HEADER VIRUS LIKE PARTICLE/IMMUNE SYSTEM 03-SEP-25 9WMQ TITLE THE CRYO-ELECTRON MICROSCOPY COMPLEX STRUCTURE OF PCV3 VLPS AND TITLE 2 ANTIBODY 2B5 COMPND MOL_ID: 1; COMPND 2 MOLECULE: CAP; COMPND 3 CHAIN: F; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: HEAVY CHAIN OF ANTIBODY 2B5; COMPND 7 CHAIN: H; COMPND 8 OTHER_DETAILS: DUE TO PATENT PROTECTION, WE ONLY PROVIDE THE CDR COMPND 9 REGIONS OF THE ANTIBODY THAT ARE INVOLVED IN KEY INTERACTIONS.; COMPND 10 MOL_ID: 3; COMPND 11 MOLECULE: LIGHT CHAIN OF ANTIBODY 2B5; COMPND 12 CHAIN: L; COMPND 13 OTHER_DETAILS: DUE TO PATENT PROTECTION, WE ONLY PROVIDE THE CDR COMPND 14 REGIONS OF THE ANTIBODY THAT ARE INVOLVED IN KEY INTERACTIONS. 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; SOURCE 7 MOL_ID: 2; SOURCE 8 ORGANISM_SCIENTIFIC: MUS; SOURCE 9 ORGANISM_TAXID: 10088; SOURCE 10 MOL_ID: 3; SOURCE 11 ORGANISM_SCIENTIFIC: MUS; SOURCE 12 ORGANISM_TAXID: 10088 KEYWDS PORCINE CIRCOVIRUS 3, CRYO-EM, PCV3 VLP, IMMUNOCOMPLEXES, VIRUS LIKE KEYWDS 2 PARTICLE/IMMUNE SYSTEM, VIRUS LIKE PARTICLE-IMMUNE SYSTEM COMPLEX EXPDTA ELECTRON MICROSCOPY AUTHOR J.SU,Y.JIANG,S.LI,Q.ZHENG REVDAT 1 01-JUL-26 9WMQ 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. 1.73 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) : 1.730 REMARK 3 NUMBER OF PARTICLES : 197071 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 9WMQ 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_1300063163. 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 : PCV3 VLP:2B5 COMPLEX; PCV3 CAP; REMARK 245 THE FAB OF 2B5 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 : TFS KRIOS REMARK 245 DETECTOR TYPE : GATAN K3 (6K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 300.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 1568.00 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) : 4800.00 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: TRIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: F, H, L 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 GLN H 1 REMARK 465 ALA H 2 REMARK 465 GLN H 3 REMARK 465 LEU H 4 REMARK 465 GLN H 5 REMARK 465 GLN H 6 REMARK 465 PRO H 7 REMARK 465 GLY H 8 REMARK 465 ALA H 9 REMARK 465 GLU H 10 REMARK 465 LEU H 11 REMARK 465 VAL H 12 REMARK 465 ARG H 13 REMARK 465 PRO H 14 REMARK 465 GLY H 15 REMARK 465 ALA H 16 REMARK 465 SER H 17 REMARK 465 VAL H 18 REMARK 465 LYS H 19 REMARK 465 LEU H 20 REMARK 465 SER H 21 REMARK 465 CYS H 22 REMARK 465 LYS H 23 REMARK 465 ALA H 24 REMARK 465 SER H 25 REMARK 465 GLY H 26 REMARK 465 TYR H 27 REMARK 465 THR H 28 REMARK 465 PHE H 29 REMARK 465 SER H 30 REMARK 465 SER H 31 REMARK 465 TYR H 32 REMARK 465 TRP H 33 REMARK 465 MET H 34 REMARK 465 ASN H 35 REMARK 465 TRP H 36 REMARK 465 VAL H 37 REMARK 465 LYS H 38 REMARK 465 GLN H 39 REMARK 465 ARG H 40 REMARK 465 PRO H 41 REMARK 465 GLU H 42 REMARK 465 GLN H 43 REMARK 465 GLY H 44 REMARK 465 LEU H 45 REMARK 465 GLU H 46 REMARK 465 TRP H 47 REMARK 465 ILE H 48 REMARK 465 ASN H 61 REMARK 465 GLN H 62 REMARK 465 LYS H 63 REMARK 465 PHE H 64 REMARK 465 LYS H 65 REMARK 465 ASP H 66 REMARK 465 LYS H 67 REMARK 465 ALA