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- EMDB-5990: Electron cryo-microscopy of quasi-human papillomavirus 16 complex... -

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Basic information

Entry
Database: EMDB / ID: EMD-5990
TitleElectron cryo-microscopy of quasi-human papillomavirus 16 complexed with Fab H16.1A
Map dataReconstruction of quasi-HPV16-Fab1A complex
Sample
  • Sample: Quasi-HPV16 complex with Fab H16.1A
  • Virus: Human papillomavirus 16
  • Protein or peptide: H16.1A Fab
Keywordsneutralization / quasi-human papillomavirus 16 / H16.1A
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 speciesunidentified (others) / Human papillomavirus 16
Methodsingle particle reconstruction / cryo EM / Resolution: 14.0 Å
AuthorsGuan J / Brendle S / Bywaters S / Lee H / Ashley RE / Conway JF / Makhov AM / Christensen N / Hafenstein S
CitationJournal: Virology / Year: 2015
Title: Structural comparison of four different antibodies interacting with human papillomavirus 16 and mechanisms of neutralization.
Authors: Jian Guan / Stephanie M Bywaters / Sarah A Brendle / Hyunwook Lee / Robert E Ashley / Alexander M Makhov / James F Conway / Neil D Christensen / Susan Hafenstein /
Abstract: Cryo-electron microscopy (cryo-EM) was used to solve the structures of human papillomavirus type 16 (HPV16) complexed with fragments of antibody (Fab) from three different neutralizing monoclonals ...Cryo-electron microscopy (cryo-EM) was used to solve the structures of human papillomavirus type 16 (HPV16) complexed with fragments of antibody (Fab) from three different neutralizing monoclonals (mAbs): H16.1A, H16.14J, and H263.A2. The structure-function analysis revealed predominantly monovalent binding of each Fab with capsid interactions that involved multiple loops from symmetry related copies of the major capsid protein. The residues identified in each Fab-virus interface map to a conformational groove on the surface of the capsomer. In addition to the known involvement of the FG and HI loops, the DE loop was also found to constitute the core of each epitope. Surprisingly, the epitope mapping also identified minor contributions by EF and BC loops. Complementary immunological assays included mAb and Fab neutralization. The specific binding characteristics of mAbs correlated with different neutralizing behaviors in pre- and post-attachment neutralization assays.
History
DepositionJun 20, 2014-
Header (metadata) releaseJul 30, 2014-
Map releaseMay 6, 2015-
UpdateJun 3, 2015-
Current statusJun 3, 2015Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.6
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.6
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-3j8z
  • Surface level: 1.2
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-3j8z
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_5990.jpg

Downloads & links

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Map

FileDownload / File: emd_5990.map.gz / Format: CCP4 / Size: 808.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of quasi-HPV16-Fab1A complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.3 Å/pix.
x 601 pix.
= 781.3 Å		1.3 Å/pix.
x 601 pix.
= 781.3 Å		1.3 Å/pix.
x 601 pix.
= 781.3 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.3 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.0 / Movie #1: 0.6
Minimum - Maximum-1.82998371 - 4.16103792
Average (Standard dev.)0.00000001 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-300-300-300
Dimensions601601601
Spacing601601601
CellA=B=C: 781.3 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.31.31.3
M x/y/z601601601
origin x/y/z0.0000.0000.000
length x/y/z781.300781.300781.300
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-300-300-300
NC/NR/NS601601601
D min/max/mean-1.8304.1610.000

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Supplemental data

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Sample components

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Entire : Quasi-HPV16 complex with Fab H16.1A

EntireName: Quasi-HPV16 complex with Fab H16.1A
Components
  • Sample: Quasi-HPV16 complex with Fab H16.1A
  • Virus: Human papillomavirus 16
  • Protein or peptide: H16.1A Fab

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Supramolecule #1000: Quasi-HPV16 complex with Fab H16.1A

SupramoleculeName: Quasi-HPV16 complex with Fab H16.1A / type: sample / ID: 1000
Oligomeric state: Three hundred H16.1A Fabs bind to one HPV16 capsid
Number unique components: 2

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Supramolecule #1: Human papillomavirus 16

SupramoleculeName: Human papillomavirus 16 / type: virus / ID: 1 / Details: Isolated by gradient centrifugation. / NCBI-ID: 337041 / Sci species name: Human papillomavirus 16 / Database: NCBI / Virus type: VIRION / Virus isolate: OTHER / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Homo sapiens (human) / synonym: VERTEBRATES
Molecular weightTheoretical: 27.8 MDa
Virus shellShell ID: 1 / Name: L1 L2 / Diameter: 720 Å / T number (triangulation number): 7

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Macromolecule #1: H16.1A Fab

MacromoleculeName: H16.1A Fab / type: protein_or_peptide / ID: 1 / Recombinant expression: Yes / Database: NCBI
Source (natural)Organism: unidentified (others)

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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
VitrificationCryogen name: ETHANE-PROPANE MIXTURE / Instrument: FEI VITROBOT MARK III

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Electron microscopy

MicroscopeFEI TECNAI F20
DateJan 9, 2013
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: NIKON SUPER COOLSCAN 9000 / Number real images: 50
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 50000 / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal magnification: 50000
Sample stageSpecimen holder model: GATAN LIQUID NITROGEN
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: auto3dem
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 14.0 Å / Resolution method: OTHER / Software - Name: auto3dem / Number images used: 2300

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Atomic model buiding 1

Initial modelPDB ID:

3oae
PDB Unreleased entry

SoftwareName: Chimera, Situs
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-3j8z:
Cryo-EM reconstruction of quasi-HPV16 complex with H16.1A Fab

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