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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 / 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 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-electron Microscopy.
Authors: Jian Guan / Stephanie M Bywaters / Sarah A Brendle / Hyunwook Lee / Robert E Ashley / Neil D Christensen / Susan Hafenstein /
Abstract: The human papillomavirus (HPV) major structural protein L1 composes capsomers that are linked together through interactions mediated by the L1 C terminus to constitute a T=7 icosahedral capsid. H16. ...The human papillomavirus (HPV) major structural protein L1 composes capsomers that are linked together through interactions mediated by the L1 C terminus to constitute a T=7 icosahedral capsid. H16.U4 is a type-specific monoclonal antibody recognizing a conformation-dependent neutralizing epitope of HPV thought to include the L1 protein C terminus. The structure of human papillomavirus 16 (HPV16) complexed with H16.U4 fragments of antibody (Fab) was solved by cryo-electron microscopy (cryo-EM) image reconstruction. Atomic structures of virus and Fab were fitted into the corresponding cryo-EM densities to identify the antigenic epitope. The antibody footprint mapped predominately to the L1 C-terminal arm with an additional contact point on the side of the capsomer. This footprint describes an epitope that is presented capsid-wide. However, although the H16.U4 epitope suggests the presence of 360 potential binding sites exposed in the capsid valley between each capsomer, H16.U4 Fab bound only to epitopes located around the icosahedral five-fold vertex of the capsid. Thus, the binding characteristics of H16.U4 defined in this study showed a distinctive selectivity for local conformation-dependent interactions with specific L1 invading arms between five-fold related capsomers.
IMPORTANCE: Human papillomavirus 16 (HPV16) is the most prevalent oncogenic genotype in HPV-associated anogenital and oral cancers. Here we use cryo-EM reconstruction techniques to solve the ...IMPORTANCE: Human papillomavirus 16 (HPV16) is the most prevalent oncogenic genotype in HPV-associated anogenital and oral cancers. Here we use cryo-EM reconstruction techniques to solve the structures of the HPV16 capsid complexes using H16.U4 fragment of antibody (Fab). Different from most other antibodies directed against surface loops, H16.U4 monoclonal antibody is unique in targeting the C-terminal arm of the L1 protein. This monoclonal antibody (MAb) is used throughout the HPV research community in HPV serological and vaccine development and to define mechanisms of HPV uptake. The unique binding mode of H16.U4 defined here shows important conformation-dependent interactions within the HPV16 capsid. By targeting an important structural and conformational epitope, H16.U4 may identify subtle conformational changes in different maturation stages of the HPV capsid and provide a key probe to analyze the mechanisms of HPV uptake during the early stages of virus infection. Our analyses precisely define important conformational epitopes on HPV16 capsids that are key targets for successful HPV prophylactic vaccines.
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
Supplemental images

400_6424.gif

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
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.33 Å/pix.
x 384 pix.
= 894.72 Å		2.33 Å/pix.
x 384 pix.
= 894.72 Å		2.33 Å/pix.
x 384 pix.
= 894.72 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.33 Å
Density

Histogram

Histogram (log scale)
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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