.N.BURTON-SMITH,H.K.N.REDDY,M.SVENDA,C.ABERGEL,K.OKAMOTO, JRNL AUTH 2 K.MURATA JRNL TITL THE 4.4A STRUCTURE OF THE GIANT MELBOURNEVIRUS VIRION JRNL TITL 2 BELONGING TO THE MARSEILLEVIRIDAE FAMILY JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 4.42 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : NULL REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : NULL REMARK 3 REFINEMENT SPACE : NULL REMARK 3 REFINEMENT PROTOCOL : NULL 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) : 4.420 REMARK 3 NUMBER OF PARTICLES : 187440 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 7YJL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 27-JUL-22. REMARK 100 THE DEPOSITION ID IS D_1300031061. 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 : MELBOURNEVIRUS 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 : NULL 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 : GATAN K2 SUMMIT (4K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 2000.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 3000.00 REMARK 245 MINIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 NOMINAL CS : 2.70 REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 2640.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : NULL 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 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 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 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 OD1 ASN A 404 H SER A 406 1.39 REMARK 500 OE1 GLU A 121 HE ARG A 215 1.47 REMARK 500 HH12 ARG A 57 OG SER A 60 1.54 REMARK 500 HE22 GLN A 301 O ALA A 304 1.55 REMARK 500 OD1 ASN A 413 H GLN A 414 1.58 REMARK 500 OD1 ASP A 243 OG1 THR A 247 1.89 REMARK 500 OG SER A 300 OG SER A 425 1.92 REMARK 500 OG1 THR A 178 OE1 GLU A 180 1.98 REMARK 500 OG SER A 389 O SER A 391 2.02 REMARK 500 NH1 ARG A 75 O ALA A 202 2.03 REMARK 500 OD1 ASP A 78 NH1 ARG A 274 2.06 REMARK 500 OG SER A 391 O LYS A 400 2.09 REMARK 500 OD2 ASP A 141 OH TYR A 335 2.16 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 ALA A 13 -60.72 -91.73 REMARK 500 PHE A 16 -5.84 69.78 REMARK 500 LEU A 29 -60.51 -94.10 REMARK 500 PHE A 65 -40.70 -138.64 REMARK 500 ASP A 78 -54.56 -120.61 REMARK 500 PHE A 115 -65.49 -92.84 REMARK 500 ASN A 128 -6.76 78.36 REMARK 500 ASP A 129 -1.24 -141.63 REMARK 500 LEU A 130 -169.18 -168.58 REMARK 500 GLN A 145 -62.06 -94.47 REMARK 500 ASN A 147 33.87 -98.53 REMARK 500 PRO A 164 7.08 -64.39 REMARK 500 PHE A 189 6.22 85.99 REMARK 500 TYR A 190 54.85 -140.18 REMARK 500 GLU A 192 36.11 -99.23 REMARK 500 ALA A 197 76.07 -101.90 REMARK 500 GLN A 239 170.17 -59.68 REMARK 500 GLN A 288 -170.98 -170.91 REMARK 500 LEU A 302 -167.17 -75.21 REMARK 500 TYR A 319 144.02 -172.18 REMARK 500 SER A 326 -70.17 -37.71 REMARK 500 SER A 327 19.39 53.65 REMARK 500 THR A 337 49.37 -86.69 REMARK 500 ALA A 350 -175.11 -69.45 REMARK 500 THR A 357 53.80 38.89 REMARK 500 TYR A 388 144.57 -172.55 REMARK 500 THR A 431 35.38 72.79 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-31529 RELATED DB: EMDB DBREF1 7YJL A 10 468 UNP A0A097I267_9VIRU DBREF2 7YJL A A0A097I267 10 468 SEQRES 1 A 459 VAL THR ALA ALA SER GLY PHE VAL ASP LEU ALA THR PHE SEQRES 2 A 459 SER ASP LEU GLU ALA TYR LEU TYR GLY GLY CYS SER ALA SEQRES 3 A 459 VAL THR TYR PHE VAL ARG ALA ILE LYS LYS ALA ASN TRP SEQRES 4 A 459 PHE SER PHE LEU PRO VAL VAL LEU ARG ASN ILE SER GLY SEQRES 5 A 459 LEU PRO GLY PHE GLY SER GLU PHE SER ALA SER VAL ASN SEQRES 6 A 459 ARG SER GLY ASP TYR