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- EMDB-72342: NER dual incision complex - noG focused Core7 map -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-72342
TitleNER dual incision complex - noG focused Core7 map
Map datanoG focus Core7 map
Sample
  • Complex: NER dual incision complex without XPG
KeywordsNER / XPA / XPG / XPF / DNA binding protein
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.3 Å
AuthorsKim J / Li 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: Pre-incision structures reveal principles of nucleotide excision DNA repair
Authors: Kim J / Li CL / Yang W
History
DepositionAug 26, 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_72342.png

Downloads & links

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Map

FileDownload / File: emd_72342.map.gz / Format: CCP4 / Size: 40.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationnoG focus Core7 map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.66 Å/pix.
x 220 pix.
= 365.2 Å		1.66 Å/pix.
x 220 pix.
= 365.2 Å		1.66 Å/pix.
x 220 pix.
= 365.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.66 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.023
Minimum - Maximum-0.01960996 - 0.08612964
Average (Standard dev.)0.00041377536 (±0.004064591)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions220220220
Spacing220220220
CellA=B=C: 365.19998 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Additional Map

Fileemd_72342_additional_1.map
AnnotationAdditional Map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: noG focus Core7 half1 map

Fileemd_72342_half_map_1.map
AnnotationnoG focus Core7 half1 map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: noG focus Core7 half2 map

Fileemd_72342_half_map_2.map
AnnotationnoG focus Core7 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 without XPG

EntireName: NER dual incision complex without XPG
Components
  • Complex: NER dual incision complex without XPG

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Supramolecule #1: NER dual incision complex without XPG

SupramoleculeName: NER dual incision complex without XPG / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#15
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 880 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

Concentration0.6 mg/mL
BufferpH: 7.9
Component:
ConcentrationFormulaName
25.0 mMHEPES(4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid)
100.0 mMKClPotassium Chloride
2.0 mMCaCl2Calcium Chloride
2.0 mMTCEP(Tris(2-carboxyethyl)phospine)
1.0 %GlycerolGlycerol
0.05 %C14H28O6Octyl Glucoside
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) / Average electron dose: 55.8 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) / Resolution.type: BY AUTHOR / Resolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0) / Number images used: 74129
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

8ebs

source_name: PDB, initial_model_type: experimental model

8ebt

source_name: PDB, initial_model_type: experimental model

8ebu

source_name: PDB, initial_model_type: experimental model
RefinementSpace: REAL / Protocol: AB INITIO MODEL

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