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- PDB-3iyk: Bluetongue virus structure reveals a sialic acid binding domain, ... -

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Basic information

Entry
Database: PDB / ID: 3iyk
TitleBluetongue virus structure reveals a sialic acid binding domain, amphipathic helices and a central coiled coil in the outer capsid proteins
Components
  • VP2
  • VP5
KeywordsVIRUS / Icosahedral virus
Function / homology
Function and homology information


virion component => GO:0044423 / viral capsid / structural molecule activity
Similarity search - Function
Outer capsid protein VP2, Orbivirus / Orbivirus outer capsid protein VP2 / Outer capsid protein VP5, Orbivirus / Orbivirus outer capsid protein VP5
Similarity search - Domain/homology
2-O-methyl-5-N-acetyl-alpha-D-neuraminic acid / Outer capsid protein VP2 / Outer capsid protein VP5
Similarity search - Component
Biological speciesBluetongue virus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 7 Å
AuthorsZhang, X. / Boyce, M. / Bhattacharya, B. / Zhang, X. / Schein, S. / Roy, P. / Zhou, Z.H.
CitationJournal: Proc Natl Acad Sci U S A / Year: 2010
Title: Bluetongue virus coat protein VP2 contains sialic acid-binding domains, and VP5 resembles enveloped virus fusion proteins.
Authors: Xing Zhang / Mark Boyce / Bishnupriya Bhattacharya / Xiaokang Zhang / Stan Schein / Polly Roy / Z Hong Zhou /
Abstract: Bluetongue virus (BTV) is transmitted by blood-feeding insects (Culicoides sp.) and causes hemorrhagic diseases in livestock. BTV is a nonenveloped, double-stranded RNA (dsRNA) virus with two capsids: ...Bluetongue virus (BTV) is transmitted by blood-feeding insects (Culicoides sp.) and causes hemorrhagic diseases in livestock. BTV is a nonenveloped, double-stranded RNA (dsRNA) virus with two capsids: a well-studied, stable core enclosing the dsRNA genome and a highly unstable, poorly studied coat responsible for host cell attachment and entry. Here, based on cryo-electron microscopy (cryoEM), we report a 7-A resolution structure of the infectious BTV virion, including the coat proteins. We show that unlike other dsRNA viruses, the VP2 attachment trimer has a triskelion shape composed of three tip domains branching from a central hub domain. We identify three putative sialic acid-binding pockets in the hub and present supporting biochemical data indicating sugar moiety binding is important for BTV infection. Despite being a nonenveloped virus, the putative VP5 membrane penetration trimer, located slightly inward of the VP2 attachment trimer, has a central coiled-coil alpha-helical bundle, similar to the fusion proteins of many enveloped viruses (e.g., HIV, herpesviruses, vesicular stomatitis virus, and influenza virus). Moreover, mapping of the amino acid sequence of VP5 to the secondary structural elements identified by cryoEM locates 15 amphipathic alpha-helical regions on the external surface of each VP5 trimer. The cryoEM density map also reveals few, weak interactions between the VP5 trimer and both the outer-coat VP2 trimer and the underlying core VP7 trimer, suggesting that the surface of VP5 could unfurl like an umbrella during penetration and shedding of the coat to release the transcriptionally active core particle.
History
DepositionJan 25, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 7, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 18, 2018Group: Data collection / Category: em_image_scans / em_software / Item: _em_software.image_processing_id / _em_software.name
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Feb 21, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _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

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Structure visualization

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  • 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-5147
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  • Superimposition on EM map
  • EMDB-5147
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Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: VP5
B: VP5
C: VP5
D: VP5
E: VP5
F: VP5
G: VP2
I: VP2
K: VP2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)566,89112
Polymers565,9229
Non-polymers9703
Water0
1
A: VP5
B: VP5
C: VP5
D: VP5
E: VP5
F: VP5
G: VP2
I: VP2
K: VP2
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)34,013,485720
Polymers33,955,291540
Non-polymers58,193180
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: VP5
B: VP5
C: VP5
D: VP5
E: VP5
F: VP5
G: VP2
I: VP2
K: VP2
hetero molecules
x 5


  • icosahedral pentamer
  • 2.83 MDa, 45 polymers
Theoretical massNumber of molelcules
Total (without water)2,834,45760
Polymers2,829,60845
Non-polymers4,84915
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: VP5
B: VP5
C: VP5
D: VP5
E: VP5
F: VP5
G: VP2
I: VP2
K: VP2
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 3.4 MDa, 54 polymers
Theoretical massNumber of molelcules
Total (without water)3,401,34872
Polymers3,395,52954
Non-polymers5,81918
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
VP5 / Coordinate model: Cα atoms only


Mass: 59070.371 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Bluetongue virus / References: UniProt: C5IWW1
#2: Protein VP2 / Coordinate model: Cα atoms only


Mass: 70499.766 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Bluetongue virus / References: UniProt: C5IWV8
#3: Sugar ChemComp-MNA / 2-O-methyl-5-N-acetyl-alpha-D-neuraminic acid / 2-O-METHYL-5-N-ACETYL-ALPHA-D- NEURAMINIC ACID


Type: D-saccharide / Mass: 323.296 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C12H21NO9
IdentifierTypeProgram
2-O-methyl-5-N-acetyl-a-D-neuraminic acidIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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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: Bluetongue VirusBluetongue disease / Type: VIRUS / Details: Icosahedron. The sample was monodisperse in ice
Details of virusEmpty: NO / Enveloped: NO / Host category: VERTEBRATES / Isolate: STRAIN / Type: VIRION
Natural hostOrganism: Bos taurus
Buffer solutionpH: 8 / Details: PBS
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: PBS
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Temp: 90 K

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F20
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 80000 X / Calibrated magnification: 79787 X / Cs: 2 mm / Camera length: 0 mm
Specimen holderSpecimen holder model: GATAN LIQUID NITROGEN / Specimen holder type: Gatan 626 / Temperature: 90 K / Tilt angle max: 0 ° / Tilt angle min: 0 °
Image recordingElectron dose: 25 e/Å2 / Film or detector model: GENERIC CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

EM software
IDNameCategory
1FREALIGN3D reconstruction
2IMIRS3D reconstruction
CTF correctionDetails: Each particle
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionMethod: projection matching / Resolution: 7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 3400 / Symmetry type: POINT
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms2265 0 66 0 2331

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