[English] 日本語
Yorodumi
- PDB-1jey: Crystal Structure of the Ku heterodimer bound to DNA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1jey
TitleCrystal Structure of the Ku heterodimer bound to DNA
Components
  • DNA (34-MER)
  • DNA (5'-D(*GP*TP*TP*TP*TP*TP*AP*GP*TP*TP*TP*AP*TP*TP*GP*GP*GP*CP*GP*CP*G)-3')
  • Ku70
  • Ku80
KeywordsDNA BINDING PROTEIN/DNA / double-strand DNA break repair / non-homologous end-joining / protein-nucleic acid complex / alpha/beta domain / beta barrel / helical C-terminal arm / SAP domain / DNA BINDING PROTEIN-DNA COMPLEX
Function / homology
Function and homology information


Ku70:Ku80 complex / negative regulation of t-circle formation / DNA end binding / small-subunit processome assembly / positive regulation of lymphocyte differentiation / DNA-dependent protein kinase complex / DNA-dependent protein kinase-DNA ligase 4 complex / nonhomologous end joining complex / regulation of smooth muscle cell proliferation / cellular response to X-ray ...Ku70:Ku80 complex / negative regulation of t-circle formation / DNA end binding / small-subunit processome assembly / positive regulation of lymphocyte differentiation / DNA-dependent protein kinase complex / DNA-dependent protein kinase-DNA ligase 4 complex / nonhomologous end joining complex / regulation of smooth muscle cell proliferation / cellular response to X-ray / nuclear telomere cap complex / double-strand break repair via classical nonhomologous end joining / Cytosolic sensors of pathogen-associated DNA / IRF3-mediated induction of type I IFN / positive regulation of neurogenesis / recombinational repair / regulation of telomere maintenance / protein localization to chromosome, telomeric region / U3 snoRNA binding / cellular hyperosmotic salinity response / 2-LTR circle formation / telomeric DNA binding / hematopoietic stem cell proliferation / positive regulation of protein kinase activity / Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases / site of DNA damage / 5'-deoxyribose-5-phosphate lyase activity / hematopoietic stem cell differentiation / ATP-dependent activity, acting on DNA / telomere maintenance via telomerase / neurogenesis / telomere maintenance / activation of innate immune response / DNA helicase activity / cyclin binding / cellular response to leukemia inhibitory factor / small-subunit processome / Nonhomologous End-Joining (NHEJ) / enzyme activator activity / cellular response to gamma radiation / protein-DNA complex / double-strand break repair via nonhomologous end joining / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / double-strand break repair / double-stranded DNA binding / scaffold protein binding / secretory granule lumen / DNA recombination / transcription regulator complex / ficolin-1-rich granule lumen / damaged DNA binding / chromosome, telomeric region / transcription cis-regulatory region binding / ribonucleoprotein complex / innate immune response / negative regulation of DNA-templated transcription / DNA damage response / ubiquitin protein ligase binding / Neutrophil degranulation / positive regulation of DNA-templated transcription / protein-containing complex binding / nucleolus / positive regulation of transcription by RNA polymerase II / protein-containing complex / ATP hydrolysis activity / DNA binding / RNA binding / extracellular region / nucleoplasm / ATP binding / nucleus / membrane / plasma membrane / cytosol
Similarity search - Function
Ku70, bridge and pillars / Ku70, bridge and pillars / Ku70; Chain: A; Domain 2 - #10 / Ku70; Chain: A; Domain 2 / Ku70; Chain: A; domain 4 / Ku70; Chain: A; domain 4 - #10 / Ku70, bridge and pillars domain superfamily / : / Ku70 / Ku, C-terminal ...Ku70, bridge and pillars / Ku70, bridge and pillars / Ku70; Chain: A; Domain 2 - #10 / Ku70; Chain: A; Domain 2 / Ku70; Chain: A; domain 4 / Ku70; Chain: A; domain 4 - #10 / Ku70, bridge and pillars domain superfamily / : / Ku70 / Ku, C-terminal / Ku, C-terminal domain superfamily / Ku C terminal domain like / Ku80 / Ku70/Ku80 C-terminal arm / Ku70/Ku80 C-terminal arm / Ku70/Ku80, N-terminal alpha/beta / Ku70/Ku80 N-terminal alpha/beta domain / Ku70/Ku80 beta-barrel domain / Ku70 and Ku80 are 70kDa and 80kDa subunits of the Lupus Ku autoantigen / Ku70/Ku80 beta-barrel domain / SPOC-like, C-terminal domain superfamily / SAP domain superfamily / SAP motif profile. / SAP domain / Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation / SAP domain / von Willebrand factor, type A domain / von Willebrand factor (vWF) type A domain / von Willebrand factor, type A / von Willebrand factor A-like domain superfamily / Few Secondary Structures / Irregular / Beta Barrel / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / X-ray repair cross-complementing protein 6 / X-ray repair cross-complementing protein 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsWalker, J.R. / Corpina, R.A. / Goldberg, J.
CitationJournal: Nature / Year: 2001
Title: Structure of the Ku heterodimer bound to DNA and its implications for double-strand break repair.
Authors: Walker, J.R. / Corpina, R.A. / Goldberg, J.
History
DepositionJun 19, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 10, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2018Group: Experimental preparation / Category: exptl_crystal_grow
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp
Revision 1.4Aug 16, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
C: DNA (5'-D(*GP*TP*TP*TP*TP*TP*AP*GP*TP*TP*TP*AP*TP*TP*GP*GP*GP*CP*GP*CP*G)-3')
D: DNA (34-MER)
A: Ku70
B: Ku80


