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- PDB-8hi2: Structure of EV71 VLP frozen at -183 degree embedded in crystalli... -

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Basic information

Entry
Database: PDB / ID: 8hi2
TitleStructure of EV71 VLP frozen at -183 degree embedded in crystalline ice
Components
  • (Genome polyprotein (Fragment)) x 2
  • Genome polyprotein
KeywordsVIRUS
Function / homology
Function and homology information


symbiont genome entry into host cell via pore formation in plasma membrane / viral capsid / host cell cytoplasm / symbiont-mediated suppression of host gene expression / symbiont entry into host cell / virion attachment to host cell / structural molecule activity
Similarity search - Function
Jelly Rolls - #20 / Picornavirus coat protein / Picornavirus coat protein VP4 / Picornavirus coat protein (VP4) / Picornavirus capsid / picornavirus capsid protein / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Genome polyprotein / Genome polyprotein / Genome polyprotein
Similarity search - Component
Biological speciesEnterovirus A71
MethodELECTRON MICROSCOPY / single particle reconstruction / Resolution: 3.2 Å
AuthorsShi, H. / Wu, C. / Zhang, X.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, China)32150010 China
CitationJournal: Structure / Year: 2023
Title: Addressing compressive deformation of proteins embedded in crystalline ice.
Authors: Huigang Shi / Chunling Wu / Xinzheng Zhang /
Abstract: For cryoelectron microscopy (cryo-EM), high cooling rates have been required for preparation of protein samples to vitrify the surrounding water and avoid formation of damaging crystalline ice. ...For cryoelectron microscopy (cryo-EM), high cooling rates have been required for preparation of protein samples to vitrify the surrounding water and avoid formation of damaging crystalline ice. Whether and how crystalline ice affects single-particle cryo-EM is still unclear. Here, single-particle cryo-EM was used to analyze three-dimensional structures of various proteins and viruses embedded in crystalline ice formed at various cooling rates. Low cooling rates led to shrinkage deformation and density distortions on samples having loose structures. Higher cooling rates reduced deformations. Deformation-free proteins in crystalline ice were obtained by modifying the freezing conditions, and reconstructions from these samples revealed a marked improvement over vitreous ice. This procedure also increased the efficiency of cryo-EM structure determinations and was essential for high-resolution reconstructions.
History
DepositionNov 18, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 1, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 15, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Jul 3, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.3Jul 2, 2025Group: Data collection / Structure summary / Category: em_software / pdbx_entry_details / Item: _em_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Genome polyprotein
B: Genome polyprotein (Fragment)
C: Genome polyprotein (Fragment)


Theoretical massNumber of molelcules
Total (without water)77,4613
Polymers77,4613
Non-polymers00
Water00
1
A: Genome polyprotein
B: Genome polyprotein (Fragment)
C: Genome polyprotein (Fragment)
x 60


Theoretical massNumber of molelcules
Total (without water)4,647,659180
Polymers4,647,659180
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: Genome polyprotein
B: Genome polyprotein (Fragment)
C: Genome polyprotein (Fragment)
x 5


  • icosahedral pentamer
  • 387 kDa, 15 polymers
Theoretical massNumber of molelcules
Total (without water)387,30515
Polymers387,30515
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: Genome polyprotein
B: Genome polyprotein (Fragment)
C: Genome polyprotein (Fragment)
x 6


  • icosahedral 23 hexamer
  • 465 kDa, 18 polymers
Theoretical massNumber of molelcules
Total (without water)464,76618
Polymers464,76618
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 Genome polyprotein


Mass: 25347.824 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterovirus A71
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A2D2CKV5
#2: Protein Genome polyprotein (Fragment)


Mass: 25987.320 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterovirus A71
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A1P8LK26
#3: Protein Genome polyprotein (Fragment)


Mass: 26125.834 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterovirus A71
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: D7RHC1
Has protein modificationN

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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: Enterovirus A71 / Type: VIRUS / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Enterovirus A71
Source (recombinant)Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Details of virusEmpty: YES / Enveloped: NO / Isolate: OTHER / Type: VIRUS-LIKE PARTICLE
Buffer solutionpH: 6.8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: NO

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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: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.20_4459: / Classification: refinement
EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 5219 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 34.97 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0044880
ELECTRON MICROSCOPYf_angle_d0.6046668
ELECTRON MICROSCOPYf_dihedral_angle_d4.357647
ELECTRON MICROSCOPYf_chiral_restr0.046734
ELECTRON MICROSCOPYf_plane_restr0.006853

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