[English] 日本語
Yorodumi
- PDB-6erg: Complex of XLF and heterodimer Ku bound to DNA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6erg
TitleComplex of XLF and heterodimer Ku bound to DNA
Components
  • (X-ray repair cross-complementing protein ...) x 2
  • DNA (21-MER)
  • DNA (34-MER)
  • Non-homologous end-joining factor 1
KeywordsDNA BINDING PROTEIN / DNA repair complex NHEJ
Function / homology
Function and homology information


positive regulation of ligase activity / DNA ligase IV complex / DNA ligation involved in DNA repair / 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 ...positive regulation of ligase activity / DNA ligase IV complex / DNA ligation involved in DNA repair / 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 / cellular response to X-ray / immunoglobulin V(D)J recombination / nonhomologous end joining complex / DNA ligation / nuclear telomere cap complex / regulation of smooth muscle cell proliferation / Cytosolic sensors of pathogen-associated DNA / double-strand break repair via classical nonhomologous end joining / IRF3-mediated induction of type I IFN / recombinational repair / regulation of telomere maintenance / U3 snoRNA binding / positive regulation of neurogenesis / protein localization to chromosome, telomeric region / cellular response to fatty acid / hematopoietic stem cell proliferation / cellular hyperosmotic salinity response / response to ionizing radiation / telomeric DNA binding / positive regulation of catalytic activity / 2-LTR circle formation / site of DNA damage / Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases / enzyme activator activity / 5'-deoxyribose-5-phosphate lyase activity / T cell differentiation / hematopoietic stem cell differentiation / positive regulation of protein kinase activity / ATP-dependent activity, acting on DNA / DNA polymerase binding / positive regulation of telomerase activity / positive regulation of telomere maintenance via telomerase / DNA helicase activity / telomere maintenance / activation of innate immune response / cellular response to leukemia inhibitory factor / small-subunit processome / neurogenesis / cyclin binding / B cell differentiation / central nervous system development / protein-DNA complex / Nonhomologous End-Joining (NHEJ) / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / cellular response to gamma radiation / fibrillar center / double-strand break repair via nonhomologous end joining / double-strand break repair / site of double-strand break / double-stranded DNA binding / scaffold protein binding / secretory granule lumen / DNA recombination / ficolin-1-rich granule lumen / transcription regulator complex / damaged DNA binding / chromosome, telomeric region / transcription cis-regulatory region binding / response to xenobiotic stimulus / ribonucleoprotein complex / innate immune response / negative regulation of DNA-templated transcription / DNA damage response / ubiquitin protein ligase binding / Neutrophil degranulation / protein-containing complex binding / nucleolus / positive regulation of DNA-templated transcription / ATP hydrolysis activity / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / RNA binding / extracellular region / nucleoplasm / ATP binding / membrane / nucleus / plasma membrane / cytosol
Similarity search - Function
Ku70; Chain: A; domain 4 / Ku70; Chain: A; domain 4 - #10 / Ku70, bridge and pillars / Ku70, bridge and pillars / Ku70; Chain: A; Domain 2 - #10 / Ku70; Chain: A; Domain 2 / XLF, N-terminal / XLF-Cernunnos, XRcc4-like factor, NHEJ component / XRCC4-like, N-terminal domain superfamily / Ku70, bridge and pillars domain superfamily ...Ku70; Chain: A; domain 4 / Ku70; Chain: A; domain 4 - #10 / Ku70, bridge and pillars / Ku70, bridge and pillars / Ku70; Chain: A; Domain 2 - #10 / Ku70; Chain: A; Domain 2 / XLF, N-terminal / XLF-Cernunnos, XRcc4-like factor, NHEJ component / XRCC4-like, N-terminal domain superfamily / 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, N-terminal alpha/beta / Ku70/Ku80 beta-barrel domain / Ku70/Ku80 C-terminal arm / Ku70/Ku80 N-terminal alpha/beta 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 domain / SAP motif profile. / 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 / Non-homologous end-joining factor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.9 Å
AuthorsNemoz, C. / Legrand, P. / Ropars, V. / Charbonnier, J.B.
Funding support France, 2items
OrganizationGrant numberCountry
INCAPLBIO 2012-280 France
French National Research AgencyANR-12-SVSE8-012 France
CitationJournal: Nat. Struct. Mol. Biol. / Year: 2018
Title: XLF and APLF bind Ku80 at two remote sites to ensure DNA repair by non-homologous end joining.
Authors: Nemoz, C. / Ropars, V. / Frit, P. / Gontier, A. / Drevet, P. / Yu, J. / Guerois, R. / Pitois, A. / Comte, A. / Delteil, C. / Barboule, N. / Legrand, P. / Baconnais, S. / Yin, Y. / Tadi, S. / ...Authors: Nemoz, C. / Ropars, V. / Frit, P. / Gontier, A. / Drevet, P. / Yu, J. / Guerois, R. / Pitois, A. / Comte, A. / Delteil, C. / Barboule, N. / Legrand, P. / Baconnais, S. / Yin, Y. / Tadi, S. / Barbet-Massin, E. / Berger, I. / Le Cam, E. / Modesti, M. / Rothenberg, E. / Calsou, P. / Charbonnier, J.B.
History
DepositionOct 18, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 17, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2019Group: Data collection / Source and taxonomy / Category: entity_src_gen / pdbx_seq_map_depositor_info
Item: _entity_src_gen.pdbx_host_org_cell_line / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.2Jan 17, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_residues
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: X-ray repair cross-complementing protein 6
B: X-ray repair cross-complementing protein 5
C: Non-homologous end-joining factor 1
D: X-ray repair cross-complementing protein 6
E: X-ray repair cross-complementing protein 5
F: Non-homologous end-joining factor 1
H: DNA (21-MER)
K: DNA (21-MER)
M: DNA (34-MER)
R: DNA (34-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)292,99913
Polymers292,71010
Non-polymers2883
Water36020
1
A: X-ray repair cross-complementing protein 6
B: X-ray repair cross-complementing protein 5
F: Non-homologous end-joining factor 1
H: DNA (21-MER)
R: DNA (34-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,4516
Polymers146,3555
Non-polymers961
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27130 Å2
ΔGint-173 kcal/mol
Surface area55170 Å2
MethodPISA
2
C: Non-homologous end-joining factor 1
D: X-ray repair cross-complementing protein 6
E: X-ray repair cross-complementing protein 5
K: DNA (21-MER)
M: DNA (34-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,5477
Polymers146,3555
Non-polymers1922
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27680 Å2
ΔGint-182 kcal/mol
Surface area55470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.710, 114.260, 127.170
Angle α, β, γ (deg.)90.000, 93.140, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