H 68 REMARK 465 ILE H 69 REMARK 465 LEU H 70 REMARK 465 THR H 71 REMARK 465 VAL H 72 REMARK 465 ASP H 73 REMARK 465 LYS H 74 REMARK 465 SER H 75 REMARK 465 SER H 76 REMARK 465 SER H 77 REMARK 465 THR H 78 REMARK 465 ALA H 79 REMARK 465 TYR H 80 REMARK 465 MET H 81 REMARK 465 GLN H 82 REMARK 465 LEU H 83 REMARK 465 SER H 84 REMARK 465 SER H 85 REMARK 465 LEU H 86 REMARK 465 THR H 87 REMARK 465 SER H 88 REMARK 465 GLU H 89 REMARK 465 ASP H 90 REMARK 465 SER H 91 REMARK 465 ALA H 92 REMARK 465 VAL H 93 REMARK 465 TYR H 94 REMARK 465 TYR H 95 REMARK 465 CYS H 96 REMARK 465 ALA H 97 REMARK 465 GLU H 108 REMARK 465 ARG H 109 REMARK 465 TRP H 110 REMARK 465 GLY H 111 REMARK 465 GLN H 112 REMARK 465 GLY H 113 REMARK 465 THR H 114 REMARK 465 THR H 115 REMARK 465 LEU H 116 REMARK 465 THR H 117 REMARK 465 VAL H 118 REMARK 465 SER H 119 REMARK 465 SER H 120 REMARK 465 ASP L 1 REMARK 465 ILE L 2 REMARK 465 VAL L 3 REMARK 465 MET L 4 REMARK 465 THR L 5 REMARK 465 GLN L 6 REMARK 465 SER L 7 REMARK 465 GLN L 8 REMARK 465 LYS L 9 REMARK 465 PHE L 10 REMARK 465 MET L 11 REMARK 465 SER L 12 REMARK 465 THR L 13 REMARK 465 SER L 14 REMARK 465 VAL L 15 REMARK 465 GLY L 16 REMARK 465 GLU L 17 REMARK 465 ARG L 18 REMARK 465 VAL L 19 REMARK 465 SER L 20 REMARK 465 VAL L 21 REMARK 465 THR L 22 REMARK 465 CYS L 23 REMARK 465 LYS L 24 REMARK 465 ALA L 25 REMARK 465 SER L 26 REMARK 465 GLN L 27 REMARK 465 ASN L 28 REMARK 465 VAL L 29 REMARK 465 TYR L 36 REMARK 465 GLN L 37 REMARK 465 GLN L 38 REMARK 465 LYS L 39 REMARK 465 PRO L 40 REMARK 465 GLY L 41 REMARK 465 GLN L 42 REMARK 465 SER L 43 REMARK 465 PRO L 44 REMARK 465 GLN L 45 REMARK 465 PRO L 46 REMARK 465 LEU L 47 REMARK 465 ILE L 48 REMARK 465 TYR L 49 REMARK 465 SER L 50 REMARK 465 ALA L 51 REMARK 465 SER L 52 REMARK 465 TYR L 53 REMARK 465 ARG L 54 REMARK 465 TYR L 55 REMARK 465 SER L 56 REMARK 465 GLY L 57 REMARK 465 VAL L 58 REMARK 465 PRO L 59 REMARK 465 ASP L 60 REMARK 465 ARG L 61 REMARK 465 PHE L 62 REMARK 465 THR L 63 REMARK 465 GLY L 64 REMARK 465 SER L 65 REMARK 465 GLY L 66 REMARK 465 SER L 67 REMARK 465 GLY L 68 REMARK 465 THR L 69 REMARK 465 ASP L 70 REMARK 465 PHE L 71 REMARK 465 THR L 72 REMARK 465 LEU L 73 REMARK 465 THR L 74 REMARK 465 ILE L 75 REMARK 465 SER L 76 REMARK 465 ASP L 77 REMARK 465 VAL L 78 REMARK 465 GLN L 79 REMARK 465 SER L 80 REMARK 465 GLU L 81 REMARK 465 ASP L 82 REMARK 465 LEU L 83 REMARK 465 ALA L 84 REMARK 465 GLU L 85 REMARK 465 TYR L 86 REMARK 465 PHE L 87 REMARK 465 CYS L 88 REMARK 465 GLN L 89 REMARK 465 GLN L 90 REMARK 465 TYR L 91 REMARK 465 ASN L 92 REMARK 465 SER L 93 REMARK 465 TYR L 94 REMARK 465 PRO L 95 REMARK 465 LEU L 96 REMARK 465 ALA L 97 REMARK 465 PHE L 98 REMARK 465 GLY L 99 REMARK 465 GLY L 100 REMARK 465 GLY L 101 REMARK 465 THR L 102 REMARK 465 LYS L 103 REMARK 465 LEU L 104 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 F 167 -66.22 -95.97 REMARK 500 GLU H 99 116.83 -160.01 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-66101 RELATED DB: EMDB REMARK 900 THE CRYO-ELECTRON MICROSCOPY COMPLEX STRUCTURE OF PCV3 VLPS AND REMARK 900 ANTIBODY 2B5 DBREF1 9WMQ F 33 214 