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- EMDB-6620: Electron cryo-microscopy of Human Papillomavirus -

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Basic information

Entry
Database: EMDB / ID: EMD-6620
TitleElectron cryo-microscopy of Human Papillomavirus
Map dataReconstruction of HPV16
Sample
  • Sample: Human papillomavirus
  • Virus: Human papillomavirus 16
KeywordsDED high resolution map / L1 plus L2 / quasivirus
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
Similarity search - Component
Biological speciesHuman papillomavirus 16
Methodsingle particle reconstruction / cryo EM / Resolution: 4.3 Å
AuthorsGuan J / Bywaters SM / Brendle SA / Ashley RE / Makhov AM / Conway JF / Christensen ND / Hafenstein S
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
DepositionMar 15, 2016-
Header (metadata) releaseMay 11, 2016-
Map releaseJan 25, 2017-
UpdateMar 29, 2017-
Current statusMar 29, 2017Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.5
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 1.5
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5kep
  • Surface level: 3
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-5kep
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

400_6620.gif

Downloads & links

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Map

FileDownload / File: emd_6620.map.gz / Format: CCP4 / Size: 1.1 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of HPV16
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.15 Å/pix.
x 668 pix.
= 766.196 Å		1.15 Å/pix.
x 668 pix.
= 766.196 Å		1.15 Å/pix.
x 668 pix.
= 766.196 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.147 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.0 / Movie #1: 1.5
Minimum - Maximum-9.32545376 - 17.7339077
Average (Standard dev.)0.0 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-334-334-334
Dimensions668668668
Spacing668668668
CellA=B=C: 766.196 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.1471.1471.147
M x/y/z668668668
origin x/y/z0.0000.0000.000
length x/y/z766.196766.196766.196
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-334-334-334
NC/NR/NS668668668
D min/max/mean-9.32517.734-0.000

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Supplemental data

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Sample components

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Entire : Human papillomavirus

EntireName: Human papillomavirus
Components
  • Sample: Human papillomavirus
  • Virus: Human papillomavirus 16

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Supramolecule #1000: Human papillomavirus

SupramoleculeName: Human papillomavirus / type: sample / ID: 1000 / Number unique components: 1
Molecular weightTheoretical: 29.8 MDa

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Supramolecule #1: Human papillomavirus 16

SupramoleculeName: Human papillomavirus 16 / type: virus / ID: 1 / Name.synonym: HPV16 / NCBI-ID: 337041 / Sci species name: Human papillomavirus 16 / Database: NCBI / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: SEROTYPE / Virus enveloped: No / Virus empty: No / Syn species name: HPV16 / Sci species serotype: HPV16
Host (natural)Organism: Homo sapiens (human) / synonym: VERTEBRATES
Molecular weightTheoretical: 29.8 MDa
Virus shellShell ID: 1 / Name: L1 plus L2 / Diameter: 580 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

Concentration1.2 mg/mL
BufferpH: 7.4 / Details: 1 M NaCl, 200 mM Tris
GridDetails: glow-discharged holey carbon support grid
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 102 K / Instrument: GATAN CRYOPLUNGE 3

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Electron microscopy

MicroscopeFEI POLARA 300
DateFeb 16, 2015
Image recordingCategory: CCD / Film or detector model: FEI FALCON II (4k x 4k) / Number real images: 9137
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal magnification: 93000
Sample stageSpecimen holder model: GATAN LIQUID NITROGEN
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

DetailsThe particles were selected using semi-automatic program e2boxer.py.
CTF correctionDetails: ctffind for whole image
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 4.3 Å / Resolution method: OTHER / Software - Name: auto3dem / Number images used: 57556
Final two d classificationNumber classes: 10

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Atomic model buiding 1

Initial modelPDB ID:

3oae
PDB Unreleased entry

SoftwareName: Phenix, Situs, NAMD
RefinementSpace: REAL
Output model

PDB-5kep:
High resolution cryo-EM maps of Human Papillomavirus 16 reveal L2 location and heparin-induced conformational changes

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Atomic model buiding 2

Initial modelPDB ID:

3j6r

SoftwareName: Phenix, Situs, NAMD
RefinementSpace: REAL
Output model

PDB-5kep:
High resolution cryo-EM maps of Human Papillomavirus 16 reveal L2 location and heparin-induced conformational changes

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