[English] 日本語
Yorodumi
- EMDB-1113: A quasi-atomic model of human adenovirus type 5 capsid. -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-1113
TitleA quasi-atomic model of human adenovirus type 5 capsid.
Map dataAdenovirus structure
Sample
  • Sample: Human adenovirus type 5
  • Virus: unidentified adenovirus
Function / homology
Function and homology information


T=25 icosahedral viral capsid / microtubule-dependent intracellular transport of viral material towards nucleus / viral capsid / host cell / clathrin-dependent endocytosis of virus by host cell / symbiont entry into host cell / virion attachment to host cell / host cell nucleus / structural molecule activity
Similarity search - Function
Adenovirus hexon protein / Adenovirus Pll, hexon, N-terminal / Adenovirus Pll, hexon, C-terminal / Adenovirus Pll, hexon, subdomain 2 / Hexon, adenovirus major coat protein, N-terminal domain / Hexon, adenovirus major coat protein, C-terminal domain / Adenovirus penton base protein / Adenovirus penton base protein / Group II dsDNA virus coat/capsid protein
Similarity search - Domain/homology
Penton protein / Hexon protein
Similarity search - Component
Biological speciesunidentified adenovirus
Methodsingle particle reconstruction / cryo EM / negative staining / Resolution: 10.3 Å
AuthorsFabry CM / Rosa-Calatrava M / Conway JF / Zubieta C / Cusack S / Ruigrok RW / Schoehn G
CitationJournal: 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
DepositionFeb 23, 2005-
Header (metadata) releaseFeb 25, 2005-
Map releaseJun 7, 2005-
UpdateMay 26, 2011-
Current statusMay 26, 2011Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 180
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 180
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-4v4u
  • Surface level: 180
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-4v4u
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1113.gif

Downloads & links

-
Map

FileDownload / File: emd_1113.map.gz / Format: CCP4 / Size: 335 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationAdenovirus structure
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesY (Sec.)X (Row.)Z (Col.)
2.45 Å/pix.
x 448 pix.
= 1097.6 Å		2.45 Å/pix.
x 448 pix.
= 1097.6 Å		2.45 Å/pix.
x 448 pix.
= 1097.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.45 Å
Density

Histogram

Histogram (log scale)
Contour Level1: 180.0 / Movie #1: 180
Minimum - Maximum-343.0 - 475.0
Average (Standard dev.)14.7233 (±79.529600000000002)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZXY
Origin-224-224-224
Dimensions448448448
Spacing448448448
CellA=B=C: 1097.6 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.452.452.45
M x/y/z448448448
origin x/y/z0.0000.0000.000
length x/y/z1097.6001097.6001097.600
α/β/γ90.00090.00090.000
start NX/NY/NZ-224-224-224
NX/NY/NZ448448448
MAP C/R/S312
start NC/NR/NS-224-224-224
NC/NR/NS448448448
D min/max/mean-343.000475.00014.723

-
Supplemental data

-
Sample components

-
Entire : Human adenovirus type 5

EntireName: Human adenovirus type 5
Components
  • Sample: Human adenovirus type 5
  • Virus: unidentified adenovirus

-
Supramolecule #1000: Human adenovirus type 5

SupramoleculeName: Human adenovirus type 5 / type: sample / ID: 1000 / Number unique components: 1
Molecular weightTheoretical: 150.0 MDa

-
Supramolecule #1: unidentified adenovirus

SupramoleculeName: unidentified adenovirus / type: virus / ID: 1 / NCBI-ID: 10535 / Sci species name: unidentified adenovirus / Virus type: VIRION / Virus isolate: SEROTYPE / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Homo sapiens (human) / synonym: VERTEBRATES
Molecular weightExperimental: 150 MDa / Theoretical: 150 MDa
Virus shellShell ID: 1 / Name: adenovirus / Diameter: 900 Å / T number (triangulation number): 25

-
Experimental details

-
Structure determination

Methodnegative staining, cryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration3.0 mg/mL
BufferpH: 7.5 / Details: 150 mM NaCl 20 mM Tris-HCl pH 7.5
StainingType: NEGATIVE / Details: Cryo EM
GridDetails: Quantifoil grid
VitrificationCryogen name: ETHANE / Chamber temperature: 87 K / Instrument: OTHER / Details: Vitrification instrument: Zeiss plunger / Method: Manual blot for 1 second before plunging

-
Electron microscopy

MicroscopeFEI/PHILIPS CM200T
TemperatureMin: 90 K / Max: 90 K / Average: 90 K
Alignment procedureLegacy - Astigmatism: objective lens astigmatism was corrected at 100,000 times magnification
DateOct 1, 2003
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7 µm / Number real images: 21 / Average electron dose: 10 e/Å2 / Od range: 1.2 / Bits/pixel: 8
Electron beamAcceleration voltage: 200 kV / Electron source: LAB6
Electron opticsCalibrated magnification: 28600 / Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus max: 0.25 µm / Nominal defocus min: 0.1 µm / Nominal magnification: 27500
Sample stageSpecimen holder: Eucentric / Specimen holder model: GATAN LIQUID NITROGEN

-
Image processing

CTF correctionDetails: CTFMIX
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 10.3 Å / Resolution method: FSC 0.33 CUT-OFF / Software - Name: PFT EM3DR / Details: Final maps were calculated from 4100 single images / Number images used: 4100

-
Atomic model buiding 1

SoftwareName: URO SITUS
DetailsProtocol: Rigid Body. Penton bases were fitted using SITUS Hexons from the asymetric unit were fitted togheter using URO
RefinementSpace: RECIPROCAL / Protocol: RIGID BODY FIT / Target criteria: R-factor
Output model

PDB-4v4u:
The quasi-atomic model of Human Adenovirus type 5 capsid

+
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.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
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

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
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.
  • 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

-
Yorodumi

Thousand views of thousand structures

  • 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

Read more