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- EMDB-1024: Six molecules of SV40 large T antigen assemble in a propeller-sha... -

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Basic information

Entry
Database: EMDB / ID: EMD-1024
TitleSix molecules of SV40 large T antigen assemble in a propeller-shaped particle around a channel.
Map dataSV40 T antigen
Sample
  • Sample: SV40 T antigen
  • Protein or peptide: Large T antigen
Function / homologyT antigen, Ori-binding / DNA replication origin binding
Function and homology information
Biological speciesSimian virus 40
Methodsingle particle reconstruction / negative staining / Resolution: 29.0 Å
AuthorsSan Martin C
CitationJournal: J Mol Biol / Year: 1997
Title: Six molecules of SV40 large T antigen assemble in a propeller-shaped particle around a channel.
Authors: M C San Martín / C Gruss / J M Carazo /
Abstract: The large T antigen of simian virus 40 (SV40) is a multifunctional regulatory protein, responsible for both the control of viral infection and the required alterations of cellular processes. T ...The large T antigen of simian virus 40 (SV40) is a multifunctional regulatory protein, responsible for both the control of viral infection and the required alterations of cellular processes. T antigen is the only viral protein required for viral DNA replication. It binds specifically to the viral origin and as a helicase unwinds the SV40 DNA bidirectionally. The functional complex is a double hexameric oligomer. In the absence of DNA, but in the presence of ATP or a non-hydrolyzable analog, T antigen assembles into hexamers, which are active as a helicase when a partially single-stranded (3') entry site exists on the substrate. We have used negative staining electron microscopy, single particle image processing and three-dimensional reconstruction with a new algebraic reconstruction techniques (ART) algorithm to study the structure of these hexameric particles in the presence of different nucleotide cofactors (ATP, ADP, and the non-hydrolyzable analogs ATPgammaS and AMP-PNP). In every case a strong 6-fold structure was found, with the six density maxima arranged in a ring-like particle around a channel, and a well-defined vorticity. Because these structural features have recently been found in other prokaryotic helicases, they seem to be strongly related to the activity of the protein, which suggests a general functional model conserved through evolution.
History
DepositionFeb 12, 2003-
Header (metadata) releaseFeb 12, 2003-
Map releaseFeb 12, 2003-
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: 14.104508243
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 14.104508243
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1024.gif

Downloads & links

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Map

FileDownload / File: emd_1024.map.gz / Format: CCP4 / Size: 478.5 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSV40 T antigen
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.8 Å/pix.
x 50 pix.
= 190. Å		3.8 Å/pix.
x 50 pix.
= 190. Å		3.8 Å/pix.
x 50 pix.
= 190. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.8 Å
Density

Histogram

Histogram (log scale)
Contour Level1: 11.5 / Movie #1: 14.1045082
Minimum - Maximum-20.978200000000001 - 26.756599999999999
Average (Standard dev.)-0.00284247 (±5.642)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions505050
Spacing505050
CellA=B=C: 190 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.83.83.8
M x/y/z505050
origin x/y/z0.0000.0000.000
length x/y/z190.000190.000190.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS505050
D min/max/mean-20.97826.757-0.003

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Supplemental data

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Sample components

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Entire : SV40 T antigen

EntireName: SV40 T antigen
Components
  • Sample: SV40 T antigen
  • Protein or peptide: Large T antigen

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Supramolecule #1000: SV40 T antigen

SupramoleculeName: SV40 T antigen / type: sample / ID: 1000 / Oligomeric state: homohexamer / Number unique components: 1
Molecular weightTheoretical: 500 KDa

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Macromolecule #1: Large T antigen

MacromoleculeName: Large T antigen / type: protein_or_peptide / ID: 1 / Name.synonym: T antigen / Number of copies: 6 / Oligomeric state: homohexamer / Recombinant expression: Yes
Source (natural)Organism: Simian virus 40 / synonym: SV40
Molecular weightTheoretical: 500 KDa
Recombinant expressionOrganism: AcNPV
SequenceGO: DNA replication origin binding / InterPro: T antigen, Ori-binding

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Experimental details

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Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration.06 mg/mL
BufferpH: 7.5
Details: 20 mM Tris.HCl pH 7.5 5 mM KCl 1.5 mM MgCl2 0.1 mM DTT 4 mM ADP
StainingType: NEGATIVE / Details: 2% Uranyl Acetate
VitrificationCryogen name: NONE

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Electron microscopy

MicroscopeJEOL 1200EXII
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: EIKONIX IEEE 488 / Number real images: 8 / Average electron dose: 10 e/Å2 / Bits/pixel: 8
Electron beamAcceleration voltage: 120 kV / Electron source: TUNGSTEN HAIRPIN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 5.6 mm / Nominal magnification: 60000
Sample stageSpecimen holder: Jeol / Specimen holder model: JEOL / Tilt angle max: 55

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Image processing

Final reconstructionApplied symmetry - Point group: C6 (6 fold cyclic) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 29.0 Å / Resolution method: OTHER / Software - Name: Xmipp / Number images used: 1472

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