Theoretical massNumber of molelcules
Total (without water)150,9674
Polymers150,9674
Non-polymers00
Water4,594255
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)83.920, 126.305, 126.436
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: DNA chain DNA (5'-D(*GP*TP*TP*TP*TP*TP*AP*GP*TP*TP*TP*AP*TP*TP*GP*GP*GP*CP*GP*CP*G)-3')


Mass: 6506.188 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain DNA (34-MER)


Mass: 10325.685 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein Ku70 / HOMO SAPIENS THYROID AUTOANTIGEN 70KD


Mass: 69945.039 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: G22P1 / Plasmid: pFASTBAC HT / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P12956
#4: Protein Ku80 / DNA REPAIR PROTEIN XRCC5


Mass: 64190.543 Da / Num. of mol.: 1 / Fragment: residues 1-565
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: XRCC5 / Plasmid: pFASTBAC HT / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P13010
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 255 / 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: 2.23 Å3/Da / Density % sol: 45 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 26% polyethylene glycol 350 monomethyl ether, 50 mM Tris-HCL pH 8.0, 5 mM magnesium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 350 monomethyl ether11
2Tris-HCl11
3MgCl211
Crystal grow
*PLUS
Temperature: 22 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
118 mg/mlprotein1drop
226 %PEG350MME1reservoir
350 mMTris-HCl1reservoirpH8.0
45 mM1reservoirMgCl2

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9A / Wavelength: 0.97921 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 7, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97921 Å / Relative weight: 1
ReflectionResolution: 2.5→25 Å / Num. all: 46460 / Num. obs: 46176 / % possible obs: 96.4 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.1 % / Biso Wilson estimate: 28.2 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 17.5
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.306 / Mean I/σ(I) obs: 3.6 / Num. unique all: 46385 / % possible all: 67.5
Reflection
*PLUS
Highest resolution: 2.5 Å / Num. obs: 46385 / Num. measured all: 141891
Reflection shell
*PLUS
% possible obs: 82.3 % / Rmerge(I) obs: 0.311

-
Processing

Software
NameVersionClassification
AMoREphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1JEQ

1jeq


Resolution: 2.5→24.74 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 2533650.68 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.28 2304 5 %RANDOM
Rwork0.218 ---
all0.22 46176 --
obs0.22 46176 97.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 34.46 Å2 / ksol: 0.36 e/Å3
Displacement parametersBiso mean: 40.1 Å2
Baniso -1Baniso -2Baniso -3
1-5.62 Å20 Å20 Å2
2---3.7 Å20 Å2
3----1.92 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.4 Å0.27 Å
Refinement stepCycle: LAST / Resolution: 2.5→24.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8224 993 0 255 9472
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.8
X-RAY DIFFRACTIONc_improper_angle_d1.24
X-RAY DIFFRACTIONc_mcbond_it1.551.5
X-RAY DIFFRACTIONc_mcangle_it2.652
X-RAY DIFFRACTIONc_scbond_it1.972
X-RAY DIFFRACTIONc_scangle_it2.972.5
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.345 348 4.6 %
Rwork0.261 7271 -
obs--98.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 25 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.218 / Rfactor Rfree: 0.276
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 40.1 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.22
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.24
X-RAY DIFFRACTIONc_mcbond_it1.551.5
X-RAY DIFFRACTIONc_scbond_it1.972
X-RAY DIFFRACTIONc_mcangle_it2.652
X-RAY DIFFRACTIONc_scangle_it2.972.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.345 / % reflection Rfree: 4.6 % / Rfactor Rwork: 0.261

+
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