HEADER VIRAL PROTEIN 03-FEB-23 8I8A TITLE CRYO-EM STRUCTURE OF THE MAJOR CAPSID PROTEIN VP39 OF AUTOGRAPHA TITLE 2 CALIFORNICA MULTIPLE NUCLEOPOLYHEDROVIRUS (ACMNPV) COMPND MOL_ID: 1; COMPND 2 MOLECULE: MAJOR VIRAL CAPSID PROTEIN; COMPND 3 CHAIN: A, B SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: AUTOGRAPHA CALIFORNICA MULTIPLE SOURCE 3 NUCLEOPOLYHEDROVIRUS; SOURCE 4 ORGANISM_TAXID: 307456 KEYWDS VIRUS, CAPSID PROTEIN, VIRAL PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR X.JIA,Q.ZHANG REVDAT 2 16-OCT-24 8I8A 1 REMARK REVDAT 1 13-DEC-23 8I8A 0 JRNL AUTH X.JIA,Y.GAO,Y.HUANG,L.SUN,S.LI,H.LI,X.ZHANG,Y.LI,J.HE,W.WU, JRNL AUTH 2 H.VENKANNAGARI,K.YANG,M.L.BAKER,Q.ZHANG JRNL TITL ARCHITECTURE OF THE BACULOVIRUS NUCLEOCAPSID REVEALED BY JRNL TITL 2 CRYO-EM. JRNL REF NAT COMMUN V. 14 7481 2023 JRNL REFN ESSN 2041-1723 JRNL PMID 37980340 JRNL DOI 10.1038/S41467-023-43284-1 REMARK 2 REMARK 2 RESOLUTION. 3.21 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) : 3.210 REMARK 3 NUMBER OF PARTICLES : 163500 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 8I8A COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 08-FEB-23. REMARK 100 THE DEPOSITION ID IS D_1300034638. 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 : AUTOGRAPHA CALIFORNICA MULTIPLE REMARK 245 NUCLEOPOLYHEDROVIRUS 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 : 7.00 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) : 1500.00 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 : NULL REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 5000.00 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: DIMERIC 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 MET A 1 REMARK 465 ALA A 2 REMARK 465 LEU A 3 REMARK 465 VAL A 4 REMARK 465 PRO A 5 REMARK 465 VAL A 6 REMARK 465 GLY A 7 REMARK 465 MET A 8 REMARK 465 ALA A 9 REMARK 465 PRO A 10 REMARK 465 ARG A 11 REMARK 465 GLN A 12 REMARK 465 MET A 13 REMARK 465 PRO A 321 REMARK 465 ASN A 322 REMARK 465 ALA A 323 REMARK 465 THR A 324 REMARK 465 LEU A 325 REMARK 465 GLY A 326 REMARK 465 GLY A 327 REMARK 465 GLY A 328 REMARK 465 ALA A 329 REMARK 465 VAL A 330 REMARK 465 ALA A 331 REMARK 465 GLY A 332 REMARK 465 PRO A 333 REMARK 465 ALA A 334 REMARK 465 PRO A 335 REMARK 465 GLY A 336 REMARK 465 VAL A 337 REMARK 465 ALA A 338 REMARK 465 GLY A 339 REMARK 465 GLU A 340 REMARK 465 ALA A 341 REMARK 465 GLY A 342 REMARK 465 GLY A 343 REMARK 465 GLY A 344 REMARK 465 ILE A 345 REMARK 465 ALA A 346 REMARK 465 VAL A 347 REMARK 465 MET B 1 REMARK 465 ALA B 2 REMARK 465 LEU B 3 REMARK 465 VAL B 4 REMARK 