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- PDB-5kep: High resolution cryo-EM maps of Human Papillomavirus 16 reveal L2... -

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Basic information

Entry
Database: PDB / ID: 5kep
TitleHigh resolution cryo-EM maps of Human Papillomavirus 16 reveal L2 location and heparin-induced conformational changes
ComponentsMajor capsid protein L1
KeywordsVIRUS LIKE PARTICLE / HPV16 / L1 protein / asymmetric unit
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 16
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.3 Å
AuthorsGuan, J. / Bywaters, S.M. / Brendle, S.A. / Ashley, R.E. / Makhov, A.M. / Conway, J.F. / Christensen, N.D. / Hafenstein, S.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/Office of the DirectorS10OD019995 United States
National Institutes of Health/Office of the DirectorS10OD011986 United States
CitationJournal: Structure / Year: 2017
Title: Cryoelectron Microscopy Maps of Human Papillomavirus 16 Reveal L2 Densities and Heparin Binding Site.
Authors: Jian Guan / Stephanie M Bywaters / Sarah A Brendle / Robert E Ashley / Alexander M Makhov / James F Conway / Neil D Christensen / Susan Hafenstein /
Abstract: Human papillomavirus (HPV) is a significant health burden and leading cause of virus-induced cancers. The current commercial vaccines are genotype specific and provide little therapeutic benefit to ...Human papillomavirus (HPV) is a significant health burden and leading cause of virus-induced cancers. The current commercial vaccines are genotype specific and provide little therapeutic benefit to patients with existing HPV infections. Host entry mechanisms represent an excellent target for alternative therapeutics, but HPV receptor use, the details of cell attachment, and host entry are inadequately understood. Here we present near-atomic resolution structures of the HPV16 capsid and HPV16 in complex with heparin, both determined from cryoelectron micrographs collected with direct electron detection technology. The structures clarify details of capsid architecture for the first time, including variation in L1 major capsid protein conformation and putative location of L2 minor protein. Heparin binds specifically around the capsid icosahedral vertices and may recapitulate the earliest stage of infection, providing a framework for continuing biochemical, genetic, and biophysical studies.
History
DepositionJun 10, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 25, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 22, 2017Group: Database references
Revision 1.2Sep 13, 2017Group: Author supporting evidence / Data collection / Category: em_image_scans / pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 6, 2017Group: Database references / Category: pdbx_database_related / Item: _pdbx_database_related.db_id
Revision 1.4Apr 5, 2023Group: Database references / Derived calculations
Category: database_2 / pdbx_database_related / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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-6620
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  • Superimposition on EM map
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Structure viewerMolecule:
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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)323,6536
Polymers323,6536
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)19,419,159360
Polymers19,419,159360
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
  • 1.62 MDa, 30 polymers
Theoretical massNumber of molelcules
Total (without water)1,618,26330
Polymers1,618,26330
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
  • 1.94 MDa, 36 polymers
Theoretical massNumber of molelcules
Total (without water)1,941,91636
Polymers1,941,91636
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 / HPV16 L1 protein


Mass: 53942.109 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human papillomavirus type 16 / Gene: L1 / Production host: Simian virus 40 / References: UniProt: P03101

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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 16Papillomaviridae / Type: VIRUS / Entity ID: all
Details of virusEmpty: NO / Enveloped: NO / Isolate: SEROCOMPLEX / Type: VIRUS-LIKE PARTICLE
Buffer solutionpH: 7.4
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: Tecnai Polara / Image courtesy: FEI Company
MicroscopyModel: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingAverage exposure time: 1.23 sec. / Electron dose: 7 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)

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Processing

CTF correctionType: NONE
3D reconstructionResolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 57556 / Num. of class averages: 10 / Symmetry type: POINT

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