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- EMDB-6424: The U4 antibody epitope on human papillomavirus 16 identified by ... -

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Basic information

Entry
Database: EMDB / ID: EMD-6424
TitleThe U4 antibody epitope on human papillomavirus 16 identified by cryo-EM
Map dataQuasi-HPV16 complexed with H16.U4
Sample
  • Sample: Quasi-HPV16 complexed with H16.U4 Fab
  • Virus: Human papillomavirus type 16
  • Protein or peptide: H16.U4 antibody
KeywordsHPV16 / antibody / cryoEM / U4 / neutralization / Fab
Function / homology
Function and homology information


T=7 icosahedral viral capsid / endocytosis involved in viral entry into host cell / virion attachment to host cell / host cell nucleus / 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 speciesMus musculus (house mouse) / Human papillomavirus type 16
Methodsingle particle reconstruction / cryo EM / Resolution: 12.0 Å
AuthorsGuan J / Bywaters SM / Brendle SA / Lee H / Ashley RE / Christensen ND / Hafenstein S
CitationJournal: J.VIROL. / Year: 2015
Title: The U4 antibody epitope on human papillomavirus 16 identified by cryo-EM
Authors: Guan J / Bywaters SM / Brendle SA / Lee H / Ashley RE / Christensen ND / Hafenstein S
History
DepositionAug 11, 2015-
Header (metadata) releaseSep 23, 2015-
Map releaseOct 7, 2015-
UpdateNov 25, 2015-
Current statusNov 25, 2015Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 1
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-3jba
  • Surface level: 1
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-3jba
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol

Downloads & links

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Map

FileDownload / File: emd_6424.map.gz / Format: CCP4 / Size: 210.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationQuasi-HPV16 complexed with H16.U4
Voxel sizeX=Y=Z: 2.33 Å
Density
Contour LevelBy AUTHOR: 1.0 / Movie #1: 1
Minimum - Maximum-2.1312201 - 6.05018234
Average (Standard dev.)0.0 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-192-192-192
Dimensions384384384
Spacing384384384
CellA=B=C: 894.72 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.332.332.33
M x/y/z384384384
origin x/y/z0.0000.0000.000
length x/y/z894.720894.720894.720
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-192-192-192
NC/NR/NS384384384
D min/max/mean-2.1316.0500.000

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Supplemental data

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Sample components

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Entire : Quasi-HPV16 complexed with H16.U4 Fab

EntireName: Quasi-HPV16 complexed with H16.U4 Fab
Components
  • Sample: Quasi-HPV16 complexed with H16.U4 Fab
  • Virus: Human papillomavirus type 16
  • Protein or peptide: H16.U4 antibody

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Supramolecule #1000: Quasi-HPV16 complexed with H16.U4 Fab

SupramoleculeName: Quasi-HPV16 complexed with H16.U4 Fab / type: sample / ID: 1000 / Number unique components: 2
Molecular weightTheoretical: 32.8 MDa

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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 / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: SEROTYPE / Virus enveloped: No / Virus empty: No / Sci species serotype: HPV16
Host (natural)Organism: Homo sapiens (human) / synonym: VERTEBRATES
Host systemOrganism: Homo sapiens (human) / Recombinant strain: HEK293TT / Recombinant plasmid: SV40
Molecular weightTheoretical: 32.8 MDa
Virus shellShell ID: 1 / Name: L1 L2 / Diameter: 590 Å / T number (triangulation number): 7

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Macromolecule #1: H16.U4 antibody

MacromoleculeName: H16.U4 antibody / type: protein_or_peptide / ID: 1 / Number of copies: 60 / Recombinant expression: No / Database: NCBI
Source (natural)Organism: Mus musculus (house mouse) / synonym: mouse

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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

MicroscopeJEOL 2100
TemperatureAverage: 95 K
DateJul 22, 2014
Image recordingCategory: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Number real images: 151 / Average electron dose: 15 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: LAB6
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus max: 5.43 µm / Nominal defocus min: 1.6 µm / Nominal magnification: 50000
Sample stageSpecimen holder model: GATAN LIQUID NITROGEN

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Image processing

DetailsThe particles were selected using semi-automatic program e2boxer.py (EMAN2).
CTF correctionDetails: each particle
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 12.0 Å / Resolution method: OTHER / Software - Name: auto3dem, RELION, EMAN2 / Number images used: 5806

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Atomic model buiding 1

Initial modelPDB ID:

3j6r


Chain - #0 - Chain ID: A / Chain - #1 - Chain ID: B / Chain - #2 - Chain ID: C / Chain - #3 - Chain ID: D / Chain - #4 - Chain ID: E / Chain - #5 - Chain ID: F
SoftwareName: Situs, Chimera
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-3jba:
The U4 antibody epitope on human papillomavirus 16 identified by cryo-EM

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