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- EMDB-45852: Focused map of XRCC4/Ligase IV on the supportive side of the liga... -

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Basic information

Entry
Database: EMDB / ID: EMD-45852
TitleFocused map of XRCC4/Ligase IV on the supportive side of the ligation complex in the NHEJ pathway
Map dataFocused map of the supportive XRCC4/Ligase IV in the ligation complex I
Sample
  • Complex: Ligation complex in the NHEJ pathway
    • Protein or peptide: human XRCC4
    • Protein or peptide: human Ligase IV
KeywordsNHEJ / ligation / XLF / PAXX / DNA repair / Ligase IV / DNA BINDING PROTEIN
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 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 21, 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_45852.png

Downloads & links

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Map

FileDownload / File: emd_45852.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFocused map of the supportive XRCC4/Ligase IV in the ligation complex I
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: 0.18
Minimum - Maximum-0.7330653 - 1.8294219
Average (Standard dev.)-0.0010674548 (±0.018634884)
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_45852_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_45852_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_45852_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 : Ligation complex in the NHEJ pathway

EntireName: Ligation complex in the NHEJ pathway
Components
  • Complex: Ligation complex in the NHEJ pathway
    • Protein or peptide: human XRCC4
    • Protein or peptide: human Ligase IV

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Supramolecule #1: Ligation complex in the NHEJ pathway

SupramoleculeName: Ligation complex in the NHEJ pathway / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 854 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)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GPVMAASQTS QTVASHVPFA DLCSTLERIQ KSKGRAEKIR HFREFLDSWR KFHDALHKNH KDV TDSFYP AMRLILPQLE RERMAYGIKE TMLAKLYIEL LNLPRDGKDA LKLLNYRTPT GTHGDAGDFA MIAYFVLKPR CLQKGSLTIQ QVNDLLDSIA SNNSAKRKDL ...String:
GPVMAASQTS QTVASHVPFA DLCSTLERIQ KSKGRAEKIR HFREFLDSWR KFHDALHKNH KDV TDSFYP AMRLILPQLE RERMAYGIKE TMLAKLYIEL LNLPRDGKDA LKLLNYRTPT GTHGDAGDFA MIAYFVLKPR CLQKGSLTIQ QVNDLLDSIA SNNSAKRKDL IKKSLLQLIT QSSALEQKWL IRMIIKDLKL GVSQQTIFSV FHNDAAELHN VTTDLEKVCR QLHDPSVGLS DISI TLFSA FKPMLAAIAD IEHIEKDMKH QSFYIETKLD GERMQMHKDG DVYKYFSRNG YNYTD QFGA SPTEGSLTPF IHNAFKADIQ ICILDGEMMA YNPNTQTFMQ KGTKFDIKRM VEDSDL QTC YCVFDVLMVN NKKLGHETLR KRYEILSSIF TPIPGRIEIV QKTQAHTKNE VIDALNE AI DKREEGIMVK QPLSIYKPDK RGEGWLKIKP EYVSGLMDEL DILIVGGYWG KGSRGGMM S HFLCAVAEKP PPGEKPSVFH TLSRVGSGCT MKELYDLGLK LAKYWKPFHR KAPPSSILC GTEKPEVYIE PCNSVIVQIK AAEIVPSDMY KTGCTLRFPR IEKIRDDKEW HECMTLDDLE QLRGKASGK LASKHLYIGG DDEPQEKKRK AAPKMKKVIG IIEHLKAPNL TNVNKISNIF E DVEFCVMS GTDSQPKPDL ENRIAEFGGY IVQNPGPDTY CVIAGSENIR VKNIILSNKH DV VKPAWLL ECFKTKSFVP WQPRFMIHMC PSTKEHFARE YDCYGDSYFI DTDLNQLKEV FSG IKNSNE QTPEEMASLI ADLEYRYSWD CSPLSMFRRH TVYLDSYAVI NDLSTKNEGT RLAI KALEL RFHGAKVVSC LAEGVSHVII GEDHSRVADF KAFRRTFKRK FKILKESWVT DSIDK CELQ EENQYLI

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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: 42.2 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: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 500830
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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