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- EMDB-71510: NER dual incision complex - DuIM local AR map -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-71510
TitleNER dual incision complex - DuIM local AR map
Map dataDuIM local AR map
Sample
  • Complex: NER dual incision complex
KeywordsNER / XPA / XPG / XPF / DNA BINDING PROTEIN
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.0 Å
AuthorsLi CL / 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)DK075037 United States
CitationJournal: To Be Published
Title: Nucleotide Excision Repair Uncovered by Pre-incision Complex Structures
Authors: Li CL / Kim J / Yang W
History
DepositionJun 28, 2025-
Header (metadata) releaseFeb 18, 2026-
Map releaseFeb 18, 2026-
UpdateFeb 18, 2026-
Current statusFeb 18, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_71510.png

Downloads & links

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Map

FileDownload / File: emd_71510.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationDuIM local AR map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 320 pix.
= 266.56 Å		0.83 Å/pix.
x 320 pix.
= 266.56 Å		0.83 Å/pix.
x 320 pix.
= 266.56 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: 0.009
Minimum - Maximum-0.008130968 - 0.023259697
Average (Standard dev.)0.000102237645 (±0.0010501171)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 266.56 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: DuIM local AR half1 map

Fileemd_71510_half_map_1.map
AnnotationDuIM local AR half1 map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: DuIM local AR half2 map

Fileemd_71510_half_map_2.map
AnnotationDuIM local AR half2 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 : NER dual incision complex

EntireName: NER dual incision complex
Components
  • Complex: NER dual incision complex

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Supramolecule #1: NER dual incision complex

SupramoleculeName: NER dual incision complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#17
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 800 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

Concentration0.4 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
100.0 mMKOAcpotassium acetate
25.0 mMTris2-Amino-2-(hydroxymethyl)propane-1,3-diol
2.0 mMCaCl2calcium chloride
2.0 mMTCEP(Tris(2-carboxyethyl)phospine)
1.0 %Glycerolglycerol
0.05 %C14H28O6Octyl glucoside
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 6 / Number real images: 52926 / Average exposure time: 3.0 sec. / Average electron dose: 52.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: Gctf / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 140332
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChainDetails

8ebt

source_name: PDB, initial_model_type: experimental modelC7CAD

6sxa

source_name: PDB, initial_model_type: experimental modelXPF/ERCC1

1l1o

source_name: PDB, initial_model_type: experimental modelRPA trimerization core

1jmc

source_name: PDB, initial_model_type: experimental modelRPA70

6tus

source_name: PDB, initial_model_type: experimental modelXPG catalytic domain
RefinementSpace: REAL / Protocol: AB INITIO MODEL

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