Journal: EMBO J / Year: 2005 Title: A quasi-atomic model of human adenovirus type 5 capsid. Authors: Céline M S Fabry / Manuel Rosa-Calatrava / James F Conway / Chloé Zubieta / Stephen Cusack / Rob W H Ruigrok / Guy Schoehn / Abstract: Adenoviruses infect a wide range of vertebrates including humans. Their icosahedral capsids are composed of three major proteins: the trimeric hexon forms the facets and the penton, a noncovalent ...Adenoviruses infect a wide range of vertebrates including humans. Their icosahedral capsids are composed of three major proteins: the trimeric hexon forms the facets and the penton, a noncovalent complex of the pentameric penton base and trimeric fibre proteins, is located at the 12 capsid vertices. Several proteins (IIIa, VI, VIII and IX) stabilise the capsid. We have obtained a 10 A resolution map of the human adenovirus 5 by image analysis from cryo-electron micrographs (cryoEMs). This map, in combination with the X-ray structures of the penton base and hexon, was used to build a quasi-atomic model of the arrangement of the two major capsid components and to analyse the hexon-hexon and hexon-penton interactions. The secondary proteins, notably VIII, were located by comparing cryoEM maps of native and pIX deletion mutant virions. Minor proteins IX and IIIa are located on the outside of the capsid, whereas protein VIII is organised with a T=2 lattice on the inner face of the capsid. The capsid organisation is compared with the known X-ray structure of bacteriophage PRD1.
History
Deposition
Feb 25, 2005
-
Header (metadata) release
Feb 25, 2005
-
Map release
Jun 7, 2005
-
Update
May 26, 2011
-
Current status
May 26, 2011
Processing site: PDBe / Status: Released
-
Structure visualization
Movie
Surface view with section colored by density value
Organism: Homo sapiens (human) / synonym: VERTEBRATES
Molecular weight
Experimental: 150 MDa / Theoretical: 150 MDa
Virus shell
Shell ID: 1 / Name: adenovirus / Diameter: 900 Å / T number (triangulation number): 25
-
Experimental details
-
Structure determination
Method
negative staining, cryo EM
Processing
single particle reconstruction
Aggregation state
particle
-
Sample preparation
Concentration
1.0 mg/mL
Buffer
pH: 7.5 / Details: 150 mM NaCl 20 mM Tris-HCl pH 7.5
Staining
Type: NEGATIVE / Details: Cryo EM
Grid
Details: Quantifoil grid
Vitrification
Cryogen name: ETHANE / Chamber temperature: 90 K / Instrument: OTHER / Details: Vitrification instrument: Zeiss plunger / Method: Manual blot for 1-2 seconds before plunging
-
Electron microscopy
Microscope
FEI/PHILIPS CM200T
Temperature
Min: 90 K / Max: 90 K / Average: 90 K
Alignment procedure
Legacy - Astigmatism: objective lens astigmatism was corrected at 100,000 times magnification
Date
Dec 1, 2003
Image recording
Category: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7 µm / Number real images: 22 / Average electron dose: 10 e/Å2 / Od range: 1.2 / Bits/pixel: 8
Electron beam
Acceleration voltage: 200 kV / Electron source: LAB6
Applied symmetry - Point group: I (icosahedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 15.5 Å / Resolution method: FSC 0.33 CUT-OFF / Software - Name: PFT EM3DR / Details: Final maps were calculated from 1060 single images / Number images used: 1060
+
About Yorodumi
-
News
-
Feb 9, 2022. New format data for meta-information of EMDB entries
New format data for meta-information of EMDB entries
Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.
In the structure databanks used in Yorodumi, some data are registered as the other names, "COVID-19 virus" and "2019-nCoV". Here are the details of the virus and the list of structure data.
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)
EMDB accession codes are about to change! (news from PDBe EMDB page)
The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
The EM Navigator/Yorodumi systems omit the EMD- prefix.
Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator
Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.
Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi