HEADER VIRUS LIKE PARTICLE 03-SEP-25 9WMR TITLE CRYO-EM STRUCTURE OF PCV3 VLPS COMPND MOL_ID: 1; COMPND 2 MOLECULE: CAP; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PORCINE CIRCOVIRUS 3; SOURCE 3 ORGANISM_TAXID: 1868221; SOURCE 4 GENE: ORF2; SOURCE 5 EXPRESSION_SYSTEM: BACULOVIRUS EXPRESSION VECTOR PFASTBAC1-HM; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 274590 KEYWDS PORCINE CIRCOVIRUS 3, CRYO-EM, PCV3 VLP, VIRUS LIKE PARTICLE EXPDTA ELECTRON MICROSCOPY AUTHOR J.SU,Y.JIANG,S.LI,Q.ZHENG REVDAT 1 01-JUL-26 9WMR 0 JRNL AUTH J.SU,X.TONG,Y.JIANG,Y.LI,H.YAN,Y.LIU,Y.WANG,X.SU,Z.SUN, JRNL AUTH 2 M.WANG,N.XIA,M.BOSTINA,S.LI,W.PANG,Q.ZHENG,K.TIAN JRNL TITL STRUCTURAL BASIS AND IMMUNOGENIC EFFICACY OF PORCINE JRNL TITL 2 CIRCOVIRUS TYPE 3 VIRUS-LIKE PARTICLE. JRNL REF NAT COMMUN 2026 JRNL REFN ESSN 2041-1723 JRNL PMID 42303972 JRNL DOI 10.1038/S41467-026-74388-Z REMARK 2 REMARK 2 RESOLUTION. 2.48 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : CRYOSPARC, CRYOSPARC 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) : 2.480 REMARK 3 NUMBER OF PARTICLES : 39064 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 9WMR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 07-SEP-25. REMARK 100 THE DEPOSITION ID IS D_1300062002. 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 : PORCINE CIRCOVIRUS 3 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 : 9.60 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 TECNAI F30 REMARK 245 DETECTOR TYPE : GATAN K3 (6K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 300.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 3872.00 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) : 4000.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : NULL REMARK 245 CALIBRATED MAGNIFICATION : NULL REMARK 245 SOURCE : OTHER 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 MET A 1 REMARK 465 VAL A 2 REMARK 465 TYR A 3 REMARK 465 ARG A 4 REMARK 465 ARG A 5 REMARK 465 ARG A 6 REMARK 465 ARG A 7 REMARK 465 ARG A 8 REMARK 465 SER A 9 REMARK 465 SER A 10 REMARK 465 THR A 11 REMARK 465 GLY A 12 REMARK 465 THR A 13 REMARK 465 THR A 14 REMARK 465 TYR A 15 REMARK 465 GLY A 16 REMARK 465 SER A 17 REMARK 465 THR A 18 REMARK 465 ARG A 19 REMARK 465 ARG A 20 REMARK 465 ARG A 21 REMARK 465 ARG A 22 REMARK 465 TYR A 23 REMARK 465 ALA A 24 REMARK 465 ARG A 25 REMARK 465 ARG A 26 REMARK 465 ARG A 27 REMARK 465 LEU A 28 REMARK 465 PHE A 29 REMARK 465 ILE A 30 REMARK 465 ARG A 31 REMARK 465 ARG A 32 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ARG A 168 CG CD NE CZ NH1 NH2 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 167 -72.30 -124.27 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-66102 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF PCV3 VLPS DBREF1 9WMR A 20 214 UNP A0A6B9EZK0_9CIRC DBREF2 9WMR A A0A6B9EZK0 20 214 SEQADV 9WMR MET A 1 UNP A0A6B9EZK INITIATING