[English] 日本語
Yorodumi
- PDB-9ox8: NHEJ Short-range complex with Polymerase lambda -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9ox8
TitleNHEJ Short-range complex with Polymerase lambda
Components
  • (DNA (34-MER)) x 2
  • (X-ray repair cross-complementing protein ...) x 2
  • DNA ligase 4
  • DNA polymerase lambda
  • DNA repair protein XRCC4
  • Non-homologous end-joining factor 1
  • Protein PAXX
KeywordsDNA BINDING PROTEIN/DNA / DNA repair / NHEJ / Complex / Polymerase / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


FHA domain binding / positive regulation of chromosome organization / DN2 thymocyte differentiation / positive regulation of ligase activity / DNA ligase IV complex / DNA ligase activity / DNA double-strand break attachment to nuclear envelope / Ku70:Ku80 complex / T cell receptor V(D)J recombination / DNA ligase (ATP) ...FHA domain binding / positive regulation of chromosome organization / DN2 thymocyte differentiation / positive regulation of ligase activity / DNA ligase IV complex / DNA ligase activity / DNA double-strand break attachment to nuclear envelope / Ku70:Ku80 complex / T cell receptor V(D)J recombination / DNA ligase (ATP) / pro-B cell differentiation / negative regulation of t-circle formation / DNA end binding / DNA ligase (ATP) activity / small-subunit processome assembly / positive regulation of lymphocyte differentiation / DNA-dependent protein kinase complex / 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 / regulation of smooth muscle cell proliferation / cellular response to X-ray / double-strand break repair via classical nonhomologous end joining / isotype switching / Cytosolic sensors of pathogen-associated DNA / protein localization to site of double-strand break / nuclear telomere cap complex / IRF3-mediated induction of type I IFN / recombinational repair / regulation of telomere maintenance / protein localization to chromosome, telomeric region / U3 snoRNA binding / positive regulation of neurogenesis / cellular response to lithium ion / cellular hyperosmotic salinity response / 2-LTR circle formation / DNA biosynthetic process / AMP binding / response to ionizing radiation / hematopoietic stem cell proliferation / ligase activity / telomeric repeat DNA binding / Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases / DNA 3'-5' helicase / T cell differentiation / somatic stem cell population maintenance / 5'-deoxyribose-5-phosphate lyase activity / chromosome organization / hematopoietic stem cell differentiation / response to X-ray / ATP-dependent activity, acting on DNA / telomere maintenance via telomerase / somatic hypermutation of immunoglobulin genes / SUMOylation of DNA damage response and repair proteins / site of DNA damage / base-excision repair, gap-filling / condensed chromosome / DNA polymerase binding / activation of innate immune response / neurogenesis / B cell differentiation / telomere maintenance / cyclin binding / stem cell proliferation / DNA-(apurinic or apyrimidinic site) lyase / DNA helicase activity / cellular response to leukemia inhibitory factor / cellular response to ionizing radiation / response to gamma radiation / central nervous system development / nucleotide-excision repair / Nonhomologous End-Joining (NHEJ) / small-subunit processome / protein-DNA complex / cellular response to gamma radiation / establishment of integrated proviral latency / base-excision repair / double-strand break repair via homologous recombination / double-strand break repair via nonhomologous end joining / positive regulation of fibroblast proliferation / fibrillar center / enzyme activator activity / T cell differentiation in thymus / double-strand break repair / site of double-strand break / double-stranded DNA binding / neuron apoptotic process / fibroblast proliferation / scaffold protein binding / DNA recombination / secretory granule lumen / transcription regulator complex / DNA-directed DNA polymerase / molecular adaptor activity / in utero embryonic development / ficolin-1-rich granule lumen / damaged DNA binding
Similarity search - Function
Protein PAXX / : / PAXX, PAralog of XRCC4 and XLF, also called C9orf142 / XLF, N-terminal / : / : / XLF N-terminal domain / XLF protein coiled-coil region / DNA ligase IV domain / DNA ligase IV ...Protein PAXX / : / PAXX, PAralog of XRCC4 and XLF, also called C9orf142 / XLF, N-terminal / : / : / XLF N-terminal domain / XLF protein coiled-coil region / 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 / Ku70, bridge and pillars domain superfamily / : / Ku70 / DNA ligase, ATP-dependent / DNA ligase, ATP-dependent, N-terminal / Ku, C-terminal / Ku, C-terminal domain superfamily / DNA ligase, ATP-dependent, N-terminal domain superfamily / DNA ligase N terminus / 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 / 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 / Ku70/Ku80 beta-barrel domain / Ku70 and Ku80 are 70kDa and 80kDa subunits of the Lupus Ku autoantigen / Ku70/Ku80 beta-barrel domain / ATP-dependent DNA ligase family profile. / SPOC-like, C-terminal domain superfamily / DNA ligase, ATP-dependent, central / ATP dependent DNA ligase domain / SAP domain superfamily / DNA repair protein XRCC4-like, C-terminal / SAP motif profile. / SAP domain / Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation / SAP domain / BRCA1 C Terminus (BRCT) domain / DNA polymerase family X, beta-like / DNA polymerase beta, palm domain / DNA polymerase beta palm / DNA polymerase lambda, fingers domain / Fingers domain of DNA polymerase lambda / DNA-directed DNA polymerase X / DNA polymerase X family / breast cancer carboxy-terminal domain / DNA polymerase family X, binding site / DNA polymerase family X signature. / DNA polymerase beta-like, N-terminal domain / DNA polymerase lambda lyase domain superfamily / Helix-hairpin-helix domain / DNA polymerase family X / DNA polymerase beta, thumb domain / DNA polymerase, thumb domain superfamily / DNA polymerase beta thumb / von Willebrand factor (vWF) type A domain / BRCT domain profile. / BRCT domain / BRCT domain superfamily / von Willebrand factor, type A / Nucleotidyltransferase superfamily / von Willebrand factor A-like domain superfamily / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA repair protein Ku70 / DNA repair protein Ku80 / DNA ligase 4 / DNA repair protein XRCC4 / Protein PAXX / Non-homologous end-joining factor 1 / DNA polymerase lambda
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 7.23 Å
AuthorsVogt, A. / He, Y.
Funding support United States, 7items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM135651 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM144559 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5T32GM008382 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)P01CA092584 United States
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)1ZIC ES102645 United States
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)Z01 ES065070 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R24GM154185 United States
CitationJournal: To Be Published
Title: End Processing in NHEJ by Polymerase lambda and PNKP is coordinated during short-range synapsis
Authors: Vogt, A. / Kaminski, A.M. / Pedersen, L.C. / Naila, T. / Tomkinson, A.E. / Lees-Miller, S.P. / Kunkel, T.A. / He, Y.
History
DepositionJun 3, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2026Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNA ligase 4
B: Non-homologous end-joining factor 1
C: X-ray repair cross-complementing protein 6
D: X-ray repair cross-complementing protein 5
E: DNA polymerase lambda
F: DNA polymerase lambda
G: DNA repair protein XRCC4
H: DNA repair protein XRCC4
I: Non-homologous end-joining factor 1
J: X-ray repair cross-complementing protein 6
K: X-ray repair cross-complementing protein 5
L: DNA (34-MER)
M: DNA (34-MER)
N: DNA (34-MER)
O: DNA repair protein XRCC4
P: DNA repair protein XRCC4
Q: DNA (34-MER)
T: Protein PAXX
U: Protein PAXX
X: DNA ligase 4


