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- EMDB-6119: Electron cryo-microscopy of human papillomavirus 16 and H16.V5 Fa... -

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Basic information

Database: EMDB / ID: 6119
TitleElectron cryo-microscopy of human papillomavirus 16 and H16.V5 Fab fragments
Keywordsvirus-Fab complex / neutralization antibody / maturation
SampleMature HPV16 quasivirus capsid complexed with H16.V5 Fabs
SourceHuman papillomavirus 16 / virus
Mus musculus / mammal / House mouse /
Map dataReconstruction of mature human papillomavirus 16 capsid complexed with Fab fragments after 1 hr incubation
Methodsingle particle (icosahedral) reconstruction, at 14.7 Å resolution
AuthorsLee H / Brendle SA / Bywaters SM / Guan J / Ashley RE / Yoder JD / Makhov AM / Conway JF / Christensen ND / Hafenstein S
CitationJ. Virol., 2015, 89, 1428-1438

J. Virol., 2015, 89, 1428-1438 Yorodumi Papers
A cryo-electron microscopy study identifies the complete H16.V5 epitope and reveals global conformational changes initiated by binding of the neutralizing antibody fragment.
Hyunwook Lee / Sarah A Brendle / Stephanie M Bywaters / Jian Guan / Robert E Ashley / Joshua D Yoder / Alexander M Makhov / James F Conway / Neil D Christensen / Susan Hafenstein

DateDeposition: Sep 30, 2014 / Header (metadata) release: Oct 8, 2014 / Map release: Dec 3, 2014 / Last update: May 27, 2015

Structure visualization

  • 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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3D viewer
Supplemental images

Downloads & links


Fileemd_6119.map.gz (map file in CCP4 format, 117502 KB)
Projections & slices

Image control

AxesZ (Sec.)Y (Row.)X (Col.)
311 pix
2.86 Å/pix.
= 889.46 Å
311 pix
2.86 Å/pix.
= 889.46 Å
311 pix
2.86 Å/pix.
= 889.46 Å



Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 2.86 Å
Contour Level:1 (by author), 1 (movie #1):
Minimum - Maximum-5.48643637 - 6.0805316
Average (Standard dev.)0E-8 (0.99999994)


Space Group Number1
Map Geometry
Axis orderXYZ
CellA=B=C: 889.45996 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.862.862.86
M x/y/z311311311
origin x/y/z0.0000.0000.000
length x/y/z889.460889.460889.460
start NX/NY/NZ
MAP C/R/S123
start NC/NR/NS-155-155-155
D min/max/mean-5.4866.081-0.000

Supplemental data

Sample components

Entire Mature HPV16 quasivirus capsid complexed with H16.V5 Fabs

EntireName: Mature HPV16 quasivirus capsid complexed with H16.V5 Fabs
Number of components: 2
Oligomeric State: Three hundred H16.V5 Fabs bind to one HPV16 capsid
MassTheoretical: 42 MDa

Component #1: virus, Human papillomavirus 16

VirusName: Human papillomavirus 16 / Class: VIRION
Details: The virus sample was incubated with excessive Fab fragments for 1 hr.
Enveloped: No / Empty: No / Isolate: OTHER
MassTheoretical: 27 MDa
SpeciesSpecies: Human papillomavirus 16 / virus
Source (natural)Host Species: Homo sapiens / human / / Host category: VERTEBRATES
Shell #1Name of element: L1/L2 / Diameter: 600 Å / T number(triangulation number): 7

Component #2: protein, H16.V5 Fab

ProteinName: H16.V5 Fab / Oligomeric Details: monomer / Recombinant expression: No / Number of Copies: 300
MassTheoretical: 50 kDa
SourceSpecies: Mus musculus / mammal / House mouse /
Source (natural)Cell: hybridoma

Experimental details

Sample preparation

Specimen stateparticle
Sample solutionSpecimen conc.: 1 mg/ml
Buffer solution: 137 mM NaCl, 2.7 mM KCl, 10 mM Na2HPO4, 1.8 mM KH2PO4
pH: 7.4
Support filmglow-discharged holey carbon Quantifoil grids
VitrificationInstrument: GATAN CRYOPLUNGE 3 / Cryogen name: ETHANE / Temperature: 102 K / Humidity: 90 % / Method: Blot for 0.7 seconds before plunging.

Electron microscopy imaging

ImagingMicroscope: JEOL 2100 / Date: Aug 13, 2014
Electron gunElectron source: LAB6 / Accelerating voltage: 200 kV / Electron dose: 15 e/Å2 / Illumination mode: SPOT SCAN
LensMagnification: 40000 X (nominal) / Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 1190 - 5670 nm
Specimen HolderModel: GATAN LIQUID NITROGEN / Temperature: 95 K
CameraDetector: GATAN ULTRASCAN 4000 (4k x 4k)

Image acquisition

Image acquisitionNumber of digital images: 138

Image processing

ProcessingMethod: single particle (icosahedral) reconstruction / Applied symmetry: I (icosahedral) / Number of projections: 2075
Details: The particles were selected using semi-automatic program e2boxer.py (EMAN2).
3D reconstructionAlgorithm: Cross-common lines / Software: Auto3dem / CTF correction: Each particle
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 to perform contrast transfer function (CTF) correction were assessed using Robem for the extracted particles. The icosahedrally averaged reconstructions were initiated using a random model generated with setup_rmc and reached 14 A resolution estimated at a Fourier Shell Correlation (FSC) of 0.5. For the last step of refinement, the final maps were CTF-corrected using a B factor of 200 A2.
Resolution: 14.7 Å / Resolution method: FSC 0.5, semi-independent

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