465 PRO B 5 REMARK 465 VAL B 6 REMARK 465 GLY B 7 REMARK 465 MET B 8 REMARK 465 ALA B 9 REMARK 465 PRO B 10 REMARK 465 ARG B 11 REMARK 465 GLN B 12 REMARK 465 MET B 13 REMARK 465 PRO B 321 REMARK 465 ASN B 322 REMARK 465 ALA B 323 REMARK 465 THR B 324 REMARK 465 LEU B 325 REMARK 465 GLY B 326 REMARK 465 GLY B 327 REMARK 465 GLY B 328 REMARK 465 ALA B 329 REMARK 465 VAL B 330 REMARK 465 ALA B 331 REMARK 465 GLY B 332 REMARK 465 PRO B 333 REMARK 465 ALA B 334 REMARK 465 PRO B 335 REMARK 465 GLY B 336 REMARK 465 VAL B 337 REMARK 465 ALA B 338 REMARK 465 GLY B 339 REMARK 465 GLU B 340 REMARK 465 ALA B 341 REMARK 465 GLY B 342 REMARK 465 GLY B 343 REMARK 465 GLY B 344 REMARK 465 ILE B 345 REMARK 465 ALA B 346 REMARK 465 VAL B 347 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 SER A 22 31.77 -94.54 REMARK 500 ALA A 28 -6.96 70.92 REMARK 500 SER A 34 80.42 -160.38 REMARK 500 ASP A 43 59.00 -94.42 REMARK 500 ASN A 106 58.32 34.50 REMARK 500 THR A 167 -142.95 45.87 REMARK 500 ARG A 171 48.96 -91.85 REMARK 500 PHE A 180 49.75 -90.95 REMARK 500 ARG A 186 54.46 -91.06 REMARK 500 ASP A 220 -95.58 56.52 REMARK 500 ILE A 253 -60.69 64.00 REMARK 500 ARG A 254 -123.85 64.12 REMARK 500 ILE A 268 -53.61 63.02 REMARK 500 TYR A 291 75.05 52.69 REMARK 500 ARG A 318 161.88 65.28 REMARK 500 ALA B 28 -4.07 68.47 REMARK 500 SER B 34 79.56 -162.38 REMARK 500 ASP B 43 54.18 -90.64 REMARK 500 LEU B 94 -61.42 -93.30 REMARK 500 ASN B 106 58.14 34.44 REMARK 500 THR B 167 -140.70 42.86 REMARK 500 ARG B 171 50.04 -92.21 REMARK 500 PHE B 180 48.65 -91.64 REMARK 500 ARG B 186 53.70 -91.30 REMARK 500 ASP B 220 -95.62 56.60 REMARK 500 THR B 237 30.76 -92.19 REMARK 500 ILE B 253 -58.13 66.13 REMARK 500 ARG B 254 -117.90 62.11 REMARK 500 ILE B 268 -54.08 61.35 REMARK 500 GLU B 290 -35.23 -39.34 REMARK 500 TYR B 291 75.19 51.59 REMARK 500 ARG B 318 156.48 65.38 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-35245 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF THE MAJOR CAPSID PROTEIN VP39 OF AUTOGRAPHA REMARK 900 CALIFORNICA MULTIPLE NUCLEOPOLYHEDROVIRUS (ACMNPV) REMARK 900 RELATED ID: EMD-35242 RELATED DB: EMDB DBREF1 8I8A A 1 347 UNP A0A0N6WHR0_9ABAC DBREF2 8I8A A A0A0N6WHR0 1 347 DBREF1 8I8A B 1 347 UNP A0A0N6WHR0_9ABAC DBREF2 8I8A B A0A0N6WHR0 1 347 SEQRES 1 A 347 MET ALA LEU VAL PRO VAL GLY MET ALA PRO ARG GLN MET SEQRES 2 A 347 ARG VAL ASN ARG CYS ILE PHE ALA SER ILE VAL SER PHE SEQRES 3 A 347 ASP ALA CYS ILE THR TYR LYS SER PRO CYS SER PRO ASP SEQRES 4 A 347 ALA TYR HIS ASP ASP GLY TRP PHE ILE CYS ASN ASN HIS SEQRES 5 A 347 LEU ILE LYS ARG