Theoretical massNumber of molelcules
Total (without water)944,07020
Polymers944,07020
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

-
Protein , 5 types, 12 molecules AXBIEFGHOPTU

#1: Protein DNA ligase 4 / DNA ligase IV / Polydeoxyribonucleotide synthase [ATP] 4


Mass: 104124.953 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LIG4 / Cell line (production host): HELA / Production host: Homo sapiens (human) / References: UniProt: P49917, DNA ligase (ATP)
#2: Protein Non-homologous end-joining factor 1 / Protein cernunnos / XRCC4-like factor


Mass: 33372.234 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NHEJ1, XLF / Production host: Escherichia coli (E. coli) / References: UniProt: Q9H9Q4
#5: Protein DNA polymerase lambda / Pol Lambda / DNA polymerase beta-2 / Pol beta2 / DNA polymerase kappa


Mass: 63571.238 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: POLL / Production host: Escherichia coli (E. coli)
References: UniProt: Q9UGP5, DNA-directed DNA polymerase, Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases
#6: Protein
DNA repair protein XRCC4 / X-ray repair cross-complementing protein 4


Mass: 38337.703 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: XRCC4 / Cell line (production host): HELA / Production host: Homo sapiens (human) / References: UniProt: Q13426
#9: Protein Protein PAXX / Paralog of XRCC4 and XLF / XRCC4-like small protein


Mass: 21663.498 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PAXX, C9orf142, XLS / Production host: Escherichia coli (E. coli) / References: UniProt: Q9BUH6

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

#3: 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 / CTC75 / 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: 68872.875 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: XRCC6, G22P1 / Production host: unidentified baculovirus
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
#4: Protein X-ray repair cross-complementing protein 5


Mass: 82812.438 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: unidentified baculovirus / References: UniProt: P13010

-
DNA chain , 2 types, 4 molecules LNMQ

#7: DNA chain DNA (34-MER)


Mass: 10567.767 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#8: DNA chain DNA (34-MER)


Mass: 10374.722 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

-
Details

Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: NHEJ Short-range complex with Polymerase lambda / Type: COMPLEX / Entity ID: all / Source: MULTIPLE SOURCES
Molecular weightExperimental value: NO
Buffer solutionpH: 7.9
Buffer component
IDConc.NameFormulaBuffer-ID
150 mMPotassium ChlorideKCl1
210 mMHEPES1
35 percentglycerol1
41 mMDTT1
50.01 percentNP-401
65 mMMagnesium ChlorideMgCl21
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: Sample stabilized by GraFix
Specimen supportGrid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 4000 nm / Nominal defocus min: 1500 nm / Cs: 2.7 mm / Alignment procedure: BASIC
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 3.61 sec. / Electron dose: 66 e/Å2 / Film or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Num. of grids imaged: 1
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 10 eV

-
Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2SerialEM4.1.2image acquisition
4cryoSPARC4.6.2CTF correction
10cryoSPARC4.6.2initial Euler assignment
13cryoSPARC4.6.23D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1506486
3D reconstructionResolution: 7.23 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 179057 / Num. of class averages: 1 / Symmetry type: POINT

+
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