[English] 日本語
Yorodumi
- PDB-1xna: NMR SOLUTION STRUCTURE OF THE SINGLE-STRAND BREAK REPAIR PROTEIN ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1xna
TitleNMR SOLUTION STRUCTURE OF THE SINGLE-STRAND BREAK REPAIR PROTEIN XRCC1-N-TERMINAL DOMAIN
ComponentsPROTEIN (DNA-REPAIR PROTEIN XRCC1)
KeywordsDNA BINDING PROTEIN / XRCC1 / 3D NMR / DNA REPAIR / SINGLE-STRAND BREAK DNA BINDING / DNA POLYMERASE-BETA BINDING / BETA SANDWICH
Function / homology
Function and homology information


3' overhang single-stranded DNA endodeoxyribonuclease activity / oxidized DNA binding / telomeric DNA-containing double minutes formation / ERCC4-ERCC1 complex / negative regulation of protection from non-homologous end joining at telomere / ADP-D-ribose modification-dependent protein binding / negative regulation of protein ADP-ribosylation / poly-ADP-D-ribose binding / regulation of base-excision repair / single strand break repair ...3' overhang single-stranded DNA endodeoxyribonuclease activity / oxidized DNA binding / telomeric DNA-containing double minutes formation / ERCC4-ERCC1 complex / negative regulation of protection from non-homologous end joining at telomere / ADP-D-ribose modification-dependent protein binding / negative regulation of protein ADP-ribosylation / poly-ADP-D-ribose binding / regulation of base-excision repair / single strand break repair / HDR through MMEJ (alt-NHEJ) / response to hydroperoxide / Resolution of AP sites via the single-nucleotide replacement pathway / APEX1-Independent Resolution of AP Sites via the Single Nucleotide Replacement Pathway / site of DNA damage / Gap-filling DNA repair synthesis and ligation in GG-NER / hippocampus development / base-excision repair / double-strand break repair via nonhomologous end joining / Gap-filling DNA repair synthesis and ligation in TC-NER / double-strand break repair / chromosome, telomeric region / chromatin / nucleolus / enzyme binding / nucleoplasm / nucleus
Similarity search - Function
DNA-repair protein Xrcc1, N-terminal / XRCC1, first (central) BRCT domain / XRCC1 N terminal domain / BRCT domain / BRCA1 C Terminus (BRCT) domain / breast cancer carboxy-terminal domain / Galactose-binding domain-like / BRCT domain profile. / BRCT domain / BRCT domain superfamily ...DNA-repair protein Xrcc1, N-terminal / XRCC1, first (central) BRCT domain / XRCC1 N terminal domain / BRCT domain / BRCA1 C Terminus (BRCT) domain / breast cancer carboxy-terminal domain / Galactose-binding domain-like / BRCT domain profile. / BRCT domain / BRCT domain superfamily / Galactose-binding-like domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
DNA repair protein XRCC1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsMarintchev, A. / Mullen, G.P.
CitationJournal: Nat.Struct.Biol. / Year: 1999
Title: Solution structure of the single-strand break repair protein XRCC1 N-terminal domain.
Authors: Marintchev, A. / Mullen, M.A. / Maciejewski, M.W. / Pan, B. / Gryk, M.R. / Mullen, G.P.
History
DepositionFeb 27, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Sep 1, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PROTEIN (DNA-REPAIR PROTEIN XRCC1)


Theoretical massNumber of molelcules
Total (without water)20,2461
Polymers20,2461
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)1 / -MINIMIZED AVERAGE STRUCTURE OF 23 CONFORMERS
Representative

-
Components

#1: Protein PROTEIN (DNA-REPAIR PROTEIN XRCC1) / XRCC1-NTD


Mass: 20245.672 Da / Num. of mol.: 1
Fragment: N-TERMINAL DOMAIN, RESIDUES 1-183. RESIDUES 152-183 ARE DISORDERED AND NOT SHOWN.
Mutation: D179E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cellular location: NUCLEUS / Gene: XRCC1 / Plasmid: PET23A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21[DE3]PLYSS / References: UniProt: P18887

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D HN(CA)CB
121CBCA(CO)NH
131HNCA
141HN(CO)CA
15115N-EDITED TOCSY
161HCC(CO)NH
171CC(CO)NH
181(H)CCH TOCSY
191HNCO
1101HNHA
1111HNHB
11212D (HB)CB(CGCD)HD
11311H-15N-HSQC
11411H-13C-HSQC
11511H-TOCSY
1161AROMATIC 1H-13C-HSQC
1171HMQC-J
11813D 15N-NOESY
11913D 13C-NOESY
NMR detailsText: THE STRUCTURE WAS DETERMINED USING TRIPLE-AND DOUBLE-RESONANCE NMR SPECTROSCOPY ON 13C-, 15N-LABELED XRCC1-N-TERMINAL DOMAIN

-
Sample preparation

DetailsContents: H2O AND D2O
Sample conditionsIonic strength: 0.4 / pH: 6.8 / Pressure: 1 atm / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

-
Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.851BRUNGERrefinement
DYANA1.5structure solution
RefinementMethod: torsion angle dynamics / Software ordinal: 1
Details: REFINEMENT DETAILS CAN BE FOUND IN THE JOURNAL CITATION ABOVE.
NMR ensembleConformer selection criteria: MINIMIZED AVERAGE STRUCTURE OF 23 CONFORMERS
Conformers submitted total number: 1

+
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://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