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- EMDB-6121: Cryo-EM reconstruction of quasi-HPV16 complexed with H16.14J Fab -

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Basic information

Entry
Database: EMDB / ID: EMD-6121
TitleCryo-EM reconstruction of quasi-HPV16 complexed with H16.14J Fab
Map dataReconstruction of quasi-HPV16 complexed with H16.14J Fab
Sample
  • Sample: Quasi-human papillomavirus 16 complexed with H16.14J Fab
  • Virus: Human papillomavirus 16
  • Protein or peptide: H16.14J Fab
Keywordsquasi-HPV16 / L1 capsomer / H16.14J 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 16
Methodsingle particle reconstruction / cryo EM / Resolution: 13.9 Å
AuthorsGuan J / Bywaters SM / Brendle SA / Lee H / Ashley RE / Conway JF / Makhov AM / Christensen ND / 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
DepositionOct 2, 2014-
Header (metadata) releaseNov 5, 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: 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-3j8v
  • Surface level: 1.5
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-3j8v
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_6121.tif

Downloads & links

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Map

FileDownload / File: emd_6121.map.gz / Format: CCP4 / Size: 379.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of quasi-HPV16 complexed with H16.14J Fab
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.33 Å/pix.
x 467 pix.
= 1088.11 Å		2.33 Å/pix.
x 467 pix.
= 1088.11 Å		2.33 Å/pix.
x 467 pix.
= 1088.11 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-8.250259399999999 - 8.402011870000001
Average (Standard dev.)0.0 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-233-233-233
Dimensions467467467
Spacing467467467
CellA=B=C: 1088.11 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.332.332.33
M x/y/z467467467
origin x/y/z0.0000.0000.000
length x/y/z1088.1101088.1101088.110
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-233-233-233
NC/NR/NS467467467
D min/max/mean-8.2508.4020.000

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Supplemental data

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Sample components

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Entire : Quasi-human papillomavirus 16 complexed with H16.14J Fab

EntireName: Quasi-human papillomavirus 16 complexed with H16.14J Fab
Components
  • Sample: Quasi-human papillomavirus 16 complexed with H16.14J Fab
  • Virus: Human papillomavirus 16
  • Protein or peptide: H16.14J Fab

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Supramolecule #1000: Quasi-human papillomavirus 16 complexed with H16.14J Fab

SupramoleculeName: Quasi-human papillomavirus 16 complexed with H16.14J Fab
type: sample / ID: 1000 / Oligomeric state: 300 H16.14J Fabs bind to one HPV16 capsid / Number unique components: 2
Molecular weightTheoretical: 44.7 MDa

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Supramolecule #1: Human papillomavirus 16

SupramoleculeName: Human papillomavirus 16 / type: virus / ID: 1 / NCBI-ID: 337041 / Sci species name: Human papillomavirus 16 / Virus type: VIRION / Virus isolate: OTHER / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Homo sapiens (human) / synonym: VERTEBRATES
Host systemOrganism: Homo sapiens (human) / Recombinant cell: 293TT / Recombinant plasmid: SV40
Molecular weightTheoretical: 27.7 MDa
Virus shellShell ID: 1 / Name: L1 L2 / Diameter: 600 Å / T number (triangulation number): 7

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Macromolecule #1: H16.14J Fab

MacromoleculeName: H16.14J Fab / type: protein_or_peptide / ID: 1 / 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

Concentration1.0 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 / Method: Blot for 0.7 seconds before plunging.

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Electron microscopy

MicroscopeJEOL 2100
TemperatureAverage: 95 K
DateAug 27, 2014
Image recordingCategory: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Number real images: 385 / 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: 4.69 µm / Nominal defocus min: 0.62 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: 13.9 Å / Resolution method: OTHER / Software - Name: Auto3dem
Details: Semi-automatic particle selection was performed using e2boxer.py to obtain the particle coordinates, followed by particle boxing, linearization, normalization, and apodization of the images ...Details: Semi-automatic particle selection was performed using e2boxer.py to obtain the particle coordinates, followed by particle boxing, linearization, normalization, and apodization of the images using Robem. Defocus and astigmatism values necessary to perform contrast transfer function (CTF) correction for the extracted particles were assessed using Robem. The icosahedrally averaged reconstruction was initiated using a random model generated with setup_rmc. For the last step of refinement, the final maps were CTF-corrected using a B factor of 200 A2.
Number images used: 5642

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Atomic model buiding 1

Initial modelPDB ID:

3oae
PDB Unreleased entry


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

PDB-3j8v:
Cryo-EM reconstruction of quasi-HPV16 complex with H16.14J Fab

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