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- PDB-9mpz: Complex of FMDV Asia1/JS/05 and porcine-derived neutralizing mono... -

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Basic information

Entry
Database: PDB / ID: 9mpz
TitleComplex of FMDV Asia1/JS/05 and porcine-derived neutralizing monoclonal antibody PAS12
Components
  • (Capsid protein ...) x 4
  • PAS12 Fv Heavy chain
  • PAS12 Fv Light chain
KeywordsVIRUS/IMMUNE SYSTEM / Foot-and-mouth disease virus Asia1 / Sus scrofa / VIRUS / VIRUS-IMMUNE SYSTEM complex
Function / homology
Function and homology information


L-peptidase / symbiont-mediated perturbation of host chromatin organization / picornain 3C / T=pseudo3 icosahedral viral capsid / ribonucleoside triphosphate phosphatase activity / host cell cytoplasmic vesicle membrane / regulation of translation / nucleoside-triphosphate phosphatase / channel activity / monoatomic ion transmembrane transport ...L-peptidase / symbiont-mediated perturbation of host chromatin organization / picornain 3C / T=pseudo3 icosahedral viral capsid / ribonucleoside triphosphate phosphatase activity / host cell cytoplasmic vesicle membrane / regulation of translation / nucleoside-triphosphate phosphatase / channel activity / monoatomic ion transmembrane transport / clathrin-dependent endocytosis of virus by host cell / RNA helicase activity / viral protein processing / host cell endoplasmic reticulum membrane / RNA-directed RNA polymerase / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / DNA-templated transcription / virion attachment to host cell / host cell nucleus / structural molecule activity / proteolysis / RNA binding / ATP binding / membrane
Similarity search - Function
Peptidase C28, foot-and-mouth virus L-proteinase / Foot-and-mouth virus L-proteinase / Aphthovirus leader protease (L(pro)) domain profile. / Foot-and-mouth disease virus VP1 coat / Capsid protein VP4, Picornavirus / Viral protein VP4 subunit / Capsid protein VP4 superfamily, Picornavirus / Helicase/polymerase/peptidase polyprotein, Calicivirus-type / Picornavirus coat protein / Papain-like cysteine peptidase superfamily ...Peptidase C28, foot-and-mouth virus L-proteinase / Foot-and-mouth virus L-proteinase / Aphthovirus leader protease (L(pro)) domain profile. / Foot-and-mouth disease virus VP1 coat / Capsid protein VP4, Picornavirus / Viral protein VP4 subunit / Capsid protein VP4 superfamily, Picornavirus / Helicase/polymerase/peptidase polyprotein, Calicivirus-type / Picornavirus coat protein / Papain-like cysteine peptidase superfamily / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Picornavirus capsid / picornavirus capsid protein / Helicase, superfamily 3, single-stranded RNA virus / Superfamily 3 helicase of positive ssRNA viruses domain profile. / Helicase, superfamily 3, single-stranded DNA/RNA virus / RNA helicase / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / Reverse transcriptase/Diguanylate cyclase domain / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Biological speciesFoot-and-mouth disease virus Asia 1
Sus scrofa (pig)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.14 Å
AuthorsWu, S. / Lei, D.
Funding support China, 5items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32373028 China
National Natural Science Foundation of China (NSFC)32171300 China
National Natural Science Foundation of China (NSFC)32072873 China
Other government2021YFD1800304
Other governmentlzujbky-2021-ct05
CitationJournal: To Be Published
Title: Porcine B cell receptor repertoire uncovers immunodominant properties of antigenic structures on serotype Asia1 foot-and-mouth disease virus
Authors: Huang, S. / Wu, S. / Li, K. / Li, F. / Li, P. / Cao, Y. / Bao, H. / Dong, K. / Yang, J. / Zhao, Q. / Sun, Y. / Li, D. / Sun, P. / Bai, X. / Fu, Y. / Yuan, H. / Ma, X. / Zhao, Z. / Zhang, J. ...Authors: Huang, S. / Wu, S. / Li, K. / Li, F. / Li, P. / Cao, Y. / Bao, H. / Dong, K. / Yang, J. / Zhao, Q. / Sun, Y. / Li, D. / Sun, P. / Bai, X. / Fu, Y. / Yuan, H. / Ma, X. / Zhao, Z. / Zhang, J. / Wang, J. / Liu, Z. / Hua, J. / Zhang, Q. / Lei, D. / Lu, Z.
History
DepositionJan 1, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 21, 2026Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Capsid protein VP1
B: Capsid protein VP2
C: Capsid protein VP3
D: Capsid protein VP4
H: PAS12 Fv Heavy chain
L: PAS12 Fv Light chain


