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- EMDB-1112: A quasi-atomic model of human adenovirus type 5 capsid. -

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Basic information

Entry
Database: EMDB / ID: EMD-1112
TitleA quasi-atomic model of human adenovirus type 5 capsid.
Map dataStructure of Adenovirus pIX deletion mutant (single frozen and thawed sample)
Sample
  • Sample: Human adenovirus type 5 pIX deletion mutant
  • 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 / clathrin-dependent endocytosis of virus by host cell / symbiont entry into host cell / host cell nucleus / structural molecule activity / virion attachment to host cell
Similarity search - Function
Adenovirus Pll, hexon, subdomain 2 / Adenovirus hexon protein / Adenovirus Pll, hexon, N-terminal / Adenovirus Pll, hexon, C-terminal / 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: 15.5 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 25, 2005-
Header (metadata) releaseFeb 25, 2005-
Map releaseJun 7, 2005-
UpdateMay 26, 2011-
Current statusMay 26, 2011Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 3500
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 3500
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-4v4u
  • Surface level: 3500
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-4v4u
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1112.gif

Downloads & links

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Map

FileDownload / File: emd_1112.map.gz / Format: CCP4 / Size: 335 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationStructure of Adenovirus pIX deletion mutant (single frozen and thawed sample)
Voxel sizeX=Y=Z: 2.45 Å
Density
Contour Level1: 4660.0 / Movie #1: 3500
Minimum - Maximum-19812.0 - 21528.0
Average (Standard dev.)108.747 (±2362.059999999999945)
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-19812.00021528.000108.747

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Supplemental data

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Sample components

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Entire : Human adenovirus type 5 pIX deletion mutant

EntireName: Human adenovirus type 5 pIX deletion mutant
Components
  • Sample: Human adenovirus type 5 pIX deletion mutant
  • Virus: unidentified adenovirus

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Supramolecule #1000: Human adenovirus type 5 pIX deletion mutant

SupramoleculeName: Human adenovirus type 5 pIX deletion mutant / type: sample / ID: 1000 / Number unique components: 1
Molecular weightTheoretical: 150 MDa

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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

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Experimental details

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Structure determination

Methodnegative staining, cryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1.0 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: 90 K / Instrument: OTHER / Details: Vitrification instrument: Zeiss plunger / Method: Manual blot for 1-2 seconds before plunging

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Electron microscopy

MicroscopeFEI/PHILIPS CM200T
Electron beamAcceleration voltage: 200 kV / Electron source: LAB6
Electron opticsCalibrated magnification: 28600 / Illumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy / 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
TemperatureMin: 90 K / Max: 90 K / Average: 90 K
Alignment procedureLegacy - Astigmatism: objective lens astigmatism was corrected at 100,000 times magnification
DateDec 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: 22 / Average electron dose: 10 e/Å2 / Od range: 1.2 / Bits/pixel: 8

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Image processing

CTF correctionDetails: CTFMIX
Final reconstructionApplied 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

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