[English] 日本語
Yorodumi
- EMDB-23515: XLF, XRCC4 and LigIV BRCT in NHEJ Short-range synaptic complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-23515
TitleXLF, XRCC4 and LigIV BRCT in NHEJ Short-range synaptic complex
Map dataXLF, XRCC4 and LigIV BRCT in NHEJ Short-range synaptic complex
Sample
  • Complex: XLF, XRCC4 and LigIV BRCT in NHEJ Short-range synaptic complex
    • Protein or peptide: XRCC4_HUMAN DNA repair protein XRCC4
    • Protein or peptide: NHEJ1_HUMAN Non-homologous end-joining factor 1
    • Protein or peptide: DNLI4_HUMAN DNA ligase 4
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.8 Å
AuthorsHe Y / Chen S
Funding support United States, 6 items
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)5T32GM008382 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U24GM129547 United States
American Cancer SocietyIRG-15-173-2 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)P01CA092584 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM047251 United States
CitationJournal: Nature / Year: 2021
Title: Structural basis of long-range to short-range synaptic transition in NHEJ.
Authors: Siyu Chen / Linda Lee / Tasmin Naila / Susan Fishbain / Annie Wang / Alan E Tomkinson / Susan P Lees-Miller / Yuan He /
Abstract: DNA double-strand breaks (DSBs) are a highly cytotoxic form of DNA damage and the incorrect repair of DSBs is linked to carcinogenesis. The conserved error-prone non-homologous end joining (NHEJ) ...DNA double-strand breaks (DSBs) are a highly cytotoxic form of DNA damage and the incorrect repair of DSBs is linked to carcinogenesis. The conserved error-prone non-homologous end joining (NHEJ) pathway has a key role in determining the effects of DSB-inducing agents that are used to treat cancer as well as the generation of the diversity in antibodies and T cell receptors. Here we applied single-particle cryo-electron microscopy to visualize two key DNA-protein complexes that are formed by human NHEJ factors. The Ku70/80 heterodimer (Ku), the catalytic subunit of the DNA-dependent protein kinase (DNA-PKcs), DNA ligase IV (LigIV), XRCC4 and XLF form a long-range synaptic complex, in which the DNA ends are held approximately 115 Å apart. Two DNA end-bound subcomplexes comprising Ku and DNA-PKcs are linked by interactions between the DNA-PKcs subunits and a scaffold comprising LigIV, XRCC4, XLF, XRCC4 and LigIV. The relative orientation of the DNA-PKcs molecules suggests a mechanism for autophosphorylation in trans, which leads to the dissociation of DNA-PKcs and the transition into the short-range synaptic complex. Within this complex, the Ku-bound DNA ends are aligned for processing and ligation by the XLF-anchored scaffold, and a single catalytic domain of LigIV is stably associated with a nick between the two Ku molecules, which suggests that the joining of both strands of a DSB involves both LigIV molecules.
History
DepositionFeb 19, 2021-
Header (metadata) releaseMay 5, 2021-
Map releaseMay 5, 2021-
UpdateMay 26, 2021-
Current statusMay 26, 2021Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.03
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.03
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

-
Map

FileDownload / File: emd_23515.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationXLF, XRCC4 and LigIV BRCT in NHEJ Short-range synaptic complex
Voxel sizeX=Y=Z: 1.66 Å
Density
Contour LevelBy AUTHOR: 0.03 / Movie #1: 0.03
Minimum - Maximum-0.0066529918 - 1.1769043
Average (Standard dev.)0.00094034005 (±0.015895981)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-96-96-96
Dimensions192192192
Spacing192192192
CellA=B=C: 318.72 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.661.661.66
M x/y/z192192192
origin x/y/z0.0000.0000.000
length x/y/z318.720318.720318.720
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ360360360
MAP C/R/S123
start NC/NR/NS-96-96-96
NC/NR/NS192192192
D min/max/mean-0.0071.1770.001

-
Supplemental data

-
Sample components

-
Entire : XLF, XRCC4 and LigIV BRCT in NHEJ Short-range synaptic complex

EntireName: XLF, XRCC4 and LigIV BRCT in NHEJ Short-range synaptic complex
Components
  • Complex: XLF, XRCC4 and LigIV BRCT in NHEJ Short-range synaptic complex
    • Protein or peptide: XRCC4_HUMAN DNA repair protein XRCC4
    • Protein or peptide: NHEJ1_HUMAN Non-homologous end-joining factor 1
    • Protein or peptide: DNLI4_HUMAN DNA ligase 4

-
Supramolecule #1: XLF, XRCC4 and LigIV BRCT in NHEJ Short-range synaptic complex

SupramoleculeName: XLF, XRCC4 and LigIV BRCT in NHEJ Short-range synaptic complex
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: XLF-XRCC4-LigIV BRCT
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 280 KDa