UNP A0A6B9EZK0_9CIRC DBREF2 9WMQ F A0A6B9EZK0 33 214 DBREF 9WMQ H 1 120 PDB 9WMQ 9WMQ 1 120 DBREF 9WMQ L 1 104 PDB 9WMQ 9WMQ 1 104 SEQRES 1 F 182 PRO THR ALA GLY THR TYR TYR THR LYS LYS TYR SER THR SEQRES 2 F 182 MET ASN VAL ILE SER VAL GLY THR PRO GLN ASP ASN LYS SEQRES 3 F 182 PRO TRP HIS ALA ASN HIS PHE ILE THR ARG LEU ASN GLU SEQRES 4 F 182 TRP GLU THR ALA ILE SER PHE GLU TYR TYR LYS ILE LEU SEQRES 5 F 182 LYS MET LYS VAL THR LEU SER PRO VAL ILE SER PRO ALA SEQRES 6 F 182 GLN GLN LYS LYS THR MET PHE GLY HIS THR ALA ILE ASP SEQRES 7 F 182 LEU ASP GLY ALA TRP THR THR ASN THR TRP LEU GLN ASP SEQRES 8 F 182 ASP PRO TYR ALA GLU SER SER THR ARG LYS VAL MET THR SEQRES 9 F 182 SER LYS LYS LYS HIS SER ARG TYR PHE THR PRO LYS PRO SEQRES 10 F 182 ILE LEU ALA GLY THR THR SER ALA HIS PRO GLY GLN SER SEQRES 11 F 182 LEU PHE PHE PHE SER ARG PRO THR PRO TRP LEU ASN THR SEQRES 12 F 182 TYR ASP PRO THR VAL GLN TRP GLY ALA LEU LEU TRP SER SEQRES 13 F 182 ILE TYR VAL PRO GLU LYS THR GLY MET THR ASP PHE TYR SEQRES 14 F 182 GLY THR LYS GLU VAL TRP ILE ARG TYR LYS SER VAL LEU SEQRES 1 H 120 GLN ALA GLN LEU GLN GLN PRO GLY ALA GLU LEU VAL ARG SEQRES 2 H 120 PRO GLY ALA SER VAL LYS LEU SER CYS LYS ALA SER GLY SEQRES 3 H 120 TYR THR PHE SER SER TYR TRP MET ASN TRP VAL LYS GLN SEQRES 4 H 120 ARG PRO GLU GLN GLY LEU GLU TRP ILE GLY ARG ILE ASP SEQRES 5 H 120 PHE TYR ASP SER GLU ASN HIS TYR ASN GLN LYS PHE LYS SEQRES 6 H 120 ASP LYS ALA ILE LEU THR VAL ASP LYS SER SER SER THR SEQRES 7 H 120 ALA TYR MET GLN LEU SER SER LEU THR SER GLU ASP SER SEQRES 8 H 120 ALA VAL TYR TYR CYS ALA GLY GLU SER TYR GLY ASN TYR SEQRES 9 H 120 GLY ARG PHE GLU ARG TRP GLY GLN GLY THR THR LEU THR SEQRES 10 H 120 VAL SER SER SEQRES 1 L 104 ASP ILE VAL MET THR GLN SER GLN LYS PHE MET SER THR SEQRES 2 L 104 SER VAL GLY GLU ARG VAL SER VAL THR CYS LYS ALA SER SEQRES 3 L 104 GLN ASN VAL GLY THR ASN VAL ALA TRP TYR GLN GLN LYS SEQRES 4 L 104 PRO GLY GLN SER PRO GLN PRO LEU ILE TYR SER ALA SER SEQRES 5 L 104 TYR ARG TYR SER GLY VAL PRO ASP ARG PHE THR GLY SER SEQRES 6 L 104 GLY SER GLY THR ASP PHE THR LEU THR ILE SER ASP VAL SEQRES 7 L 104 GLN SER GLU ASP LEU ALA GLU TYR PHE CYS GLN GLN TYR SEQRES 8 L 104 ASN SER TYR PRO LEU ALA PHE GLY GLY GLY THR LYS LEU SHEET 1 AA1 4 TYR F 39 ILE F 49 0 SHEET 2 AA1 4 PHE F 200 TYR F 210 -1 O TYR F 210 N TYR F 39 SHEET 3 AA1 4 TYR F 80 PRO F 92 -1 N SER F 91 O TYR F 201 SHEET 4 AA1 4 HIS F 141 PHE F 145 -1 O HIS F 141 N LEU F 90 SHEET 1 AA2 4 TYR F 39 ILE F 49 0 SHEET 2 AA2 4 PHE F 200 TYR F 210 -1 O TYR F 210 N TYR F 39 SHEET 3 AA2 4 TYR F 80 PRO F 92 -1 N SER F 91 O TYR F 201 SHEET 4 AA2 4 LEU F 173 ASN F 174 -1 O LEU F 173 N TYR F 81 SHEET 1 AA3 5 THR F 119 LEU F 121 0 SHEET 2 AA3 5 TRP F 60 PHE F 65 -1 N TRP F 60 O LEU F 121 SHEET 3 AA3 5 ALA F 184 TYR F 190 -1 O TRP F 187 N ASN F 63 SHEET 4 AA3 5 PHE F 104 ASP F 110 -1 N ALA F 108 O LEU F 186 SHEET 5 AA3 5 LYS F 133 THR F 136 -1 O MET F 135 N GLY F 105 SHEET 1 AA4 2 ARG H 50 ILE H 51 0 SHEET 2 AA4 2 ASN H 58 HIS H 59 -1 O HIS H 59 N ARG H 50 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 321 0 0 0 15 0 0 6 1719 3 0 32 END