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- PDB-1tbd: SOLUTION STRUCTURE OF THE ORIGIN DNA BINDING DOMAIN OF SV40 T-ANT... -

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Basic information

Entry
Database: PDB / ID: 1tbd
TitleSOLUTION STRUCTURE OF THE ORIGIN DNA BINDING DOMAIN OF SV40 T-ANTIGEN, NMR, MINIMIZED AVERAGE STRUCTURE
ComponentsSV40 T-ANTIGEN
KeywordsDNA BINDING PROTEIN / DNA-BINDING PROTEIN / REPLICATION ORIGIN BINDING DOMAIN
Function / homology
Function and homology information


symbiont-mediated suppression of host JAK-STAT cascade via inhibition of JAK1 activity / bidirectional double-stranded viral DNA replication / viral DNA genome replication / DNA unwinding involved in DNA replication / DNA replication origin binding / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / helicase activity / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / single-stranded DNA binding / double-stranded DNA binding ...symbiont-mediated suppression of host JAK-STAT cascade via inhibition of JAK1 activity / bidirectional double-stranded viral DNA replication / viral DNA genome replication / DNA unwinding involved in DNA replication / DNA replication origin binding / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / helicase activity / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / single-stranded DNA binding / double-stranded DNA binding / symbiont-mediated perturbation of host ubiquitin-like protein modification / hydrolase activity / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / host cell nucleus / ATP binding / identical protein binding / metal ion binding
Similarity search - Function
Replication Protein E1; Chain: A, - #20 / Large T antigen, polyomaviridae / Replication Protein E1; Chain: A, / Large T antigen, polyomavirus, C-terminal / Zinc finger, large T-antigen D1-type / Origin of replication binding protein / Polyomavirus large T antigen C-terminus / Large T-antigen (T-ag) origin-binding domain (OBD) profile. / Zinc finger large T-antigen (T-ag) D1-type profile. / T antigen, Ori-binding ...Replication Protein E1; Chain: A, - #20 / Large T antigen, polyomaviridae / Replication Protein E1; Chain: A, / Large T antigen, polyomavirus, C-terminal / Zinc finger, large T-antigen D1-type / Origin of replication binding protein / Polyomavirus large T antigen C-terminus / Large T-antigen (T-ag) origin-binding domain (OBD) profile. / Zinc finger large T-antigen (T-ag) D1-type profile. / T antigen, Ori-binding / Zinc finger, large T-antigen D1 domain superfamily / Helicase, superfamily 3, DNA virus / Superfamily 3 helicase of DNA viruses domain profile. / DnaJ molecular chaperone homology domain / dnaJ domain profile. / Chaperone J-domain superfamily / DnaJ domain / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesSimian virus 40
MethodSOLUTION NMR / simulated annealing
AuthorsLuo, X. / Sanford, D.G. / Bullock, P.A. / Bachovchin, W.W.
CitationJournal: Nat.Struct.Biol. / Year: 1996
Title: Solution structure of the origin DNA-binding domain of SV40 T-antigen.
Authors: Luo, X. / Sanford, D.G. / Bullock, P.A. / Bachovchin, W.W.
History
DepositionNov 4, 1996Processing site: BNL
Revision 1.0Mar 12, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Structure summary
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / struct_keywords
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_keywords.text

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SV40 T-ANTIGEN


Theoretical massNumber of molelcules
Total (without water)15,4151
Polymers15,4151
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / 30TO BE GIVEN
Representative

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Components

#1: Protein SV40 T-ANTIGEN


Mass: 15414.633 Da / Num. of mol.: 1 / Fragment: DNA BINDING DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Simian virus 40 / Genus: PolyomavirusPolyomaviridae / Cell line: BL21 / Production host: Escherichia coli (E. coli) / References: UniProt: P03070

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
121TOCSY
131HNCA
141HN(CO)CA
151(H)CCH-TOCSY
NMR detailsText: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR SPECTROSCOPY ON 13C, 15N LABELED SV40 T-ANTIGEN DNA BINDING DOMAIN.

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Sample preparation

Sample conditionspH: 5.5 / Temperature: 303 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Bruker AMX500 / Manufacturer: Bruker / Model: AMX500 / Field strength: 500 MHz

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
NMR software
NameVersionDeveloperClassification
X-PLORBRUNGERrefinement
BIOSYM FELIXFELIXstructure solution
RefinementMethod: simulated annealing / Software ordinal: 1
NMR ensembleConformer selection criteria: TO BE GIVEN / Conformers calculated total number: 30 / Conformers submitted total number: 1

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