[English] 日本語
Yorodumi
- PDB-1in1: NMR STRUCTURE OF HUMAN DNA LIGASE IIIALPHA BRCT DOMAIN -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1in1
TitleNMR STRUCTURE OF HUMAN DNA LIGASE IIIALPHA BRCT DOMAIN
ComponentsDNA LIGASE III
KeywordsLIGASE / parallel beta sheet
Function / homology
Function and homology information


DNA ligase III-XRCC1 complex / negative regulation of mitochondrial DNA replication / base-excision repair, DNA ligation / DNA ligase activity / DNA ligase (ATP) / DNA ligase (ATP) activity / DNA ligation / HDR through MMEJ (alt-NHEJ) / lagging strand elongation / mitochondrial DNA repair ...DNA ligase III-XRCC1 complex / negative regulation of mitochondrial DNA replication / base-excision repair, DNA ligation / DNA ligase activity / DNA ligase (ATP) / DNA ligase (ATP) activity / DNA ligation / HDR through MMEJ (alt-NHEJ) / lagging strand elongation / mitochondrial DNA repair / Resolution of AP sites via the single-nucleotide replacement pathway / DNA biosynthetic process / double-strand break repair via alternative nonhomologous end joining / APEX1-Independent Resolution of AP Sites via the Single Nucleotide Replacement Pathway / mitochondrion organization / Gap-filling DNA repair synthesis and ligation in GG-NER / base-excision repair, gap-filling / double-strand break repair via homologous recombination / Gap-filling DNA repair synthesis and ligation in TC-NER / double-strand break repair / cell cycle / cell division / mitochondrion / DNA binding / zinc ion binding / nucleoplasm / ATP binding / nucleus
Similarity search - Function
DNA ligase 3, BRCT domain / DNA ligase 3 BRCT domain / DNA ligase, ATP-dependent / DNA ligase, ATP-dependent, N-terminal / DNA ligase, ATP-dependent, N-terminal domain superfamily / DNA ligase N terminus / ATP-dependent DNA ligase signature 2. / ATP-dependent DNA ligase AMP-binding site. / DNA ligase, ATP-dependent, C-terminal / ATP dependent DNA ligase C terminal region ...DNA ligase 3, BRCT domain / DNA ligase 3 BRCT domain / DNA ligase, ATP-dependent / DNA ligase, ATP-dependent, N-terminal / DNA ligase, ATP-dependent, N-terminal domain superfamily / DNA ligase N terminus / ATP-dependent DNA ligase signature 2. / ATP-dependent DNA ligase AMP-binding site. / DNA ligase, ATP-dependent, C-terminal / ATP dependent DNA ligase C terminal region / DNA ligase, ATP-dependent, conserved site / ATP-dependent DNA ligase family profile. / BRCT domain / Zinc finger poly(ADP-ribose) polymerase (PARP)-type signature. / Zinc finger, PARP-type superfamily / Poly(ADP-ribose) polymerase and DNA-Ligase Zn-finger region / Zinc finger poly(ADP-ribose) polymerase (PARP)-type profile. / Poly(ADP-ribose) polymerase and DNA-Ligase Zn-finger region / DNA ligase, ATP-dependent, central / ATP dependent DNA ligase domain / Zinc finger, PARP-type / breast cancer carboxy-terminal domain / BRCT domain profile. / BRCT domain / BRCT domain superfamily / Nucleic acid-binding, OB-fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / distance geometry, simulated annealing, torsion angle dynamics
AuthorsKrishnan, V.V. / Thornton, K.H. / Thelen, M.P. / Cosman, M.
Citation
Journal: Biochemistry / Year: 2001
Title: Solution structure and backbone dynamics of the human DNA ligase IIIalpha BRCT domain
Authors: Krishnan, V.V. / Thornton, K.H. / Thelen, M.P. / Cosman, M.
#1: Journal: Protein Expr.Purif. / Year: 2001
Title: Expression, purification, and biophysical characterization of the BRCT domain of human DNA ligase III alpha
Authors: Cosman, M. / Krishnan, V.V. / Thornton, K.H. / Thelen, M.P.
History
DepositionMay 11, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 25, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / 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 / _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: DNA LIGASE III


Theoretical massNumber of molelcules
Total (without water)9,9851
Polymers9,9851
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 / 299structures with the least restraint violations, target function
RepresentativeModel #1ensemble of 20 structures

-
Components

#1: Protein DNA LIGASE III / E.C.6.5.1.1 / POLYDEOXYRIBONUCLEOTIDE SYNTHASE [ATP]


Mass: 9985.422 Da / Num. of mol.: 1 / Fragment: BRCT DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: BL21(DE3) / Production host: Escherichia coli (E. coli) / References: UniProt: P49916, DNA ligase (ATP)

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1213D 13C-separated NOESY
1313D 15N-separated NOESY
141HNHA
151DQF-COSY
NMR detailsText: The structures were determined using triple-resonance NMR spectroscopy

-
Sample preparation

DetailsContents: 50 mM NaH2PO4, 150 mM NaCl, 25 mM d10-DTT / Solvent system: 90-95% H2O and 10-5% D2O
Sample conditionsIonic strength: 0.4-1.0 mM / pH: 6.6 / Pressure: ambient / Temperature: 288 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
Felix2.3MSI Inc.processing
NMRPipeBax et al.data analysis
DYANA1.5Wuthrich et al.structure solution
DYANA1.5Wuthrich et al.refinement
RefinementMethod: distance geometry, simulated annealing, torsion angle dynamics
Software ordinal: 1
Details: the structures are based on a total of 1072 restraints, 979 NOE-derived distance constraints, 25 dihedral angle restraints, 54 H bond restraints from hydrogen bonds
NMR representativeSelection criteria: ensemble of 20 structures
NMR ensembleConformer selection criteria: structures with the least restraint violations, target function
Conformers calculated total number: 299 / 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://pdbjlvh1.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