-
Macromolecule #1: XRCC4_HUMAN DNA repair protein XRCC4

MacromoleculeName: XRCC4_HUMAN DNA repair protein XRCC4 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: unidentified baculovirus
SequenceString: MERKISRIHL VSEPSITHFL QVSWEKTLES GFVITLTDGH SAWTGTVSES EISQEADDMA MEKGKYVGEL RKALLSGAGP ADVYTFNFSK ESCYFFFEKN LKDVSFRLGS FNLEKVENPA EVIRELICYC LDTIAENQAK NEHLQKENER LLRDWNDVQG RFEKCVSAKE ...String:
MERKISRIHL VSEPSITHFL QVSWEKTLES GFVITLTDGH SAWTGTVSES EISQEADDMA MEKGKYVGEL RKALLSGAGP ADVYTFNFSK ESCYFFFEKN LKDVSFRLGS FNLEKVENPA EVIRELICYC LDTIAENQAK NEHLQKENER LLRDWNDVQG RFEKCVSAKE ALETDLYKRF ILVLNEKKTK IRSLHNKLLN AAQEREKDIK QEGETAICSE MTADRDPVYD ESTDEESENQ TDLSGLASAA VSKDDSIISS LDVTDIAPSR KRRQRMQRNL GTEPKMAPQE NQLQEKENSR PDSSLPETSK KEHISAENMS LETLRNSSPE DLFDEI

-
Macromolecule #2: NHEJ1_HUMAN Non-homologous end-joining factor 1

MacromoleculeName: NHEJ1_HUMAN Non-homologous end-joining factor 1 / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: unidentified baculovirus
SequenceString: MEELEQGLLM QPWAWLQLAE NSLLAKVFIT KQGYALLVSD LQQVWHEQVD TSVVSQRAKE LNKRLTAPPA AFLCHLDNLL RPLLKDAAHP SEATFSCDCV ADALILRVRS ELSGLPFYWN FHCMLASPSL VSQHLIRPLM GMSLALQCQV RELATLLHMK DLEIQDYQES ...String:
MEELEQGLLM QPWAWLQLAE NSLLAKVFIT KQGYALLVSD LQQVWHEQVD TSVVSQRAKE LNKRLTAPPA AFLCHLDNLL RPLLKDAAHP SEATFSCDCV ADALILRVRS ELSGLPFYWN FHCMLASPSL VSQHLIRPLM GMSLALQCQV RELATLLHMK DLEIQDYQES GATLIRDRLK TEPFEENSFL EQFMIEKLPE ACSIGDGKPF VMNLQDLYMA VTTQEVQVGQ KHQGAGDPHT SNSASLQGID SQCVNQPEQL VSSAPTLSAP EKESTGTSGP LQRPQLSKVK RKKPRGLFS

-
Macromolecule #3: DNLI4_HUMAN DNA ligase 4

MacromoleculeName: DNLI4_HUMAN DNA ligase 4 / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: unidentified baculovirus
SequenceString: SNIFEDVEFC VMSGTDSQPK PDLENRIAEF GGYIVQNPGP DTYCVIAGSE NIRVKNIILS NKHDVVKPAW LLECFKTKSF VPWQPRFMIH MCPSTKEHFA REYDCYGDSY FIDTDLNQLK EVFSGIKNSN EQTPEEMASL IADLEYRYSW DCSPLSMFRR HTVYLDSYAV ...String:
SNIFEDVEFC VMSGTDSQPK PDLENRIAEF GGYIVQNPGP DTYCVIAGSE NIRVKNIILS NKHDVVKPAW LLECFKTKSF VPWQPRFMIH MCPSTKEHFA REYDCYGDSY FIDTDLNQLK EVFSGIKNSN EQTPEEMASL IADLEYRYSW DCSPLSMFRR HTVYLDSYAV INDLSTKNEG TRLAIKALEL RFHGAKVVSC LAEGVSHVII GEDHSRVADF KAFRRTFKRK FKILKESWVT DSIDKCELQE ENQYLI

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.9
Component:
ConcentrationNameFormula
10.0 mMHEPES
50.0 mMPotassium chlorideKCl
10.0 mMMagnesium chlorideMgCl2
2.5 %glycerol
1.0 mMDTT
0.05 %NP-40
GridModel: Quantifoil R3.5/1 / Material: COPPER / Mesh: 200 / Support film - Material: GRAPHENE OXIDE / Support film - topology: CONTINUOUS / Support film - Film thickness: 200.0 nm / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: OTHER / Pretreatment - Pressure: 101.325 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: DARK FIELD / Cs: 2.7 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 30000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Digitization - Dimensions - Width: 11520 pixel / Digitization - Dimensions - Height: 8184 pixel / Number grids imaged: 2 / Number real images: 32723 / Average exposure time: 0.0426 sec. / Average electron dose: 46.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Particle selectionNumber selected: 1766936
CTF correctionSoftware: (Name: Gctf, CTFFIND)
Startup modelType of model: INSILICO MODEL
In silico model: Negative staining map reconstructed ab-initio from CryoSPARC
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software: (Name: EMAN, cryoSPARC)
Final 3D classificationNumber classes: 3 / Avg.num./class: 60000 / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 7.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 47575
FSC plot (resolution estimation)

-
Atomic model buiding 1

RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: Correlation coefficient

+
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