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- PDB-3iyo: Cryo-EM model of virion-sized HEV virion-sized capsid -

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Basic information

Entry
Database: PDB / ID: 3iyo
TitleCryo-EM model of virion-sized HEV virion-sized capsid
ComponentsCapsid proteinCapsid
KeywordsVIRUS / Amino Acid Sequence / Capsid / Capsid Proteins / Cryoelectron Microscopy / Dimerization / Image Processing / Computer-Assisted / Molecular Sequence Data / hepatitis E virus / Protein Conformation / Protein Folding / Protein Structure / Recombinant viral capsid / Virus Assembly / icosahedral virus
Function / homology
Function and homology information


viral capsid / host cell surface / host cell cytoplasm / structural molecule activity / RNA binding / cytoplasm
Similarity search - Function
Hepatitis E virus structural protein 2 / Structural protein 2 nucleoplasmin-like domain / Viral coat protein subunit
Similarity search - Domain/homology
Biological speciesHepatitis E virus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 10.5 Å
AuthorsXing, L. / Mayazaki, N. / Li, T.C. / Simons, M.N. / Wall, J.S. / Moore, M. / Wang, C.Y. / Takeda, N. / Wakita, T. / Miyamura, T. / Cheng, R.H.
CitationJournal: J Biol Chem / Year: 2010
Title: Structure of hepatitis E virion-sized particle reveals an RNA-dependent viral assembly pathway.
Authors: Li Xing / Tian-Cheng Li / Naoyuki Mayazaki / Martha N Simon / Joseph S Wall / Mary Moore / Che-Yen Wang / Naokazu Takeda / Takaji Wakita / Tatsuo Miyamura / R Holland Cheng /
Abstract: Hepatitis E virus (HEV) induces acute hepatitis in humans with a high fatality rate in pregnant women. There is a need for anti-HEV research to understand the assembly process of HEV native capsid. ...Hepatitis E virus (HEV) induces acute hepatitis in humans with a high fatality rate in pregnant women. There is a need for anti-HEV research to understand the assembly process of HEV native capsid. Here, we produced a large virion-sized and a small T=1 capsid by expressing the HEV capsid protein in insect cells with and without the N-terminal 111 residues, respectively, for comparative structural analysis. The virion-sized capsid demonstrates a T=3 icosahedral lattice and contains RNA fragment in contrast to the RNA-free T=1 capsid. However, both capsids shared common decameric organization. The in vitro assembly further demonstrated that HEV capsid protein had the intrinsic ability to form decameric intermediate. Our data suggest that RNA binding is the extrinsic factor essential for the assembly of HEV native capsids.
History
DepositionMar 19, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 18, 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
Revision 1.3Feb 21, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type

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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
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  • Superimposition on EM map
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Structure viewerMolecule:
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Assembly

Deposited unit
A: Capsid protein
B: Capsid protein
D: Capsid protein


Theoretical massNumber of molelcules
Total (without water)213,0953
Polymers213,0953
Non-polymers00
Water0
1
A: Capsid protein
B: Capsid protein
D: Capsid protein
x 60


Theoretical massNumber of molelcules
Total (without water)12,785,718180
Polymers12,785,718180
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
B: Capsid protein
D: Capsid protein
x 5


  • icosahedral pentamer
  • 1.07 MDa, 15 polymers
Theoretical massNumber of molelcules
Total (without water)1,065,47615
Polymers1,065,47615
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: Capsid protein
B: Capsid protein
D: Capsid protein
x 6


  • icosahedral 23 hexamer
  • 1.28 MDa, 18 polymers
Theoretical massNumber of molelcules
Total (without water)1,278,57218
Polymers1,278,57218
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 Capsid protein / Capsid / Coordinate model: Cα atoms only


Mass: 71031.766 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Hepatitis E virus / References: UniProt: Q1AHV0

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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: Hepatitis E capsid / Type: VIRUS
Molecular weight
IDEntity assembly-IDValue (°)Experimental value
1111.8 MDaYES
2112.2 MDaNO
Details of virusEmpty: NO / Enveloped: NO / Host category: VERTEBRATES / Isolate: STRAIN / Type: VIRUS-LIKE PARTICLE
Natural hostOrganism: Homo sapiens
Buffer solutionName: MES-K buffer / pH: 6.2 / Details: 20mM MES-K
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: 20mM MES-K
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Temp: 93 K

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Electron microscopy imaging

MicroscopyModel: JEOL 2100F
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 50000 X / Cs: 2 mm / Camera length: 0 mm
Specimen holderSpecimen holder model: GATAN LIQUID NITROGEN / Specimen holder type: single-tilt / Tilt angle max: 0 ° / Tilt angle min: 0 °
Image recordingElectron dose: 10 e/Å2 / Film or detector model: TVIPS TEMCAM-F415 (4k x 4k)
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

EM software
IDNameCategory
1Situsmodel fitting
2P3DR3D reconstruction
CTF correctionDetails: each micrograph
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionMethod: Polar Fourier Transform (PFT) / Resolution: 10.5 Å / Resolution method: FSC 0.5 CUT-OFF / Num. of particles: 4348 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL / Target criteria: cross-correlation
Details: REFINEMENT PROTOCOL--Rigid Body DETAILS--Monomer C were divided into Shell and Spike domains and separately fitted by manual docking using program O and followed by Situs
Atomic model buildingPDB-ID: 2ZZQ

2zzq


Pdb chain-ID: A / Accession code: 2ZZQ / Source name: PDB / Type: experimental model
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms1397 0 0 0 1397

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