VAL LEU ASN THR TRP LEU ARG VAL SEQRES 7 A 459 ARG LEU PRO LEU VAL ALA ILE ARG PRO THR ASN THR GLY SEQRES 8 A 459 GLY ALA ILE ASN ALA ASN ALA THR ILE ARG TRP THR ARG SEQRES 9 A 459 ASN PHE MET HIS ASN LEU VAL GLU LYS VAL ASN ILE THR SEQRES 10 A 459 PHE ASN ASP LEU ILE VAL HIS GLU PHE ASP SER TYR TRP SEQRES 11 A 459 PHE ASP PHE ASN SER GLN PHE ASN ILE ASP ALA SER LYS SEQRES 12 A 459 ARG VAL GLY TYR ARG ASN MET ILE GLY ASP ILE PRO ALA SEQRES 13 A 459 MET ILE ASN PRO VAL THR THR GLY ASN PRO LEU GLY THR SEQRES 14 A 459 GLY GLU PHE PHE ASN LEU PRO ILE PRO LEU PHE TYR THR SEQRES 15 A 459 GLU ASP SER GLY LEU ALA LEU ALA VAL SER ALA LEU PRO SEQRES 16 A 459 PHE ASN ASP ILE LYS ILE ASN TYR CYS LEU ARG ARG TRP SEQRES 17 A 459 GLN ASP LEU ILE VAL LEU ASN VAL GLY VAL GLY GLY ASN SEQRES 18 A 459 PRO PRO THR TYR ASP ASP ILE VAL GLN VAL SER TYR ASP SEQRES 19 A 459 SER THR PHE THR LEU ILE TYR SER SER ASN ALA PRO ALA SEQRES 20 A 459 ILE THR ASN VAL GLU THR TRP CYS HIS TYR ALA VAL VAL SEQRES 21 A 459 HIS ASN ASP GLU ARG VAL LYS MET GLY LYS ASN PRO ARG SEQRES 22 A 459 ASP MET VAL ILE LYS GLN VAL GLN LYS VAL ASN GLU THR SEQRES 23 A 459 THR ILE ASN LEU SER GLN LEU ASN ALA LEU VAL PRO ILE SEQRES 24 A 459 ASP ILE ARG VAL SER HIS ALA VAL VAL GLY TYR PHE TYR SEQRES 25 A 459 ALA ILE ARG ASN SER SER THR THR GLY GLU TRP SER ASN SEQRES 26 A 459 TYR THR THR GLU PRO ALA TYR ALA GLY LEU ASP PRO LEU SEQRES 27 A 459 GLU ALA ALA GLN LEU VAL TYR GLU SER THR ALA ARG VAL SEQRES 28 A 459 SER ASN GLY SER ASP TYR TYR SER LEU MET VAL PRO TRP SEQRES 29 A 459 TYR TRP HIS LYS SER ILE PRO GLU GLU THR GLY TYR HIS SEQRES 30 A 459 ALA TYR SER TYR SER LEU ASP THR PHE ALA SER ASP PRO SEQRES 31 A 459 LYS GLY SER THR ASN TYR SER LYS LEU THR ASN VAL SER SEQRES 32 A 459 ASN GLN TYR VAL PRO SER THR ALA ALA VAL ASN ALA SER SEQRES 33 A 459 ALA GLY VAL THR ASN THR GLY ILE PRO ILE PRO SER ALA SEQRES 34 A 459 THR ASN PRO ALA VAL THR GLN GLN ASN GLN THR PHE GLN SEQRES 35 A 459 HIS ILE PHE ARG VAL LEU ASN PHE ASN VAL LEU ARG LEU SEQRES 36 A 459 SER GLY GLY SER HELIX 1 AA1 VAL A 17 THR A 21 5 5 HELIX 2 AA2 SER A 23 TYR A 30 1 8 HELIX 3 AA3 PHE A 115 VAL A 120 1 6 HELIX 4 AA4 ASP A 136 SER A 144 1 9 HELIX 5 AA5 LYS A 152 MET A 159 1 8 HELIX 6 AA6 ALA A 197 ALA A 202 1 6 HELIX 7 AA7 ARG A 216 ILE A 221 1 6 HELIX 8 AA8 HIS A 270 LYS A 279 1 10 HELIX 9 AA9 SER A 364 LEU A 369 1 6 HELIX 10 AB1 SER A 418 ALA A 426 1 9 SHEET 1 AA1 4 VAL A 54 VAL A 55 0 SHEET 2 AA1 4 GLU A 261 CYS A 264 -1 O CYS A 264 N VAL A 54 SHEET 3 AA1 4 TRP A 84 LEU A 89 -1 N ARG A 86 O GLU A 261 SHEET 4 AA1 4 GLU A 180 PRO A 185 -1 O LEU A 184 N LEU A 85 SHEET 1 AA2 2 VAL A 92 ALA A 93 0 SHEET 2 AA2 2 VAL A 238 GLN A 239 -1 O VAL A 238 N ALA A 93 SHEET 1 AA3 2 ASN A 124 THR A 126 0 SHEET 2 AA3 2 LYS A 209 ASN A 211 -1 O ASN A 211 N ASN A 124 SHEET 1 AA4 2 SER A 241 TYR A 242 0 SHEET 2 AA4 2 LEU A 248 ILE A 249 -1 O ILE A 249 N SER A 241 SHEET 1 AA5 2 ARG A 282 LYS A 287 0 SHEET 2 AA5 2 PHE A 459 LEU A 464 -1 O LEU A 462 N MET A 284 SHEET 1 AA6 4 THR A 295 THR A 296 0 SHEET 2 AA6 4 GLN A 451 ARG A 455 -1 O HIS A 452 N THR A 295 SHEET 3 AA6 4 TYR A 319 ARG A 324 -1 N PHE A 320 O ARG A 455 SHEET 4 AA6 4 ALA A 387 TYR A 388 -1 O TYR A 388 N TYR A 319 SHEET 1 AA7 2 ILE A 308 ASP A 309 0 SHEET 2 AA7 2 ASN A 413 GLN A 414 -1 O ASN A 413 N ASP A 309 SHEET 1 AA8 2 VAL A 428 THR A 429 0 SHEET 2 AA8 2 ILE A 433 PRO A 434 -1 O ILE A 433 N THR A 429 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 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