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- EMDB-5932: Electron cryo-microscopy of Human Papillomavirus Type 16 Capsid -

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Basic information

Entry
Database: EMDB / ID: EMD-5932
TitleElectron cryo-microscopy of Human Papillomavirus Type 16 Capsid
Map dataReconstruction of fully mature HPV16 L1/L2 capsid
Sample
  • Sample: Human Papilloma Virus type 16 capsid
  • Virus: Human papillomavirus type 16
Function / homology
Function and homology information


T=7 icosahedral viral capsid / endocytosis involved in viral entry into host cell / host cell nucleus / virion attachment to host cell / structural molecule activity
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
Methodsingle particle reconstruction / cryo EM / Resolution: 9.1 Å
AuthorsCardone G / Moyer AL / Cheng N / Thompson CD / Dvoretzky I / Lowy DR / Schiller JT / Steven AC / Buck CB / Trus BL
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, 2014-
Header (metadata) releaseJul 23, 2014-
Map releaseJul 23, 2014-
UpdateAug 27, 2014-
Current statusAug 27, 2014Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 800
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 800
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-3j6r
  • Surface level: 800
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-3j6r
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_5932.png

Downloads & links

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Map

FileDownload / File: emd_5932.map.gz / Format: CCP4 / Size: 248.5 MB / Type: IMAGE STORED AS SIGNED INTEGER (2 BYTES)
AnnotationReconstruction of fully mature HPV16 L1/L2 capsid
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.41 Å/pix.
x 511 pix.
= 720.51 Å		1.41 Å/pix.
x 511 pix.
= 720.51 Å		1.41 Å/pix.
x 511 pix.
= 720.51 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.41 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 800.0 / Movie #1: 800
Minimum - Maximum-2226.0 - 3846.0
Average (Standard dev.)22.884346010000002 (±535.922607419999963)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-255-255-255
Dimensions511511511
Spacing511511511
CellA=B=C: 720.51 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Integer*27
Å/pix. X/Y/Z1.411.411.41
M x/y/z511511511
origin x/y/z0.0000.0000.000
length x/y/z720.510720.510720.510
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ969680
MAP C/R/S123
start NC/NR/NS-255-255-255
NC/NR/NS511511511
D min/max/mean-2226.0003846.00022.884

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Supplemental data

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Sample components

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Entire : Human Papilloma Virus type 16 capsid

EntireName: Human Papilloma Virus type 16 capsid
Components
  • Sample: Human Papilloma Virus type 16 capsid
  • Virus: Human papillomavirus type 16

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Supramolecule #1000: Human Papilloma Virus type 16 capsid

SupramoleculeName: Human Papilloma Virus type 16 capsid / type: sample / ID: 1000 / Number unique components: 1

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Supramolecule #1: Human papillomavirus type 16

SupramoleculeName: Human papillomavirus type 16 / type: virus / ID: 1 / NCBI-ID: 333760 / Sci species name: Human papillomavirus type 16 / Database: NCBI / Virus type: VIRION / Virus isolate: SEROTYPE / Virus enveloped: No / Virus empty: No / Sci species serotype: 16
Host (natural)Organism: Homo sapiens (human) / synonym: VERTEBRATES
Virus shellShell ID: 1 / Diameter: 600 Å / T number (triangulation number): 7

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

VitrificationCryogen name: ETHANE / Instrument: LEICA KF80

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Electron microscopy

MicroscopeFEI/PHILIPS CM200FEG
DateFeb 2, 2010
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7 µm / Number real images: 20 / Bits/pixel: 8
Electron beamAcceleration voltage: 120 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus max: 2.175 µm / Nominal defocus min: 0.537 µm / Nominal magnification: 38000
Sample stageSpecimen holder model: GATAN LIQUID NITROGEN

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Image processing

CTF correctionDetails: each micrograph
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 9.1 Å / Resolution method: OTHER / Software - Name: Auto3DEM / Number images used: 5952

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Atomic model buiding 1

Initial modelPDB ID:

1dzl


Chain - Chain ID: A
SoftwareName: Chimera, PyMol, VMD, NAMD, MDFF, Bsoft
DetailsRigid fitting of domain copies into asymmetric unit, followed by molecular dynamics-based flexible fitting, adding symmetry as constraint
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

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

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