[English] 日本語
Yorodumi
- EMDB-6119: Electron cryo-microscopy of human papillomavirus 16 and H16.V5 Fa... -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
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 / ハツカネズミ, はつかねずみ /
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

Movie
  • Surface view with section colored by density value
  • Surface level: 1
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by radius
  • Surface level: 1
  • Imaged by UCSF CHIMERA
  • Download
3D viewer


View / / Stereo:
Center
Zoom
Scale
Slabnear <=> far

fix: /
Orientation
Orientation Rotation
Misc. /
Show/hide
Supplemental images

Downloads & links

-
Map

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

Image control

Size
Brightness
Contrast
Others
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

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

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

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions311311311
Origin-155-155-155
Limit155155155
Spacing311311311
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
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS-155-155-155
NC/NR/NS311311311
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 / ハツカネズミ, はつかねずみ /
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

+
About Yorodumi

-
News

-
Oct 4, 2017. Three pioneers of this field were awarded Nobel Prize in Chemistry 2017

Three pioneers of this field were awarded Nobel Prize in Chemistry 2017

  • Jacques Dubochet (University of Lausanne, Switzerland) is a pioneer of ice-embedding method of EM specimen (as known as cryo-EM), Most of 3DEM structures in EMDB and PDB are obtained using his method.
  • Joachim Frank (Columbia University, New York, USA) is a pioneer of single particle reconstruction, which is the most used reconstruction method for 3DEM structures in EMDB and EM entries in PDB. And also, he is a develper of Spider, which is one of the most famous software in this field, and is used for some EM Navigor data (e.g. map projection/slice images).
  • Richard Henderson (MRC Laboratory of Molecular Biology, Cambridge, UK) was determined the first biomolecule structure by EM. The first EM entry in PDB, PDB-1brd is determinedby him.

External links: The 2017 Nobel Prize in Chemistry - Press Release

-
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.

External links: wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator (legacy version) / Yorodumi (legacy version)

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi / EM Navigator (legacy version) / Yorodumi (legacy version)

Read more

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • All the functionalities will be ported from the levgacy version.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

Related info.: Yorodumi (legacy version) / EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Yorodumi Papers / Jmol/JSmol / Changes in new EM Navigator and Yorodumi

Read more