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- PDB-7dss: Complex of FMDV and M8 Nab -

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Basic information

Entry
Database: PDB / ID: 7dss
TitleComplex of FMDV and M8 Nab
Components
  • M8 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 / Nab / complex / FMDV
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesVicugna pacos (alpaca)
Foot-and-mouth disease virus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.9 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 31, 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 1.2Oct 23, 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
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  • Biological unit as icosahedral pentamer
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  • Biological unit as icosahedral 23 hexamer
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  • Deposited structure unit
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  • Simplified surface model + fitted atomic model
  • EMDB-30843
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  • Superimposition on EM map
  • EMDB-30843
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Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: M8 Nab
1: VP1 of O type FMDV capsid
2: VP2 of O-type FMDV capsid
3: VP3 of O-type FMDV capsid
4: VP4 of O-type FMDV capsid


Theoretical massNumber of molelcules
Total (without water)91,5415
Polymers91,5415
Non-polymers00
Water00
1
A: M8 Nab
1: VP1 of O type FMDV capsid
2: VP2 of O-type FMDV capsid
3: VP3 of O-type FMDV capsid
4: VP4 of O-type FMDV capsid
x 60


Theoretical massNumber of molelcules
Total (without water)5,492,443300
Polymers5,492,443300
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: M8 Nab
1: VP1 of O type FMDV capsid
2: VP2 of O-type FMDV capsid
3: VP3 of O-type FMDV capsid
4: VP4 of O-type FMDV capsid
x 5


  • icosahedral pentamer
  • 458 kDa, 25 polymers
Theoretical massNumber of molelcules
Total (without water)457,70425
Polymers457,70425
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: M8 Nab
1: VP1 of O type FMDV capsid
2: VP2 of O-type FMDV capsid
3: VP3 of O-type FMDV capsid
4: VP4 of O-type FMDV capsid
x 6


  • icosahedral 23 hexamer
  • 549 kDa, 30 polymers
Theoretical massNumber of molelcules
Total (without water)549,24430
Polymers549,24430
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 M8 Nab


Mass: 13932.477 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vicugna pacos (alpaca) / Production host: Lama glama (llama)
#2: 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
#3: 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
#4: Protein VP3 of O-type FMDV capsid


Mass: 23704.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Foot-and-mouth disease virus
#5: 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
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 M8 NabCOMPLEXall0MULTIPLE SOURCES
2M8 NabCOMPLEX#11RECOMBINANT
3FMDVCOMPLEX#2-#51NATURAL
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Vicugna pacos (alpaca)30538
32Foot-and-mouth disease virus12110
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: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 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

SoftwareName: PHENIX / Version: 1.17.1_3660: / Classification: refinement
CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 3000 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0076283
ELECTRON MICROSCOPYf_angle_d0.7198570
ELECTRON MICROSCOPYf_dihedral_angle_d13.436861
ELECTRON MICROSCOPYf_chiral_restr0.047968
ELECTRON MICROSCOPYf_plane_restr0.0051110

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