Theoretical massNumber of molelcules
Total (without water)107,3376
Polymers107,3376
Non-polymers00
Water00
1
A: Capsid protein VP1
B: Capsid protein VP2
C: Capsid protein VP3
D: Capsid protein VP4
H: PAS12 Fv Heavy chain
L: PAS12 Fv Light chain
x 60


Theoretical massNumber of molelcules
Total (without water)6,440,211360
Polymers6,440,211360
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
2


  • Idetical with deposited unit
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Capsid protein VP1
B: Capsid protein VP2
C: Capsid protein VP3
D: Capsid protein VP4
H: PAS12 Fv Heavy chain
L: PAS12 Fv Light chain
x 5


  • icosahedral pentamer
  • 537 kDa, 30 polymers
Theoretical massNumber of molelcules
Total (without water)536,68430
Polymers536,68430
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: Capsid protein VP1
B: Capsid protein VP2
C: Capsid protein VP3
D: Capsid protein VP4
H: PAS12 Fv Heavy chain
L: PAS12 Fv Light chain
x 6


  • icosahedral 23 hexamer
  • 644 kDa, 36 polymers
Theoretical massNumber of molelcules
Total (without water)644,02136
Polymers644,02136
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
5


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))

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Components

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Capsid protein ... , 4 types, 4 molecules ABCD

#1: Protein Capsid protein VP1


Mass: 23471.611 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Foot-and-mouth disease virus Asia 1 / Cell line (production host): BHK-21 / Production host: Mesocricetus auratus (golden hamster) / References: UniProt: A2I7M2
#2: Protein Capsid protein VP2 / P1B / Virion protein 2


Mass: 24471.596 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Foot-and-mouth disease virus Asia 1 / Cell line (production host): BHK-21 / Production host: Mesocricetus auratus (golden hamster) / References: UniProt: A2I7M2
#3: Protein Capsid protein VP3 / P1C / Virion protein 3


Mass: 23845.801 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Foot-and-mouth disease virus Asia 1 / Cell line (production host): BHK-21 / Production host: Mesocricetus auratus (golden hamster) / References: UniProt: A2I7M2
#4: Protein Capsid protein VP4 / P1A / Virion protein 4


Mass: 8789.116 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Foot-and-mouth disease virus Asia 1 / Cell line (production host): BHK-21 / Production host: Mesocricetus auratus (golden hamster) / References: UniProt: A2I7M2

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Antibody , 2 types, 2 molecules HL

#5: Antibody PAS12 Fv Heavy chain


Mass: 13321.924 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Production host: Homo sapiens (human)
#6: Antibody PAS12 Fv Light chain


Mass: 13436.797 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Production host: Homo sapiens (human)

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Details

Has protein modificationY
Source detailsThe virus was obtained from naturally infected animals, and was propagated in BHK-21 cells for ...The virus was obtained from naturally infected animals, and was propagated in BHK-21 cells for research purposes. The virus harvested from the infected BHK-21 cells was used for the microscopy sample.

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1Complex of FMDV Asia1/JS/05 and porcine-derived neutralizing monoclonal antibody PAS12COMPLEXall0MULTIPLE SOURCES
2FMDV Asia1/JS/05VIRUS#1-#41RECOMBINANT
3porcine-derived neutralizing monoclonal antibody PAS12COMPLEX#5-#61RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
22Foot-and-mouth disease virus Asia 1110195
33Sus scrofa (pig)9823
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-IDCell
12Mesocricetus auratus (golden hamster)10036BHK-21
23Homo sapiens (human)9606
Details of virusEmpty: NO / Enveloped: NO / Type: VIRION
Buffer solutionpH: 7.2
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 30 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.20.1_4487 / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 2.14 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 17484 / Symmetry type: POINT
RefinementHighest resolution: 2.14 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0037003
ELECTRON MICROSCOPYf_angle_d0.5329542
ELECTRON MICROSCOPYf_dihedral_angle_d11.8072498
ELECTRON MICROSCOPYf_chiral_restr0.0421071
ELECTRON MICROSCOPYf_plane_restr0.0051232

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