[English] 日本語
Yorodumi
- PDB-1ik9: CRYSTAL STRUCTURE OF A XRCC4-DNA LIGASE IV COMPLEX -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1ik9
TitleCRYSTAL STRUCTURE OF A XRCC4-DNA LIGASE IV COMPLEX
Components
  • DNA LIGASE IV
  • DNA REPAIR PROTEIN XRCC4
KeywordsGENE REGULATION/LIGASE / DNA end joining / double-strand break repair / V(D)J recombination / protein-protein complex / coiled coil / GENE REGULATION-LIGASE COMPLEX
Function / homology
Function and homology information


FHA domain binding / positive regulation of chromosome organization / positive regulation of ligase activity / DNA ligase IV complex / DNA ligase activity / DN2 thymocyte differentiation / DNA ligase (ATP) / T cell receptor V(D)J recombination / pro-B cell differentiation / DNA ligase (ATP) activity ...FHA domain binding / positive regulation of chromosome organization / positive regulation of ligase activity / DNA ligase IV complex / DNA ligase activity / DN2 thymocyte differentiation / DNA ligase (ATP) / T cell receptor V(D)J recombination / pro-B cell differentiation / DNA ligase (ATP) activity / DNA-dependent protein kinase-DNA ligase 4 complex / immunoglobulin V(D)J recombination / nonhomologous end joining complex / nucleotide-excision repair, DNA gap filling / single strand break repair / V(D)J recombination / double-strand break repair via classical nonhomologous end joining / isotype switching / protein localization to site of double-strand break / positive regulation of neurogenesis / DNA biosynthetic process / cellular response to lithium ion / 2-LTR circle formation / ligase activity / somatic stem cell population maintenance / response to X-ray / chromosome organization / SUMOylation of DNA damage response and repair proteins / condensed chromosome / neurogenesis / central nervous system development / stem cell proliferation / response to gamma radiation / cellular response to ionizing radiation / Nonhomologous End-Joining (NHEJ) / base-excision repair / double-strand break repair via nonhomologous end joining / establishment of integrated proviral latency / positive regulation of fibroblast proliferation / T cell differentiation in thymus / double-strand break repair / site of double-strand break / fibroblast proliferation / neuron apoptotic process / in utero embryonic development / negative regulation of neuron apoptotic process / chromosome, telomeric region / cell population proliferation / cell division / intracellular membrane-bounded organelle / enzyme binding / magnesium ion binding / DNA binding / nucleoplasm / ATP binding / identical protein binding / nucleus / cytosol
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #370 / DNA double-strand break repair and VJ recombination XRCC4, N-terminal / Dna Repair Protein Xrcc4; Chain: A, domain 1 / DNA ligase IV domain / DNA ligase IV / DNA ligase 4 / DNA Ligase 4, adenylation domain / XRCC4, N-terminal domain superfamily / DNA repair protein XRCC4 / : ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #370 / DNA double-strand break repair and VJ recombination XRCC4, N-terminal / Dna Repair Protein Xrcc4; Chain: A, domain 1 / DNA ligase IV domain / DNA ligase IV / DNA ligase 4 / DNA Ligase 4, adenylation domain / XRCC4, N-terminal domain superfamily / DNA repair protein XRCC4 / : / : / : / XRCC4 N-terminal domain / XRCC4 coiled-coil / XRCC4 C-terminal region / XRCC4-like, N-terminal domain superfamily / 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 AMP-binding site. / ATP-dependent DNA ligase signature 2. / 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. / DNA ligase, ATP-dependent, central / ATP dependent DNA ligase domain / DNA repair protein XRCC4-like, C-terminal / BRCA1 C Terminus (BRCT) domain / breast cancer carboxy-terminal domain / BRCT domain profile. / BRCT domain / BRCT domain superfamily / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Beta Complex / Nucleic acid-binding, OB-fold / Up-down Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
DNA ligase 4 / DNA repair protein XRCC4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAS / Resolution: 2.3 Å
AuthorsSibanda, B.L. / Critchlow, S.E. / Begun, J. / Pei, X.Y. / Jackson, S.P. / Blundell, T.L. / Pellegrini, L.
CitationJournal: Nat.Struct.Biol. / Year: 2001
Title: Crystal structure of an Xrcc4-DNA ligase IV complex.
Authors: Sibanda, B.L. / Critchlow, S.E. / Begun, J. / Pei, X.Y. / Jackson, S.P. / Blundell, T.L. / Pellegrini, L.
History
DepositionMay 3, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 21, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNA REPAIR PROTEIN XRCC4
B: DNA REPAIR PROTEIN XRCC4
C: DNA LIGASE IV