PHE LYS MET SER LYS MET VAL LEU PRO SEQRES 6 A 347 ILE PHE ASP GLU ASP ASP ASN GLN PHE LYS MET THR ILE SEQRES 7 A 347 ALA ARG HIS LEU VAL GLY ASN LYS GLU ARG GLY ILE LYS SEQRES 8 A 347 ARG ILE LEU ILE PRO SER ALA THR ASN TYR GLN ASP VAL SEQRES 9 A 347 PHE ASN LEU ASN SER MET MET GLN ALA GLU GLN LEU ILE SEQRES 10 A 347 PHE HIS LEU ILE TYR ASN ASN GLU ASN ALA VAL ASN THR SEQRES 11 A 347 ILE CYS ASP ASN LEU LYS TYR THR GLU GLY PHE THR SER SEQRES 12 A 347 ASN THR GLN ARG VAL ILE HIS SER VAL TYR ALA THR THR SEQRES 13 A 347 LYS SER ILE LEU ASP THR THR ASN PRO ASN THR PHE CYS SEQRES 14 A 347 SER ARG VAL SER ARG ASP GLU LEU ARG PHE PHE ASP VAL SEQRES 15 A 347 THR ASN ALA ARG ALA LEU ARG GLY GLY ALA GLY ASP GLN SEQRES 16 A 347 LEU PHE ASN ASN TYR SER GLY PHE LEU GLN ASN LEU ILE SEQRES 17 A 347 ARG ARG ALA VAL ALA PRO GLU TYR LEU GLN ILE ASP THR SEQRES 18 A 347 GLU GLU LEU ARG PHE ARG ASN CYS ALA THR CYS ILE ILE SEQRES 19 A 347 ASP GLU THR GLY LEU VAL ALA SER VAL PRO ASP GLY PRO SEQRES 20 A 347 GLU LEU TYR ASN PRO ILE ARG SER SER ASP ILE MET ARG SEQRES 21 A 347 SER GLN PRO ASN ARG LEU GLN ILE ARG ASN VAL LEU LYS SEQRES 22 A 347 PHE GLU GLY ASP THR ARG GLU LEU ASP ARG THR LEU SER SEQRES 23 A 347 GLY TYR GLU GLU TYR PRO THR TYR VAL PRO LEU PHE LEU SEQRES 24 A 347 GLY TYR GLN ILE ILE ASN SER GLU ASN ASN PHE LEU ARG SEQRES 25 A 347 ASN ASP PHE ILE PRO ARG ALA ASN PRO ASN ALA THR LEU SEQRES 26 A 347 GLY GLY GLY ALA VAL ALA GLY PRO ALA PRO GLY VAL ALA SEQRES 27 A 347 GLY GLU ALA GLY GLY GLY ILE ALA VAL SEQRES 1 B 347 MET ALA LEU VAL PRO VAL GLY MET ALA PRO ARG GLN MET SEQRES 2 B 347 ARG VAL ASN ARG CYS ILE PHE ALA SER ILE VAL SER PHE SEQRES 3 B 347 ASP ALA CYS ILE THR TYR LYS SER PRO CYS SER PRO ASP SEQRES 4 B 347 ALA TYR HIS ASP ASP GLY TRP PHE ILE CYS ASN ASN HIS SEQRES 5 B 347 LEU ILE LYS ARG PHE LYS MET SER LYS MET VAL LEU PRO SEQRES 6 B 347 ILE PHE ASP GLU ASP ASP ASN GLN PHE LYS MET THR ILE SEQRES 7 B 347 ALA ARG HIS LEU VAL GLY ASN LYS GLU ARG GLY ILE LYS SEQRES 8 B 347 ARG ILE LEU ILE PRO SER ALA THR ASN TYR GLN ASP VAL SEQRES 9 B 347 PHE ASN LEU ASN SER MET MET GLN ALA GLU GLN LEU ILE SEQRES 10 B 347 PHE HIS LEU ILE TYR ASN ASN GLU ASN ALA VAL ASN THR SEQRES 11 B 347 ILE CYS ASP ASN LEU LYS TYR THR GLU GLY PHE THR SER SEQRES 12 B 347 ASN THR GLN ARG VAL ILE HIS SER VAL TYR ALA THR THR SEQRES 13 B 347 LYS SER ILE LEU ASP THR THR ASN PRO ASN THR PHE CYS SEQRES 14 B 347 SER ARG VAL SER ARG ASP GLU LEU ARG PHE PHE ASP VAL SEQRES 15 B 347 THR ASN ALA ARG ALA LEU ARG GLY GLY ALA GLY ASP GLN SEQRES 16 B 347 LEU PHE ASN ASN TYR SER GLY PHE LEU GLN