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- EMDB-45846: Focused map of PAXX/XLF in a gap-filling complex with Pol mu enga... -

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Basic information

Entry
Database: EMDB / ID: EMD-45846
TitleFocused map of PAXX/XLF in a gap-filling complex with Pol mu engaged in the NHEJ pathway
Map datafocused PAXX map in a gap-filling complex in the NHEJ pathway
Sample
  • Complex: A gap-filling complex with Pol mu engaged
    • Protein or peptide: human PAXX
    • Protein or peptide: human XLF
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: 7.4 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_45846.png

Downloads & links

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Map

FileDownload / File: emd_45846.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationfocused PAXX map 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: 0.006
Minimum - Maximum-0.012177158 - 0.02420555
Average (Standard dev.)-0.0000279922 (±0.0005871708)
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_45846_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_45846_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_45846_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 PAXX
    • Protein or peptide: human XLF

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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 PAXX

MacromoleculeName: human PAXX / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGSSHHHHHH SQDPMDPLSP PLCTLPPGPE PPRFVCYCEG EESGEGDRGG FNLYVTDAAE LWSTCFTPDS LAAL KARFG LSAAEDITPR FRAACEQQAV ALTLQEDRAS LTLSGGPSAL AFDLSKVPGP EAAPR LRAL TLGLAKRVWS LERRLAAAEE TAVSPRKSPR ...String:
MGSSHHHHHH SQDPMDPLSP PLCTLPPGPE PPRFVCYCEG EESGEGDRGG FNLYVTDAAE LWSTCFTPDS LAAL KARFG LSAAEDITPR FRAACEQQAV ALTLQEDRAS LTLSGGPSAL AFDLSKVPGP EAAPR LRAL TLGLAKRVWS LERRLAAAEE TAVSPRKSPR PAGPQLFLPD PDPQRGGPGP GVRRRC PGE SLINPGFKSK KPAGGVDFDE T

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Macromolecule #2: human XLF

MacromoleculeName: human XLF / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GPVMEELEQG LLMQPWAWLQ LAENSLLAKV FITKQGYALL VSDLQQVWHE QVDTSVVSQR AKE LNKRLT APPAAFLCHL DNLLRPLLKD AAHPSEATFS CDCVADALIL RVRSELSGLP FYWN FHCML ASPSLVSQHL IRPLMGMSLA LQCQVRELAT LLHMKDLEIQ ...String:
GPVMEELEQG LLMQPWAWLQ LAENSLLAKV FITKQGYALL VSDLQQVWHE QVDTSVVSQR AKE LNKRLT APPAAFLCHL DNLLRPLLKD AAHPSEATFS CDCVADALIL RVRSELSGLP FYWN FHCML ASPSLVSQHL IRPLMGMSLA LQCQVRELAT LLHMKDLEIQ DYQESGATLI RDRLK TEPF EENSFLEQFM IEKLPEACSI GDGKPFVMNL QDLYMAVTTQ EVQVGQKHQG AGDPHT SNS ASLQGIDSQC VNQPEQLVSS APTLSAPEKE STGTSGPLQR PQLSKVKRKK PRGLFS

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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: 7.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 105280
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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