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- EMDB-7136: High-Resolution Structure Analysis of Antibody V5 and U4 Conforma... -

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Basic information

Entry
Database: EMDB / ID: EMD-7136
TitleHigh-Resolution Structure Analysis of Antibody V5 and U4 Conformational Epitope on Human Papillomavirus 16
Map dataAntibody V5 and U4 Conformational Epitope on Human Papillomavirus 16
Sample
  • Complex: Human papillomavirus type 16 / Antibody complex
    • Complex: Antibody U4
      • Protein or peptide: U4 Heavy chain
      • Protein or peptide: U4 Light chain
    • Virus: Human papillomavirus type 16
      • Protein or peptide: Major capsid protein L1
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 speciesMus musculus (house mouse) / Mouse (mice) / Human papillomavirus type 16
Methodsingle particle reconstruction / cryo EM / Resolution: 4.7 Å
AuthorsGuan J / Bywaters SM / Brendle SA / Ashley RE / Makhov AM / Conway JF / Christenson ND / Hafenstein S
CitationJournal: Viruses / Year: 2017
Title: High-Resolution Structure Analysis of Antibody V5 and U4 Conformational Epitopes on Human Papillomavirus 16.
Authors: Jian Guan / Stephanie M Bywaters / Sarah A Brendle / Robert E Ashley / Alexander M Makhov / James F Conway / Neil D Christensen / Susan Hafenstein /
Abstract: Cancers attributable to human papillomavirus (HPV) place a huge burden on the health of both men and women. The current commercial vaccines are genotype specific and provide little therapeutic ...Cancers attributable to human papillomavirus (HPV) place a huge burden on the health of both men and women. The current commercial vaccines are genotype specific and provide little therapeutic benefit to patients with existing HPV infections. Identifying the conformational epitopes on the virus capsid supports the development of improved recombinant vaccines to maximize long-term protection against multiple types of HPV. Fragments of antibody (Fab) digested from the neutralizing monoclonal antibodies H16.V5 (V5) and H16.U4 (U4) were bound to HPV16 capsids and the structures of the two virus-Fab complexes were solved to near atomic resolution using cryo-electron microscopy. The structures reveal virus conformational changes, the Fab-binding mode to the capsid, the residues comprising the epitope and indicate a potential interaction of U4 with the minor structural protein, L2. Competition enzyme-linked immunosorbent assay (ELISA) showed V5 outcompetes U4 when added sequentially, demonstrating a steric interference even though the footprints do not overlap. Combined with our previously reported immunological and structural results, we propose that the virus may initiate host entry through an interaction between the icosahedral five-fold vertex of the capsid and receptors on the host cell. The highly detailed epitopes identified for the two antibodies provide a framework for continuing biochemical, genetic and biophysical studies.
History
Header (metadata) releaseJul 27, 2016-
DepositionDec 4, 2017-
Map releaseFeb 14, 2018-
UpdateOct 24, 2018-
Current statusOct 24, 2018Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2.1
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 2.1
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6bsp
  • Surface level: 2.1
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6bsp
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_7136.png

Downloads & links

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Map

FileDownload / File: emd_7136.map.gz / Format: CCP4 / Size: 1.2 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationAntibody V5 and U4 Conformational Epitope on Human Papillomavirus 16
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.15 Å/pix.
x 680 pix.
= 779.96 Å		1.15 Å/pix.
x 680 pix.
= 779.96 Å		1.15 Å/pix.
x 680 pix.
= 779.96 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: 2.1 / Movie #1: 2.1
Minimum - Maximum-8.246546 - 14.058398
Average (Standard dev.)0.00000000187083 (±0.99999994)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-340-340-340
Dimensions680680680
Spacing680680680
CellA=B=C: 779.95996 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.1471.1471.147
M x/y/z680680680
origin x/y/z0.0000.0000.000
length x/y/z779.960779.960779.960
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-340-340-340
NC/NR/NS680680680
D min/max/mean-8.24714.0580.000

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Supplemental data

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Sample components

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Entire : Human papillomavirus type 16 / Antibody complex