ASN LEU ILE SEQRES 17 B 347 ARG ARG ALA VAL ALA PRO GLU TYR LEU GLN ILE ASP THR SEQRES 18 B 347 GLU GLU LEU ARG PHE ARG ASN CYS ALA THR CYS ILE ILE SEQRES 19 B 347 ASP GLU THR GLY LEU VAL ALA SER VAL PRO ASP GLY PRO SEQRES 20 B 347 GLU LEU TYR ASN PRO ILE ARG SER SER ASP ILE MET ARG SEQRES 21 B 347 SER GLN PRO ASN ARG LEU GLN ILE ARG ASN VAL LEU LYS SEQRES 22 B 347 PHE GLU GLY ASP THR ARG GLU LEU ASP ARG THR LEU SER SEQRES 23 B 347 GLY TYR GLU GLU TYR PRO THR TYR VAL PRO LEU PHE LEU SEQRES 24 B 347 GLY TYR GLN ILE ILE ASN SER GLU ASN ASN PHE LEU ARG SEQRES 25 B 347 ASN ASP PHE ILE PRO ARG ALA ASN PRO ASN ALA THR LEU SEQRES 26 B 347 GLY GLY GLY ALA VAL ALA GLY PRO ALA PRO GLY VAL ALA SEQRES 27 B 347 GLY GLU ALA GLY GLY GLY ILE ALA VAL HELIX 1 AA1 CYS A 18 ILE A 23 5 6 HELIX 2 AA2 SER A 37 HIS A 42 5 6 HELIX 3 AA3 CYS A 49 PHE A 57 1 9 HELIX 4 AA4 ARG A 88 LYS A 91 5 4 HELIX 5 AA5 MET A 111 TYR A 122 1 12 HELIX 6 AA6 ASN A 124 TYR A 137 1 14 HELIX 7 AA7 GLY A 140 ASN A 164 1 25 HELIX 8 AA8 GLY A 191 ASN A 198 1 8 HELIX 9 AA9 SER A 201 VAL A 212 1 12 HELIX 10 AB1 THR A 278 LEU A 285 1 8 HELIX 11 AB2 CYS B 18 ILE B 23 5 6 HELIX 12 AB3 SER B 37 HIS B 42 5 6 HELIX 13 AB4 CYS B 49 PHE B 57 1 9 HELIX 14 AB5 ARG B 88 LYS B 91 5 4 HELIX 15 AB6 MET B 111 TYR B 122 1 12 HELIX 16 AB7 ASN B 124 TYR B 137 1 14 HELIX 17 AB8 GLY B 140 ASN B 164 1 25 HELIX 18 AB9 GLY B 191 ASN B 198 1 8 HELIX 19 AC1 SER B 201 VAL B 212 1 12 HELIX 20 AC2 THR B 278 THR B 284 1 7 SHEET 1 AA1 2 MET A 62 ILE A 66 0 SHEET 2 AA1 2 PHE A 74 ILE A 78 -1 O PHE A 74 N ILE A 66 SHEET 1 AA2 3 ILE A 93 ILE A 95 0 SHEET 2 AA2 3 GLY A 238 VAL A 240 -1 O LEU A 239 N LEU A 94 SHEET 3 AA2 3 ILE A 233 ASP A 235 -1 N ILE A 233 O VAL A 240 SHEET 1 AA3 4 GLU A 176 PHE A 179 0 SHEET 2 AA3 4 TYR A 301 ILE A 304 -1 O TYR A 301 N PHE A 179 SHEET 3 AA3 4 TYR A 216 ILE A 219 1 N GLN A 218 O ILE A 304 SHEET 4 AA3 4 GLU A 222 ARG A 225 -1 O LEU A 224 N LEU A 217 SHEET 1 AA4 2 LYS B 61 ILE B 66 0 SHEET 2 AA4 2 PHE B 74 ALA B 79 -1 O PHE B 74 N ILE B 66 SHEET 1 AA5 3 ILE B 93 ILE B 95 0 SHEET 2 AA5 3 GLY B 238 VAL B 240 -1 O LEU B 239 N LEU B 94 SHEET 3 AA5 3 ILE B 233 ASP B 235 -1 N ILE B 233 O VAL B 240 SHEET 1 AA6 4 GLU B 176 PHE B 179 0 SHEET 2 AA6 4 TYR B 301 ILE B 304 -1 O TYR B 301 N PHE B 179 SHEET 3 AA6 4 TYR B 216 ILE B 219 1 N GLN B 218 O ILE B 304 SHEET 4 AA6 4 GLU B 222 ARG B 225 -1 O LEU B 224 N LEU B 217 SSBOND 1 CYS A 36 CYS A 49 1555 1555 2.03 SSBOND 2 CYS A 229 CYS B 229 1555 1555 2.03 SSBOND 3 CYS B 36 CYS B 49 1555 1555 2.03 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