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- PDB-7dst: FMDV capsid in complex with M170 Nab -

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Basic information

Entry
Database: PDB / ID: 7dst
TitleFMDV capsid in complex with M170 Nab
Components
  • M170 Nab
  • VP1 of O type FMDV capsid
  • VP2 of O type FMDV capsid
  • VP3 of O type FMDV capsid
  • VP4 of O type FMDV capsid
KeywordsVIRUS / FMDV capsid in complex with M170 Nab
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesLama glama (llama)
Foot-and-mouth disease virus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsDong, H. / Liu, P.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)No. 31941011, 12034006, 31672592, 31873023, 31811540395, 31772739, 315725153 and 1811540395 China
CitationJournal: Protein Cell / Year: 2022
Title: Structural and molecular basis for foot-and-mouth disease virus neutralization by two potent protective antibodies.
Authors: Hu Dong / Pan Liu / Manyuan Bai / Kang Wang / Rui Feng / Dandan Zhu / Yao Sun / Suyu Mu / Haozhou Li / Michiel Harmsen / Shiqi Sun / Xiangxi Wang / Huichen Guo /
History
DepositionJan 2, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 10, 2021Provider: repository / Type: Initial release
Revision 1.1May 25, 2022Group: Database references / Derived calculations / Category: citation / database_2 / pdbx_struct_oper_list
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type
Revision 1.2Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update

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Structure visualization

Movie
  • Biological unit as complete icosahedral assembly
  • Imaged by Jmol
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  • Biological unit as icosahedral pentamer
  • Imaged by Jmol
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  • Biological unit as icosahedral 23 hexamer
  • Imaged by Jmol
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  • Deposited structure unit
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  • Simplified surface model + fitted atomic model
  • EMDB-30845
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  • Superimposition on EM map
  • EMDB-30845
  • Imaged by UCSF Chimera
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Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: VP1 of O type FMDV capsid
B: VP2 of O type FMDV capsid
C: VP3 of O type FMDV capsid
D: VP4 of O type FMDV capsid
E: M170 Nab


Theoretical massNumber of molelcules
Total (without water)90,5975
Polymers90,5975
Non-polymers00
Water00
1
A: VP1 of O type FMDV capsid
B: VP2 of O type FMDV capsid
C: VP3 of O type FMDV capsid
D: VP4 of O type FMDV capsid
E: M170 Nab
x 60


Theoretical massNumber of molelcules
Total (without water)5,435,848300
Polymers5,435,848300
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: VP1 of O type FMDV capsid
B: VP2 of O type FMDV capsid
C: VP3 of O type FMDV capsid
D: VP4 of O type FMDV capsid
E: M170 Nab
x 5


  • icosahedral pentamer
  • 453 kDa, 25 polymers
Theoretical massNumber of molelcules
Total (without water)452,98725
Polymers452,98725
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: VP1 of O type FMDV capsid
B: VP2 of O type FMDV capsid
C: VP3 of O type FMDV capsid
D: VP4 of O type FMDV capsid
E: M170 Nab
x 6


  • icosahedral 23 hexamer
  • 544 kDa, 30 polymers
Theoretical massNumber of molelcules
Total (without water)543,58530
Polymers543,58530
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

#1: Protein VP1 of O type FMDV capsid


Mass: 22849.139 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Foot-and-mouth disease virus
#2: Protein VP2 of O type FMDV capsid


Mass: 23091.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Foot-and-mouth disease virus
#3: Protein VP3 of O type FMDV capsid


Mass: 23754.705 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Foot-and-mouth disease virus
#4: Protein VP4 of O type FMDV capsid


Mass: 7963.328 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Foot-and-mouth disease virus
#5: Antibody M170 Nab


Mass: 12939.211 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Lama glama (llama)
Has protein modificationY

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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
1FMDV in complex with M170COMPLEXall0NATURAL
2FMDVCOMPLEX#1-#41NATURAL
3M170COMPLEX#51RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Foot-and-mouth disease virus12110
32Lama glama (llama)9844
Source (recombinant)Organism: Lama glama (llama)
Buffer solutionpH: 7.4
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: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: DARK FIELD
Image recordingElectron dose: 30 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 3692 / Symmetry type: POINT

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