[English] 日本語
Yorodumi
- PDB-1z1d: Structural Model for the interaction between RPA32 C-terminal dom... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1z1d
TitleStructural Model for the interaction between RPA32 C-terminal domain and SV40 T antigen origin binding domain.
Components
  • Large T antigen
  • Replication protein A 32 kDa subunit
KeywordsREPLICATION / Winged Helix-turn-Helix motif / Origin binding domain / Protein-Protein Complex
Function / homology
Function and homology information


protein localization to chromosome / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of JAK1 activity / DNA replication factor A complex / regulation of DNA damage checkpoint / bidirectional double-stranded viral DNA replication / Removal of the Flap Intermediate / Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta) / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / Removal of the Flap Intermediate from the C-strand / G-rich strand telomeric DNA binding ...protein localization to chromosome / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of JAK1 activity / DNA replication factor A complex / regulation of DNA damage checkpoint / bidirectional double-stranded viral DNA replication / Removal of the Flap Intermediate / Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta) / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / Removal of the Flap Intermediate from the C-strand / G-rich strand telomeric DNA binding / viral DNA genome replication / DNA 3'-5' helicase / HDR through Single Strand Annealing (SSA) / Impaired BRCA2 binding to RAD51 / regulation of double-strand break repair via homologous recombination / telomeric DNA binding / DNA unwinding involved in DNA replication / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / DNA replication origin binding / Presynaptic phase of homologous DNA pairing and strand exchange / Activation of the pre-replicative complex / Regulation of HSF1-mediated heat shock response / PCNA-Dependent Long Patch Base Excision Repair / HSF1 activation / mismatch repair / Activation of ATR in response to replication stress / mitotic G1 DNA damage checkpoint signaling / telomere maintenance / Translesion synthesis by REV1 / Translesion synthesis by POLK / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / helicase activity / nucleotide-excision repair / Fanconi Anemia Pathway / Recognition of DNA damage by PCNA-containing replication complex / Termination of translesion DNA synthesis / Translesion Synthesis by POLH / double-strand break repair via homologous recombination / base-excision repair / G2/M DNA damage checkpoint / HDR through Homologous Recombination (HRR) / PML body / Dual Incision in GG-NER / Meiotic recombination / Formation of Incision Complex in GG-NER / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / single-stranded DNA binding / Processing of DNA double-strand break ends / double-stranded DNA binding / symbiont-mediated perturbation of host ubiquitin-like protein modification / protein phosphatase binding / DNA replication / Regulation of TP53 Activity through Phosphorylation / damaged DNA binding / chromosome, telomeric region / nuclear body / symbiont-mediated suppression of host innate immune response / hydrolase activity / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / virus-mediated perturbation of host defense response / ubiquitin protein ligase binding / host cell nucleus / chromatin / enzyme binding / nucleoplasm / ATP binding / identical protein binding / nucleus / metal ion binding
Similarity search - Function
Replication factor A protein 2 / Replication protein A, C-terminal / Replication protein A C terminal / Replication Protein E1; Chain: A, - #20 / Large T antigen, polyomaviridae / Replication factor A protein-like / Replication Protein E1; Chain: A, / Large T antigen, polyomavirus, C-terminal / Zinc finger, large T-antigen D1-type / Origin of replication binding protein ...Replication factor A protein 2 / Replication protein A, C-terminal / Replication protein A C terminal / Replication Protein E1; Chain: A, - #20 / Large T antigen, polyomaviridae / Replication factor A protein-like / 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 / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Nucleic acid-binding, OB-fold / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Large T antigen / Replication protein A 32 kDa subunit
Similarity search - Component
Biological speciesHomo sapiens (human)
Simian virus 40
MethodSOLUTION NMR / Rigid body docking, Semi-flexible simulated annealing, Refinement using explicit water
AuthorsArunkumar, A.I. / Klimovich, V. / Jiang, X. / Ott, R.D. / Mizoue, L. / Fanning, E. / Chazin, W.J.
Citation
Journal: Nat.Struct.Mol.Biol. / Year: 2005
Title: Insights into hRPA32 C-terminal domain--mediated assembly of the simian virus 40 replisome.
Authors: Arunkumar, A.I. / Klimovich, V. / Jiang, X. / Ott, R.D. / Mizoue, L. / Fanning, E. / Chazin, W.J.
#1: Journal: Cell(Cambridge,Mass.) / Year: 2000
Title: Structural basis for the recognition of DNA repair proteins UNG2, XPA, and RAD52 by replication factor A
Authors: Mer, G. / Bochkarev, A. / Gupta, R. / Bochkareva, E. / Frappier, L. / Ingles, C.M. / Edwards, A.M. / Chazin, W.J.
#2: Journal: Nat.Struct.Mol.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
DepositionMar 3, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 17, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Replication protein A 32 kDa subunit
B: Large T antigen


Theoretical massNumber of molelcules
Total (without water)26,1102
Polymers26,1102
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with acceptable covalent geometry,structures with favorable non-bond energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein Replication protein A 32 kDa subunit / RP-A / RF-A / Replication factor-A protein 2 / RPA32


Mass: 10999.127 Da / Num. of mol.: 1 / Fragment: RPA32 C-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RPA2, REPA2, RPA32 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P15927
#2: Protein Large T antigen / SV40 T antigen


Mass: 15111.362 Da / Num. of mol.: 1 / Fragment: SV40 T antigen Origin binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Simian virus 40 / Genus: Polyomavirus / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P03070

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 15N-1H HSQC
1222D 15N-1H HSQC
NMR detailsText: This model structure was obtained using ambigous chemical shift pertubation constraints and validated using residual dipolar couplings and point mutations on the interface

-
Sample preparation

Details
Solution-IDContentsSolvent system
10.2mM RPA32C U-15N, 0.6mM Tag-OBD, 20mM Tris buffer pH 7.0, 2 mM DTT, 5mM MgCl2, 90% H2O, 10% D2O90% H2O/10% D2O
20.2mM Tag-OBD U-15N, 0.6mM RPA32C, 20mM Tris buffer pH 7.0, 2mM DTT, 5mM MgCl2, 90% H2O, 10% D2O90% H2O/10% D2O
Sample conditionsIonic strength: 0.03 M / pH: 7 / Pressure: ambient / Temperature: 298 K

-
NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

-
Processing

NMR software
NameVersionDeveloperClassification
UXNMR2.3Bruker softwarecollection
Felix2000Accelrys, Incdata analysis
HADDOCK1.3Bonvin, A.M.structure solution
HADDOCK1.3Bonvin, A.M.refinement
RefinementMethod: Rigid body docking, Semi-flexible simulated annealing, Refinement using explicit water
Software ordinal: 1
Details: 1500 conformers were obtained in the rigid body docking and 200 best conformers were selected for semi-flexible simulated annealing followed by refinement.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with acceptable covalent geometry,structures with favorable non-bond energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

+
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://pdbjlc1.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