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- PDB-3j6r: Electron cryo-microscopy of Human Papillomavirus Type 16 capsid -

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Basic information

Entry
Database: PDB / ID: 3j6r
TitleElectron cryo-microscopy of Human Papillomavirus Type 16 capsid
ComponentsMajor capsid protein L1
KeywordsVIRUS / capsid protein
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 / Major capsid protein L1
Similarity search - Component
Biological speciesHuman papillomavirus type 16
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 9.1 Å
AuthorsCardone, G. / Moyer, A.L. / Cheng, N. / Thompson, C.D. / Dvoretzky, I. / Lowy, D.R. / Schiller, J.T. / Steven, A.C. / Buck, C.B. / Trus, B.L.
CitationJournal: mBio / Year: 2014
Title: Maturation of the human papillomavirus 16 capsid.
Authors: Giovanni Cardone / Adam L Moyer / Naiqian Cheng / Cynthia D Thompson / Israel Dvoretzky / Douglas R Lowy / John T Schiller / Alasdair C Steven / Christopher B Buck / Benes L Trus /
Abstract: Papillomaviruses are a family of nonenveloped DNA viruses that infect the skin or mucosa of their vertebrate hosts. The viral life cycle is closely tied to the differentiation of infected ...Papillomaviruses are a family of nonenveloped DNA viruses that infect the skin or mucosa of their vertebrate hosts. The viral life cycle is closely tied to the differentiation of infected keratinocytes. Papillomavirus virions are released into the environment through a process known as desquamation, in which keratinocytes lose structural integrity prior to being shed from the surface of the skin. During this process, virions are exposed to an increasingly oxidative environment, leading to their stabilization through the formation of disulfide cross-links between neighboring molecules of the major capsid protein, L1. We used time-lapse cryo-electron microscopy and image analysis to study the maturation of HPV16 capsids assembled in mammalian cells and exposed to an oxidizing environment after cell lysis. Initially, the virion is a loosely connected procapsid that, under in vitro conditions, condenses over several hours into the more familiar 60-nm-diameter papillomavirus capsid. In this process, the procapsid shrinks by ~5% in diameter, its pentameric capsomers change in structure (most markedly in the axial region), and the interaction surfaces between adjacent capsomers are consolidated. A C175S mutant that cannot achieve normal inter-L1 disulfide cross-links shows maturation-related shrinkage but does not achieve the fully condensed 60-nm form. Pseudoatomic modeling based on a 9-Å resolution reconstruction of fully mature capsids revealed C-terminal disulfide-stabilized "suspended bridges" that form intercapsomeric cross-links. The data suggest a model in which procapsids exist in a range of dynamic intermediates that can be locked into increasingly mature configurations by disulfide cross-linking, possibly through a Brownian ratchet mechanism. Importance: Human papillomaviruses (HPVs) cause nearly all cases of cervical cancer, a major fraction of cancers of the penis, vagina/vulva, anus, and tonsils, and genital and nongenital warts. HPV types associated with a high risk of cancer, such as HPV16, are generally transmitted via sexual contact. The nonenveloped virion of HPVs shows a high degree of stability, allowing the virus to persist in an infectious form in environmental fomites. In this study, we used cryo-electron microscopy to elucidate the structure of the HPV16 capsid at different stages of maturation. The fully mature capsid adopts a rigid, highly regular structure stabilized by intermolecular disulfide bonds. The availability of a pseudoatomic model of the fully mature HPV16 virion should help guide understanding of antibody responses elicited by HPV capsid-based vaccines.
History
DepositionMar 20, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 23, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 20, 2014Group: Database references
Revision 1.2Aug 27, 2014Group: Database references
Revision 1.3Jul 18, 2018Group: Data collection / Category: em_software / Item: _em_software.image_processing_id / _em_software.name
Revision 1.4Feb 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 / struct_ref_seq_dif
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 / _struct_ref_seq_dif.details

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Structure visualization

Movie
  • Biological unit as complete icosahedral assembly
  • Imaged by Jmol
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  • Biological unit as icosahedral pentamer
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  • Biological unit as icosahedral 23 hexamer
  • Imaged by Jmol
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  • Deposited structure unit
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  • Simplified surface model + fitted atomic model
  • EMDB-5932
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  • Superimposition on EM map
  • EMDB-5932
  • Imaged by UCSF Chimera
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Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)320,6746
Polymers320,6746
Non-polymers00
Water0
1
B: Major capsid protein L1
A: Major capsid protein L1
E: Major capsid protein L1
D: Major capsid protein L1
C: Major capsid protein L1
F: Major capsid protein L1
x 60


Theoretical massNumber of molelcules
Total (without water)19,240,422360
Polymers19,240,422360
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
B: Major capsid protein L1
A: Major capsid protein L1
E: Major capsid protein L1
D: Major capsid protein L1
C: Major capsid protein L1
F: Major capsid protein L1
x 5


  • icosahedral pentamer
  • 1.6 MDa, 30 polymers
Theoretical massNumber of molelcules
Total (without water)1,603,36930
Polymers1,603,36930
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
B: Major capsid protein L1
A: Major capsid protein L1
E: Major capsid protein L1
D: Major capsid protein L1
C: Major capsid protein L1
F: Major capsid protein L1
x 6


  • icosahedral 23 hexamer
  • 1.92 MDa, 36 polymers
Theoretical massNumber of molelcules
Total (without water)1,924,04236
Polymers1,924,04236
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 / L1 protein


Mass: 53445.617 Da / Num. of mol.: 6 / Fragment: UNP residues 35-512 / Source method: isolated from a natural source / Source: (natural) Human papillomavirus type 16 / References: UniProt: Q4VRM0, UniProt: P03101*PLUS

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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 Papilloma Virus type 16 capsid / Type: VIRUS
Details of virusEmpty: NO / Enveloped: NO / Host category: VERTEBRATES / Isolate: SEROTYPE / Type: VIRION
Natural hostOrganism: Homo sapiens
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: LEICA KF80 / Cryogen name: ETHANE / Details: Plunged into liquid ethane (LEICA KF80)

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Electron microscopy imaging

MicroscopyModel: FEI/PHILIPS CM200FEG / Date: Feb 2, 2010
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 120 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 38000 X / Nominal defocus max: 2175 nm / Nominal defocus min: 537 nm / Cs: 2 mm / Camera length: 0 mm
Specimen holderSpecimen holder model: GATAN LIQUID NITROGEN / Tilt angle max: 0 ° / Tilt angle min: 0 °
Image recordingFilm or detector model: KODAK SO-163 FILM
Image scansNum. digital images: 20
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

EM software
IDNameCategory
1MDFFmodel fitting
2NAMDmodel fitting
3PyMOLmodel fitting
4UCSF Chimeramodel fitting
5VMDmodel fitting
6Auto3DEM3D reconstruction
7Bsoft3D reconstruction
CTF correctionDetails: each micrograph
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionMethod: projection-matching, direct Fourier inversion / Resolution: 9.1 Å / Resolution method: FSC 0.33 CUT-OFF / Num. of particles: 5952 / Nominal pixel size: 1.41 Å / Actual pixel size: 1.41 Å / Details: (Single particle--Applied symmetry: I) / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Details: REFINEMENT PROTOCOL--flexible DETAILS--Rigid fitting of domain copies in asymmetric unit, followed by molecular dynamics-based flexible fitting, adding symmetry as constraint
Atomic model buildingPDB-ID: 1DZL

1dzl


Pdb chain-ID: A / Accession code: 1DZL / Source name: PDB / Type: experimental model
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms11466 0 0 0 11466

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