-
X-ray repair cross-complementing protein ... , 2 types, 4 molecules ADBE

#1: Protein X-ray repair cross-complementing protein 6 / 5'-deoxyribose-5-phosphate lyase Ku70 / 5'-dRP lyase Ku70 / 70 kDa subunit of Ku antigen / ATP- ...5'-deoxyribose-5-phosphate lyase Ku70 / 5'-dRP lyase Ku70 / 70 kDa subunit of Ku antigen / ATP-dependent DNA helicase 2 subunit 1 / ATP-dependent DNA helicase II 70 kDa subunit / CTC box-binding factor 75 kDa subunit / CTCBF / DNA repair protein XRCC6 / Lupus Ku autoantigen protein p70 / Ku70 / Thyroid-lupus autoantigen / TLAA / X-ray repair complementing defective repair in Chinese hamster cells 6


Mass: 62629.629 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: XRCC6, G22P1 / Cell line (production host): Sf21 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P12956, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement, Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases
#2: Protein X-ray repair cross-complementing protein 5 / 86 kDa subunit of Ku antigen / ATP-dependent DNA helicase 2 subunit 2 / ATP-dependent DNA helicase ...86 kDa subunit of Ku antigen / ATP-dependent DNA helicase 2 subunit 2 / ATP-dependent DNA helicase II 80 kDa subunit / CTC box-binding factor 85 kDa subunit / CTCBF / DNA repair protein XRCC5 / Ku80 / Ku86 / Lupus Ku autoantigen protein p86 / Nuclear factor IV / Thyroid-lupus autoantigen / TLAA / X-ray repair complementing defective repair in Chinese hamster cells 5 (double-strand-break rejoining)


Mass: 65356.836 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: XRCC5, G22P2 / Cell line (production host): Sf21 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P13010, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement

-
Protein/peptide , 1 types, 2 molecules CF

#3: Protein/peptide Non-homologous end-joining factor 1 / Protein cernunnos / XRCC4-like factor


