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- EMDB-45843: Focused map of XRCC4/Ligase IV complex on the supportive side of ... -

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Basic information

Entry
Database: EMDB / ID: EMD-45843
TitleFocused map of XRCC4/Ligase IV complex on the supportive side of a gap-filling complex with Pol mu engaged in the NHEJ pathway
Map dataFocused map of supportive XRCC4/Ligase IV complex in a gap-filling complex in the NHEJ pathway
Sample
  • Complex: A gap-filling complex with Pol mu engaged
    • Protein or peptide: human XRCC4
    • Protein or peptide: human Ligase IV
KeywordsNHEJ / DNA gap / fill-in synthesis / ligation / XLF / PAXX / Polymerase mu / DNA repair / Ligase IV / DNA BINDING PROTEIN
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsLi J / Liu L / Gellert M / Yang W
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK) United States
CitationJournal: Nature / Year: 2025
Title: Dynamic assemblies and coordinated reactions of non-homologous end joining.
Authors: Lan Liu / Jun Li / Metztli Cisneros-Aguirre / Arianna Merkell / Jeremy M Stark / Martin Gellert / Wei Yang /
Abstract: Non-homologous end joining (NHEJ) is the main repair pathway of double-strand DNA breaks in higher eukaryotes. Here we report reconstitution of the final steps of NHEJ and structures of DNA ...Non-homologous end joining (NHEJ) is the main repair pathway of double-strand DNA breaks in higher eukaryotes. Here we report reconstitution of the final steps of NHEJ and structures of DNA polymerase μ and ligase IV (LIG4) engaged in gap filling and end joining. These reactions take place in a flexible ω-shaped framework composed of XRCC4 and XLF. Two broken DNA ends, each encircled by Ku70-Ku80 internally, are docked onto the ω frame, mediated by LIG4. DNA polymerase and ligase attached to each ω arm repair only one broken strand of a defined polarity; the final steps of NHEJ requires coordination and toggling of a pair of such enzymes. The facilitators XLF and PAXX additively stimulate NHEJ reactions. As DNA-end sensor and protector, LIG4 replaces DNA-PKcs for end joining and bridges the two DNA ends for polymerase to fill remaining gaps. These assemblies present new targets for NHEJ inhibition to enhance efficacy of radiotherapy and accuracy of gene editing.
History
DepositionJul 20, 2024-
Header (metadata) releaseApr 23, 2025-
Map releaseApr 23, 2025-
UpdateNov 5, 2025-
Current statusNov 5, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_45843.png

Downloads & links

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Map

FileDownload / File: emd_45843.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFocused map of supportive XRCC4/Ligase IV complex in a gap-filling complex in the NHEJ pathway
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 512 pix.
= 426.496 Å		0.83 Å/pix.
x 512 pix.
= 426.496 Å		0.83 Å/pix.
x 512 pix.
= 426.496 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.833 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.25
Minimum - Maximum-1.3071779 - 2.4150891
Average (Standard dev.)-0.00044641583 (±0.023113176)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 426.496 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_45843_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half 1 map

Fileemd_45843_half_map_1.map
Annotationhalf 1 map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half 2 map

Fileemd_45843_half_map_2.map
Annotationhalf 2 map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : A gap-filling complex with Pol mu engaged

EntireName: A gap-filling complex with Pol mu engaged
Components
  • Complex: A gap-filling complex with Pol mu engaged
    • Protein or peptide: human XRCC4
    • Protein or peptide: human Ligase IV

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Supramolecule #1: A gap-filling complex with Pol mu engaged

SupramoleculeName: A gap-filling complex with Pol mu engaged / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 967 KDa

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Macromolecule #1: human XRCC4

