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Yorodumi- EMDB-1024: Six molecules of SV40 large T antigen assemble in a propeller-sha... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-1024 | |||||||||
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Title | Six molecules of SV40 large T antigen assemble in a propeller-shaped particle around a channel. | |||||||||
Map data | SV40 T antigen | |||||||||
Sample |
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Function / homology | T antigen, Ori-binding / DNA replication origin binding Function and homology information | |||||||||
Biological species | Simian virus 40 | |||||||||
Method | single particle reconstruction / negative staining / Resolution: 29.0 Å | |||||||||
Authors | San Martin C | |||||||||
Citation | Journal: 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_1024.map.gz | 443.4 KB | EMDB map data format | |
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Header (meta data) | emd-1024-v30.xml emd-1024.xml | 7.7 KB 7.7 KB | Display Display | EMDB header |
Images | 1024.gif | 9.4 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-1024 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-1024 | HTTPS FTP |
-Validation report
Summary document | emd_1024_validation.pdf.gz | 207.2 KB | Display | EMDB validaton report |
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Full document | emd_1024_full_validation.pdf.gz | 206.3 KB | Display | |
Data in XML | emd_1024_validation.xml.gz | 4.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1024 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1024 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_1024.map.gz / Format: CCP4 / Size: 478.5 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | SV40 T antigen | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 3.8 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : SV40 T antigen
Entire | Name: SV40 T antigen |
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Components |
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-Supramolecule #1000: SV40 T antigen
Supramolecule | Name: SV40 T antigen / type: sample / ID: 1000 / Oligomeric state: homohexamer / Number unique components: 1 |
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Molecular weight | Theoretical: 500 KDa |
-Macromolecule #1: Large T antigen
Macromolecule | Name: Large T antigen / type: protein_or_peptide / ID: 1 / Name.synonym: T antigen / Number of copies: 6 / Oligomeric state: homohexamer / Recombinant expression: Yes |
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Source (natural) | Organism: Simian virus 40 / synonym: SV40 |
Molecular weight | Theoretical: 500 KDa |
Recombinant expression | Organism: AcNPV |
Sequence | GO: DNA replication origin binding / InterPro: T antigen, Ori-binding |
-Experimental details
-Structure determination
Method | negative staining |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | .06 mg/mL |
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Buffer | pH: 7.5 Details: 20 mM Tris.HCl pH 7.5 5 mM KCl 1.5 mM MgCl2 0.1 mM DTT 4 mM ADP |
Staining | Type: NEGATIVE / Details: 2% Uranyl Acetate |
Vitrification | Cryogen name: NONE |
-Electron microscopy
Microscope | JEOL 1200EXII |
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Image recording | Category: 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 beam | Acceleration voltage: 120 kV / Electron source: TUNGSTEN HAIRPIN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 5.6 mm / Nominal magnification: 60000 |
Sample stage | Specimen holder: Jeol / Specimen holder model: JEOL / Tilt angle max: 55 |
-Image processing
Final reconstruction | Applied 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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