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- EMDB-53059: Cryo-EM map of apo-XPF-ERCC1-SLX4(330-555)-SLX4IP from a DNA-cont... -

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Basic information

Entry
Database: EMDB / ID: EMD-53059
TitleCryo-EM map of apo-XPF-ERCC1-SLX4(330-555)-SLX4IP from a DNA-containing sample.
Map dataPost-processed (un-sharpened, filtered) half map.
Sample
  • Complex: XPF-ERCC1-SLX4(330-555)-SLX4IP complex
KeywordsDNA repair / endonuclease / multiprotein complex / HYDROLASE
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsFeng J / Matthews-Palmer T / Greber BJ
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/V009354/1 United Kingdom
CitationJournal: To Be Published
Title: Molecular basis of XPF-ERCC1 targeting to SLX4-dependent DNA repair pathways
Authors: Feng J / Martin PR / Lecot M / Cronin NB / Matthews-Palmer T / Niedzwiedz W / Greber BJ
History
DepositionMar 9, 2025-
Header (metadata) releaseDec 17, 2025-
Map releaseDec 17, 2025-
UpdateDec 17, 2025-
Current statusDec 17, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53059.png

Downloads & links

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Map

FileDownload / File: emd_53059.map.gz / Format: CCP4 / Size: 10.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPost-processed (un-sharpened, filtered) half map.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.4 Å/pix.
x 140 pix.
= 196. Å		1.4 Å/pix.
x 140 pix.
= 196. Å		1.4 Å/pix.
x 140 pix.
= 196. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.4 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02
Minimum - Maximum-0.026808148 - 0.09180922
Average (Standard dev.)0.0005916046 (±0.0052095903)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions140140140
Spacing140140140
CellA=B=C: 196.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_53059_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Unfiltered half-map from refinement.

Fileemd_53059_half_map_1.map
AnnotationUnfiltered half-map from refinement.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Unfiltered half-map from refinement.

Fileemd_53059_half_map_2.map
AnnotationUnfiltered half-map from refinement.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : XPF-ERCC1-SLX4(330-555)-SLX4IP complex

EntireName: XPF-ERCC1-SLX4(330-555)-SLX4IP complex
Components
  • Complex: XPF-ERCC1-SLX4(330-555)-SLX4IP complex

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Supramolecule #1: XPF-ERCC1-SLX4(330-555)-SLX4IP complex

SupramoleculeName: XPF-ERCC1-SLX4(330-555)-SLX4IP complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 210 KDa

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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

Concentration0.2 mg/mL
BufferpH: 7.9
Component:
ConcentrationNameFormula
20.0 mMHEPES-KOH
200.0 mMPotassium chlorideKCl
2.0 mMManganese chlorideMnCl2
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 50 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
DetailsThe sample contained a two-fold excess of DNA fork substrate over protein complex.

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Electron microscopy

MicroscopeTFS GLACIOS
Specialist opticsEnergy filter - Name: TFS Selectris / Energy filter - Slit width: 10 eV
DetailsFringe-free imaging used.
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Number real images: 11694 / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 20.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.7 µm / Nominal defocus min: 0.4 µm / Nominal magnification: 165000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN

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Image processing

CTF correctionSoftware: (Name: cryoSPARC (ver. 4.4.1), RELION (ver. 5.0-beta))
Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: EMDB MAP
EMDB ID:

10337

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 5.0-beta) / Number images used: 72254
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.4.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 5.0-beta)
Final 3D classificationNumber classes: 2 / Software - Name: RELION (ver. 5.0-beta)

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Atomic model buiding 1

Initial modelPDB ID:

9qee


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT

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