Mass: 1536.907 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9H9Q4

-
DNA chain , 2 types, 4 molecules HKMR

#4: DNA chain DNA (21-MER)


Mass: 6506.188 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Synthetic construct (others)
#5: DNA chain DNA (34-MER)


Mass: 10325.685 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Synthetic construct (others)

-
Non-polymers , 2 types, 23 molecules

#6: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 20 / 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: 2.75 Å3/Da / Density % sol: 55.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 18% PEG 3350, 150 mM Na sulfate , 100 mM Bis-Tris-Propane

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98009 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 11, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98009 Å / Relative weight: 1
ReflectionResolution: 2.9→48.76 Å / Num. obs: 51644 / % possible obs: 72.9 % / Redundancy: 14 % / Biso Wilson estimate: 106.46 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.171 / Rpim(I) all: 0.068 / Rrim(I) all: 0.182 / Net I/σ(I): 9.7
Reflection shellResolution: 2.9→3.09 Å / Redundancy: 14.2 % / Rmerge(I) obs: 2.48 / Mean I/σ(I) obs: 1 / CC1/2: 0.51 / Rpim(I) all: 0.94 / Rrim(I) all: 2.56 / % possible all: 21

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
XSCALEdata scaling
Cootmodel building
BUSTER2.10.3refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1JEY

1jey


Resolution: 2.9→48.76 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.916 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.458
RfactorNum. reflection% reflectionSelection details
Rfree0.244 2605 5.04 %RANDOM
Rwork0.218 ---
obs0.22 51644 72.9 %-
Displacement parametersBiso max: 225.95 Å2 / Biso mean: 100.04 Å2 / Biso min: 28.61 Å2
Baniso -1Baniso -2Baniso -3
1--1.9913 Å20 Å23.0498 Å2
2--1.6561 Å20 Å2
3---0.3352 Å2
Refine analyzeLuzzati coordinate error obs: 0.47 Å
Refinement stepCycle: final / Resolution: 2.9→48.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16821 2133 0 20 18974
Biso mean---51.16 -
Num. residues----2190
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d6746SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes2986HARMONIC5
X-RAY DIFFRACTIONt_it19574HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion2530SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact20557SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d19574HARMONIC20.007
X-RAY DIFFRACTIONt_angle_deg26846HARMONIC20.94
X-RAY DIFFRACTIONt_omega_torsion2.17
X-RAY DIFFRACTIONt_other_torsion18.24
LS refinement shellResolution: 2.9→2.98 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3179 34 5.53 %
Rwork0.3136 581 -
all0.3138 615 -
obs--11.8 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.6133-0.56181.43430.2345-0.19721.097-0.07290.01630.62240.0191-0.0544-0.003-0.1224-0.12010.1273-0.0210.03480.0184-0.0317-0.15710.006438.9878-6.237153.2216
24.29110.8380.38970.43710.09531.1302-0.0576-0.51310.1009-0.0116-0.0061-0.0427-0.07710.09310.0637-0.03-0.00940.0543-0.342-0.0452-0.1068-6.1283-8.2204211.1613
36.41030.1556-1.77392.7085-0.32756.08820.01290.3805-0.2364-0.50590.05170.57180.67180.1087-0.06460.07460.0676-0.12080.28710.03920.039446.0657-18.3926137.5107
43.6443-0.7985-2.91912.7020.54357.5174-0.018-0.6442-0.24770.5680.0064-0.57910.653-0.21630.01170.1348-0.1739-0.10760.3231-0.00130.0985-13.8995-19.597227.2849
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* B|* F|* }A34 - 534
2X-RAY DIFFRACTION1{ A|* B|* F|* }B-16 - 542
3X-RAY DIFFRACTION1{ A|* B|* F|* }F293 - 299
4X-RAY DIFFRACTION2{ D|* E|* C|* }D32 - 534
5X-RAY DIFFRACTION2{ D|* E|* C|* }E-16 - 543
6X-RAY DIFFRACTION2{ D|* E|* C|* }C293 - 299
7X-RAY DIFFRACTION3{ H|* R|* }H1 - 21
8X-RAY DIFFRACTION3{ H|* R|* }R1 - 34
9X-RAY DIFFRACTION4{ K|* M|* }K1 - 21
10X-RAY DIFFRACTION4{ K|* M|* }M1 - 34

+
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