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- PDB-5jb1: Pseudo-atomic structure of Human Papillomavirus Type 59 L1 Virus-... -

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Basic information

Entry
Database: PDB / ID: 5jb1
TitlePseudo-atomic structure of Human Papillomavirus Type 59 L1 Virus-like Particle
ComponentsMajor capsid protein L1
KeywordsVIRUS / Capsid / T=7 icosahedral / Virus-like Particle
Function / homology
Function and homology information


T=7 icosahedral viral capsid / endocytosis involved in viral entry into host cell / host cell nucleus / structural molecule activity / virion attachment to host cell
Similarity search - Function
Major capsid L1 (late) protein, Papillomavirus / Major capsid L1 (late) superfamily, Papillomavirus / L1 (late) protein / Double-stranded DNA virus, group I, capsid
Similarity search - Domain/homology
Major capsid protein L1
Similarity search - Component
Biological speciesHuman papillomavirus type 59
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6 Å
AuthorsLi, Z.H. / Yan, X.D. / Yu, H. / Zheng, Q.B. / Gu, Y. / Li, S.W.
Funding support China, United States, 2items
OrganizationGrant numberCountry
National Natural Science Foundation81172885 China
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R37-GM33050 United States
CitationJournal: Structure / Year: 2016
Title: The C-Terminal Arm of the Human Papillomavirus Major Capsid Protein Is Immunogenic and Involved in Virus-Host Interaction.
Authors: Zhihai Li / Xiaodong Yan / Hai Yu / Daning Wang / Shuo Song / Yunbing Li / Maozhou He / Qiyang Hong / Qingbing Zheng / Qinjian Zhao / Ying Gu / Jun Zhang / Mandy E W Janssen / Giovanni ...Authors: Zhihai Li / Xiaodong Yan / Hai Yu / Daning Wang / Shuo Song / Yunbing Li / Maozhou He / Qiyang Hong / Qingbing Zheng / Qinjian Zhao / Ying Gu / Jun Zhang / Mandy E W Janssen / Giovanni Cardone / Norman H Olson / Timothy S Baker / Shaowei Li / Ningshao Xia /
Abstract: Cervical cancer is the second most prevalent malignant tumor among women worldwide. High-risk human papillomaviruses (HPVs) are believed to be the major causative pathogens of mucosal epithelial ...Cervical cancer is the second most prevalent malignant tumor among women worldwide. High-risk human papillomaviruses (HPVs) are believed to be the major causative pathogens of mucosal epithelial cancers including cervical cancer. The HPV capsid is made up of 360 copies of major (L1) and 72 copies of minor (L2) capsid proteins. To date, limited high-resolution structural information about the HPV capsid has hindered attempts to understand details concerning the mechanisms by which HPV assembles and infects cells. In this study, we have constructed a pseudo-atomic model of the HPV59 L1-only capsid and demonstrate that the C-terminal arm of L1 participates in virus-host interactions. Moreover, when conjugated to a scaffold protein, keyhole limpet hemocyanin (KLH), this arm is immunogenic in vivo. These results provide new insights that will help elucidate HPV biology, and hence pave a way for the design of next-generation HPV vaccines.
History
DepositionApr 13, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 18, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 6, 2016Group: Database references
Revision 1.2Oct 18, 2017Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Data processing / Database references
Category: citation / em_image_scans ...citation / em_image_scans / em_software / pdbx_audit_support
Item: _citation.journal_id_CSD / _em_software.name / _pdbx_audit_support.funding_organization
Revision 1.3Oct 23, 2019Group: Data collection / Other / Category: atom_sites / cell
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3] / _cell.Z_PDB
Revision 1.4Mar 23, 2022Group: Author supporting evidence / Database references / Derived calculations
Category: database_2 / pdbx_audit_support / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization / _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
  • EMDB-8147
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  • Superimposition on EM map
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Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Major capsid protein L1
B: Major capsid protein L1
C: Major capsid protein L1
D: Major capsid protein L1
E: Major capsid protein L1
F: Major capsid protein L1


Theoretical massNumber of molelcules
Total (without water)335,8716
Polymers335,8716
Non-polymers00
Water0
1
A: Major capsid protein L1
B: Major capsid protein L1
C: Major capsid protein L1
D: Major capsid protein L1
E: Major capsid protein L1
F: Major capsid protein L1
x 60


Theoretical massNumber of molelcules
Total (without water)20,152,230360
Polymers20,152,230360
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: Major capsid protein L1
B: Major capsid protein L1
C: Major capsid protein L1
D: Major capsid protein L1
E: Major capsid protein L1
F: Major capsid protein L1
x 5


  • icosahedral pentamer
  • 1.68 MDa, 30 polymers
Theoretical massNumber of molelcules
Total (without water)1,679,35330
Polymers1,679,35330
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: Major capsid protein L1
B: Major capsid protein L1
C: Major capsid protein L1
D: Major capsid protein L1
E: Major capsid protein L1
F: Major capsid protein L1
x 6


  • icosahedral 23 hexamer
  • 2.02 MDa, 36 polymers
Theoretical massNumber of molelcules
Total (without water)2,015,22336
Polymers2,015,22336
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
Major capsid protein L1


Mass: 55978.418 Da / Num. of mol.: 6 / Fragment: UNP RESIDUES 10-508
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human papillomavirus type 59 / Gene: ORF putative L1, L1 / Plasmid: pTO-T7 / Production host: Escherichia coli (E. coli) / Strain (production host): ER2566 / References: UniProt: Q81971

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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: Human papillomavirus type 59 / Type: VIRUS / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 19.8 MDa / Experimental value: NO
Source (natural)Organism: Human papillomavirus type 59
Source (recombinant)Organism: Escherichia coli (E. coli) / Strain: ER2566 / Plasmid: pTO-T7
Details of virusEmpty: YES / Enveloped: NO / Isolate: SEROTYPE / Type: VIRUS-LIKE PARTICLE
Natural hostOrganism: Homo sapiens
Virus shellName: Capsid / Diameter: 580 nm / Triangulation number (T number): 7
Buffer solutionpH: 7.3
Buffer component
IDConc.NameFormulaBuffer-ID
18 mg/mLsodium chlorideNaClSodium chloride1
20.2 mg/mLpotassium chlorideKCl1
31.42 mg/mLDisodium phosphateNa2HPO41
40.24 mg/mLMonopotassium phosphateKH2PO41
SpecimenConc.: 5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 281 K

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F30
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 25 e/Å2 / Film or detector model: FEI FALCON I (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1Auto3DEM4.05particle selection
4ctffind3CTF correction
7Chimera1.1model fitting
9VMDmodel refinement
13Auto3DEM4.053D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 6 Å / Resolution method: OTHER / Num. of particles: 3100
Details: The effective resolution was estimated based on the 0.5 criteria of FSC between the cryoEM structure and the final model derived from the density map.
Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL / Target criteria: Correlation coefficient

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