EntireName: Human papillomavirus type 16 / Antibody complex
Components
  • Complex: Human papillomavirus type 16 / Antibody complex
    • Complex: Antibody U4
      • Protein or peptide: U4 Heavy chain
      • Protein or peptide: U4 Light chain
    • Virus: Human papillomavirus type 16
      • Protein or peptide: Major capsid protein L1

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Supramolecule #1: Human papillomavirus type 16 / Antibody complex

SupramoleculeName: Human papillomavirus type 16 / Antibody complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all

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Supramolecule #2: Antibody U4

SupramoleculeName: Antibody U4 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2
Source (natural)Organism: Mus musculus (house mouse)

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Supramolecule #3: Human papillomavirus type 16

SupramoleculeName: Human papillomavirus type 16 / type: virus / ID: 3 / Parent: 1 / Macromolecule list: #3 / NCBI-ID: 333760 / Sci species name: Human papillomavirus type 16 / Virus type: VIRION / Virus isolate: SEROCOMPLEX / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Homo sapiens (human)

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Macromolecule #1: U4 Heavy chain

MacromoleculeName: U4 Heavy chain / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mouse (mice)
Molecular weightTheoretical: 12.108347 KDa
SequenceString:
SGGGLVKPGG SLKLSCEASG FTFSSYAMSW VRQTPEKRLE WVASISSGGN THYPDSVKGR FTISRDNARN ILYLQMSSLR SEDTAMYYC ARGLYYGYDE GSDFDYWGQG

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Macromolecule #2: U4 Light chain

MacromoleculeName: U4 Light chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mouse (mice)
Molecular weightTheoretical: 12.09953 KDa
SequenceString:
DIVMSQSPSS LAVSVGEKVT MSCKSSQSLL YSNTQKNYLA WYQQKPGQSP KLLIYWASTR ESGVPDRFTG SGSGTDFTLT ISSVKAEDL AVYYCQQYYS YPLTFGAGTK L

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Macromolecule #3: Major capsid protein L1

MacromoleculeName: Major capsid protein L1 / type: protein_or_peptide / ID: 3 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Human papillomavirus type 16
Molecular weightTheoretical: 52.387277 KDa
SequenceString: YLPPVPVSKV VSTDEYVART NIYYHAGTSR LLAVGHPYFP IKKPNNNKIL VPKVSGLQYR VFRIHLPDPN KFGFPDTSFY NPDTQRLVW ACVGVEVGRG QPLGVGISGH PLLNKLDDTE NASAYAANAG VDNRECISMD YKQTQLCLIG CKPPIGEHWG K GSPCTNVA ...String:
YLPPVPVSKV VSTDEYVART NIYYHAGTSR LLAVGHPYFP IKKPNNNKIL VPKVSGLQYR VFRIHLPDPN KFGFPDTSFY NPDTQRLVW ACVGVEVGRG QPLGVGISGH PLLNKLDDTE NASAYAANAG VDNRECISMD YKQTQLCLIG CKPPIGEHWG K GSPCTNVA VNPGDCPPLE LINTVIQDGD MVDTGFGAMD FTTLQANKSE VPLDICTSIC KYPDYIKMVS EPYGDSLFFY LR REQMFVR HLFNRAGAVG ENVPDDLYIK GSGSTANLAS SNYFPTPSGS MVTSDAQIFN KPYWLQRAQG HNNGICWGNQ LFV TVVDTT RSTNMSLCAA ISTSETTYKN TNFKEYLRHG EEYDLQFIFQ LCKITLTADV MTYIHSMNST ILEDWNFGLQ PPPG GTLED TYRFVTSQAI ACQKHTPPAP KEDPLKKYTF WEVNLKEKFS ADLDQFPLGR KFLLQAGLKA KPKF

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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

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI POLARA 300
Image recording#0 - Image recording ID: 1 / #0 - Film or detector model: FEI FALCON II (4k x 4k) / #0 - Average electron dose: 7.0 e/Å2 / #1 - Image recording ID: 2 / #1 - Film or detector model: FEI FALCON II (4k x 4k) / #1 - Average electron dose: 7.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

Image recording ID1
Startup modelType of model: OTHER / Details: Auto3dem RMC
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 17612
Initial angle assignmentType: COMMON LINE
Final angle assignmentType: COMMON LINE

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