MacromoleculeName: human XRCC4 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MERKISRIHL VSEPSITHFL QVSWEKTLES GFVITLTDGH SAWTGTVSES EISQEADDMA MEKGKYVGE LRKALLSGAG PADVYTFNFS KESCYFFFEK NLKDVSFRLG SFNLEKVENP A EVIRELIC YCLDTIAENQ AKNEHLQKEN ERLLRDWNDV QGRFEKCVSA ...String:
MERKISRIHL VSEPSITHFL QVSWEKTLES GFVITLTDGH SAWTGTVSES EISQEADDMA MEKGKYVGE LRKALLSGAG PADVYTFNFS KESCYFFFEK NLKDVSFRLG SFNLEKVENP A EVIRELIC YCLDTIAENQ AKNEHLQKEN ERLLRDWNDV QGRFEKCVSA KEALETDLYK RF ILVLNEK KTKIRSLHNK LLNAAQEREK DIKQEGETAI CSEMTADRDP VYDESTDEES ENQ TDLSGL ASAAVSKDDS IISSLDVTDI APSRKRRQRM QRNLGTEPKM APQENQLQEK ENSR PDSSL PETSKKEHIS AENMSLETLR NSSPEDLFDE I

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Macromolecule #2: human Ligase IV

MacromoleculeName: human Ligase IV / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
SequenceString: GPVMAASQTS QTVASHVPFA DLCSTLERIQ KSKGRAEKIR HFREFLDSWR KFHDALHKNH KDV TDSFYP AMRLILPQLE RERMAYGIKE TMLAKLYIEL LNLPRDGKDA LKLLNYRTPT GTHG DAGDF AMIAYFVLKP RCLQKGSLTI QQVNDLLDSI ASNNSAKRKD ...String:
GPVMAASQTS QTVASHVPFA DLCSTLERIQ KSKGRAEKIR HFREFLDSWR KFHDALHKNH KDV TDSFYP AMRLILPQLE RERMAYGIKE TMLAKLYIEL LNLPRDGKDA LKLLNYRTPT GTHG DAGDF AMIAYFVLKP RCLQKGSLTI QQVNDLLDSI ASNNSAKRKD LIKKSLLQLI TQSSA LEQK WLIRMIIKDL KLGVSQQTIF SVFHNDAAEL HNVTTDLEKV CRQLHDPSVG LSDISI TLF SAFKPMLAAI ADIEHIEKDM KHQSFYIETK LDGERMQMHK DGDVYKYFSR NGYNYTD QF GASPTEGSLT PFIHNAFKAD IQICILDGEM MAYNPNTQTF MQKGTKFDIK RMVEDSDL Q TCYCVFDVLM VNNKKLGHET LRKRYEILSS IFTPIPGRIE IVQKTQAHTK NEVIDALNE AIDKREEGIM VKQPLSIYKP DKRGEGWLKI KPEYVSGLMD ELDILIVGGY WGKGSRGGMM SHFLCAVAE KPPPGEKPSV FHTLSRVGSG CTMKELYDLG LKLAKYWKPF HRKAPPSSIL C GTEKPEVY IEPCNSVIVQ IKAAEIVPSD MYKTGCTLRF PRIEKIRDDK EWHECMTLDD LE QLRGKAS GKLASKHLYI GGDDEPQEKK RKAAPKMKKV IGIIEHLKAP NLTNVNKISN IFE DVEFCV MSGTDSQPKP DLENRIAEFG GYIVQNPGPD TYCVIAGSEN IRVKNIILSN KHDV VKPAW LLECFKTKSF VPWQPRFMIH MCPSTKEHFA REYDCYGDSY FIDTDLNQLK EVFSG IKNS NEQTPEEMAS LIADLEYRYS WDCSPLSMFR RHTVYLDSYA VINDLSTKNE GTRLAI KAL ELRFHGAKVV SCLAEGVSHV IIGEDHSRVA DFKAFRRTFK RKFKILKESW VTDSIDK CE LQEENQYLI

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.35 mg/mL
BufferpH: 7.9
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 54.4 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: EMDB MAP
EMDB ID:

23509

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 891208
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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