Theoretical massNumber of molelcules
Total (without water)53,2573
Polymers53,2573
Non-polymers00
Water4,035224
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7300 Å2
ΔGint-58 kcal/mol
Surface area25000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.062, 79.628, 242.142
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein DNA REPAIR PROTEIN XRCC4


Mass: 24466.619 Da / Num. of mol.: 2 / Fragment: XRCC4 FRAGMENT, RESIDUES 1-213 / Mutation: C93A,C128A,C130A,C165A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: XRCC4 / Plasmid: pET15a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q13426
#2: Protein/peptide DNA LIGASE IV / POLYDEOXYRIBONUCLEOTIDE SYNTHASE


Mass: 4323.684 Da / Num. of mol.: 1 / Fragment: LINKER CONNECTING BRCT DOMAINS, RESIDUES 748-784
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LIG4 / Plasmid: pTYB3 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P49917, DNA ligase (ATP)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 224 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 4.3 Å3/Da / Density % sol: 71.5 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6
Details: PEG6000, MES, xylitol, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
Details: used seeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
10.050 mMprotein1drop
210 mMTris-HCl1droppH8.0
3150 mM1dropNaCl
41.5 %(w/v)PEG60001drop
50.05 MMES1droppH6.0
71.5 %(w/v)xylitol precipitant solution1drop
86 %(w/v)PEG60001reservoir
90.1 MMES1reservoirpH6.0

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 8, 2001 / Details: mirrors
RadiationMonochromator: 111/311 Si crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.3→33.26 Å / Num. all: 34224 / Num. obs: 34224 / % possible obs: 85.5 % / Observed criterion σ(I): 0 / Redundancy: 2.1 % / Biso Wilson estimate: 56.1 Å2 / Rmerge(I) obs: 0.051 / Rsym value: 0.051 / Net I/σ(I): 17.9
Reflection shellResolution: 2.3→2.35 Å / Rmerge(I) obs: 0.229 / Mean I/σ(I) obs: 2.3 / Num. unique all: 795 / Rsym value: 0.229 / % possible all: 44.4
Reflection
*PLUS
Num. measured all: 72477
Reflection shell
*PLUS
% possible obs: 44.4 %

-
Processing

Software
NameVersionClassification
SHARPphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: SAS / Resolution: 2.3→33.26 Å / Isotropic thermal model: overall anisotropic B value / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.266 1723 -random
Rwork0.228 ---
all-34084 --
obs-34084 85.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 54.1307 Å2 / ksol: 0.340363 e/Å3
Displacement parametersBiso mean: 70.4 Å2
Baniso -1Baniso -2Baniso -3
1-35.06 Å2-12.72 Å222.34 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.38 Å
Luzzati d res low-5 Å
Luzzati sigma a0.63 Å0.68 Å
Refinement stepCycle: LAST / Resolution: 2.3→33.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3512 0 0 224 3736
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d21.3
X-RAY DIFFRACTIONc_improper_angle_d0.45
X-RAY DIFFRACTIONc_mcbond_it3.6
X-RAY DIFFRACTIONc_scbond_it6.41
LS refinement shellResolution: 2.3→2.38 Å / Rfactor Rfree error: 0.048
RfactorNum. reflection% reflection
Rfree0.467 95 -
Rwork0.466 --
obs-1980 50.4 %
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / Rfactor obs: 0.228
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 70.4 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.45
X-RAY DIFFRACTIONc_mcbond_it3.6
X-RAY DIFFRACTIONc_scbond_it6.41
LS refinement shell
*PLUS
Rfactor Rfree: 0.467 / Rfactor Rwork: 0.466

+
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