METHIONINE SEQADV 9WMR VAL A 2 UNP A0A6B9EZK EXPRESSION TAG SEQADV 9WMR TYR A 3 UNP A0A6B9EZK EXPRESSION TAG SEQADV 9WMR ARG A 4 UNP A0A6B9EZK EXPRESSION TAG SEQADV 9WMR ARG A 5 UNP A0A6B9EZK EXPRESSION TAG SEQADV 9WMR ARG A 6 UNP A0A6B9EZK EXPRESSION TAG SEQADV 9WMR ARG A 7 UNP A0A6B9EZK EXPRESSION TAG SEQADV 9WMR ARG A 8 UNP A0A6B9EZK EXPRESSION TAG SEQADV 9WMR SER A 9 UNP A0A6B9EZK EXPRESSION TAG SEQADV 9WMR SER A 10 UNP A0A6B9EZK EXPRESSION TAG SEQADV 9WMR THR A 11 UNP A0A6B9EZK EXPRESSION TAG SEQADV 9WMR GLY A 12 UNP A0A6B9EZK EXPRESSION TAG SEQADV 9WMR THR A 13 UNP A0A6B9EZK EXPRESSION TAG SEQADV 9WMR THR A 14 UNP A0A6B9EZK EXPRESSION TAG SEQADV 9WMR TYR A 15 UNP A0A6B9EZK EXPRESSION TAG SEQADV 9WMR GLY A 16 UNP A0A6B9EZK EXPRESSION TAG SEQADV 9WMR SER A 17 UNP A0A6B9EZK EXPRESSION TAG SEQADV 9WMR THR A 18 UNP A0A6B9EZK EXPRESSION TAG SEQADV 9WMR ARG A 19 UNP A0A6B9EZK EXPRESSION TAG SEQRES 1 A 214 MET VAL TYR ARG ARG ARG ARG ARG SER SER THR GLY THR SEQRES 2 A 214 THR TYR GLY SER THR ARG ARG ARG ARG TYR ALA ARG ARG SEQRES 3 A 214 ARG LEU PHE ILE ARG ARG PRO THR ALA GLY THR TYR TYR SEQRES 4 A 214 THR LYS LYS TYR SER THR MET ASN VAL ILE SER VAL GLY SEQRES 5 A 214 THR PRO GLN ASP ASN LYS PRO TRP HIS ALA ASN HIS PHE SEQRES 6 A 214 ILE THR ARG LEU ASN GLU TRP GLU THR ALA ILE SER PHE SEQRES 7 A 214 GLU TYR TYR LYS ILE LEU LYS MET LYS VAL THR LEU SER SEQRES 8 A 214 PRO VAL ILE SER PRO ALA GLN GLN LYS LYS THR MET PHE SEQRES 9 A 214 GLY HIS THR ALA ILE ASP LEU ASP GLY ALA TRP THR THR SEQRES 10 A 214 ASN THR TRP LEU GLN ASP ASP PRO TYR ALA GLU SER SER SEQRES 11 A 214 THR ARG LYS VAL MET THR SER LYS LYS LYS HIS SER ARG SEQRES 12 A 214 TYR PHE THR PRO LYS PRO ILE LEU ALA GLY THR THR SER SEQRES 13 A 214 ALA HIS PRO GLY GLN SER LEU PHE PHE PHE SER ARG PRO SEQRES 14 A 214 THR PRO TRP LEU ASN THR TYR ASP PRO THR VAL GLN TRP SEQRES 15 A 214 GLY ALA LEU LEU TRP SER ILE TYR VAL PRO GLU LYS THR SEQRES 16 A 214 GLY MET THR ASP PHE TYR GLY THR LYS GLU VAL TRP ILE SEQRES 17 A 214 ARG TYR LYS SER VAL LEU HELIX 1 AA1 ARG A 68 TRP A 72 5 5 HELIX 2 AA2 SER A 95 GLN A 99 5 5 SHEET 1 AA1 4 TYR A 39 ILE A 49 0 SHEET 2 AA1 4 PHE A 200 TYR A 210 -1 O GLY A 202 N ASN A 47 SHEET 3 AA1 4 TYR A 80 PRO A 92 -1 N SER A 91 O TYR A 201 SHEET 4 AA1 4 HIS A 141 PHE A 145 -1 O HIS A 141 N LEU A 90 SHEET 1 AA2 4 TYR A 39 ILE A 49 0 SHEET 2 AA2 4 PHE A 200 TYR A 210 -1 O GLY A 202 N ASN A 47 SHEET 3 AA2 4 TYR A 80 PRO A 92 -1 N SER A 91 O TYR A 201 SHEET 4 AA2 4 LEU A 173 ASN A 174 -1 O LEU A 173 N TYR A 81 SHEET 1 AA3 5 THR A 119 LEU A 121 0 SHEET 2 AA3 5 TRP A 60 THR A 67 -1 N TRP A 60 O LEU A 121 SHEET 3 AA3 5 TRP A 182 TYR A 190 -1 O ILE A 189 N HIS A 61 SHEET 4 AA3 5 PHE A 104 ASP A 110 -1 N ALA A 108 O LEU A 186 SHEET 5 AA3 5 LYS A 133 THR A 136 -1 O MET A 135 N GLY A 105 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 MASTER 163 0 0 2 13 0 0 6 1480 1 0 17 END