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- PDB-8hbi: FMDV (A/TUR/14/98) in complex with M688F -

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Basic information

Entry
Database: PDB / ID: 8hbi
TitleFMDV (A/TUR/14/98) in complex with M688F
Components
  • M688F nab
  • VP1 of capsid protein
  • VP2 of capsid protein
  • VP3 of capsid protein
  • VP4 of capsid protein
KeywordsVIRUS / FMDV / antibody
Function / homology
Function and homology information


icosahedral viral capsid / host cell cytoplasm / symbiont entry into host cell / virion attachment to host cell / structural molecule activity / cytoplasm
Similarity search - Function
Foot-and-mouth disease virus VP1 coat / Capsid protein VP4, Picornavirus / Viral protein VP4 subunit / Capsid protein VP4 superfamily, Picornavirus / Picornavirus capsid / picornavirus capsid protein / Picornavirus/Calicivirus coat protein / Viral coat protein subunit
Similarity search - Domain/homology
Biological speciesLama glama (llama)
Foot-and-mouth disease virus A
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsLi, H.Z. / Dong, H. / Liu, P.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Structural and in vivo studies of neutralizing antibody topographical classifications reveal mechanisms underlying differences in immunogenicity and antigenicity between 146S and 12S of foot- ...Title: Structural and in vivo studies of neutralizing antibody topographical classifications reveal mechanisms underlying differences in immunogenicity and antigenicity between 146S and 12S of foot-and-mouth disease virus
Authors: Li, H.Z. / Dong, H. / Liu, P.
History
DepositionOct 28, 2022Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jan 3, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: M688F nab
A: VP1 of capsid protein
B: VP2 of capsid protein
C: VP3 of capsid protein
D: VP4 of capsid protein


Theoretical massNumber of molelcules
Total (without water)94,6115
Polymers94,6115
Non-polymers00
Water00
1
E: M688F nab
A: VP1 of capsid protein
B: VP2 of capsid protein
C: VP3 of capsid protein
D: VP4 of capsid protein
x 60


Theoretical massNumber of molelcules
Total (without water)5,676,634300
Polymers5,676,634300
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
E: M688F nab
A: VP1 of capsid protein
B: VP2 of capsid protein
C: VP3 of capsid protein
D: VP4 of capsid protein
x 5


  • icosahedral pentamer
  • 473 kDa, 25 polymers
Theoretical massNumber of molelcules
Total (without water)473,05325
Polymers473,05325
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
E: M688F nab
A: VP1 of capsid protein
B: VP2 of capsid protein
C: VP3 of capsid protein
D: VP4 of capsid protein
x 6


  • icosahedral 23 hexamer
  • 568 kDa, 30 polymers
Theoretical massNumber of molelcules
Total (without water)567,66330
Polymers567,66330
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: Antibody M688F nab


Mass: 13861.437 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama)
Production host: Yeast centromeric expression vector p416GPD (others)
#2: Protein VP1 of capsid protein


Mass: 23111.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Foot-and-mouth disease virus A / References: UniProt: A0A7D5BJ70
#3: Protein VP2 of capsid protein


Mass: 24575.779 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Foot-and-mouth disease virus A / References: UniProt: A0A7D5BJ70
#4: Protein VP3 of capsid protein


Mass: 24284.121 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Foot-and-mouth disease virus A / References: UniProt: A0A7D5BJ70
#5: Protein VP4 of capsid protein


Mass: 8778.129 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Foot-and-mouth disease virus A / References: UniProt: A0A7D5BJ70

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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

ComponentName: FMDV capsid protein in complex with M688F nab / Type: COMPLEX / Entity ID: all / Source: MULTIPLE SOURCES
Source (natural)Organism: Foot-and-mouth disease virus A
Buffer solutionpH: 7
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: DIFFRACTION / Nominal defocus max: 2800 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 30 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 25824 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0076317
ELECTRON MICROSCOPYf_angle_d0.6418604
ELECTRON MICROSCOPYf_dihedral_angle_d16.346866
ELECTRON MICROSCOPYf_chiral_restr0.047954
ELECTRON MICROSCOPYf_plane_restr0.0051114

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