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- EMDB-56568: Multi-body refinement component 2 of the cryo-EM structure of the... -

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Basic information

Entry
Database: EMDB / ID: EMD-56568
TitleMulti-body refinement component 2 of the cryo-EM structure of the human holo-TFIIH-XPC complex bound to bulky lesion-mimic DNA
Map dataPost-processed, filtered multi-body refinement cryo-EM map used to produce composite map for coordinate refinement (body 2)
Sample
  • Complex: Human holo-TFIIH, XPC complex, and XPA with biotinylated DNA.
KeywordsNucleotide excision repair / DNA Repair / helicase / transcription factor / DNA BINDING PROTEIN
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
Authorsde Martin Garrido N / Haste CAF / Feng J / Cronin NB / Greber BJ
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/V009354/1 United Kingdom
CitationJournal: Sci Adv / Year: 2026
Title: Visualization of stepwise derepression of TFIIH in global genome nucleotide excision repair.
Authors: Natàlia de Martín Garrido / Callum A F Haste / Junjie Feng / Nora B Cronin / Basil J Greber /
Abstract: Nucleotide excision repair (NER) is a crucial DNA repair pathway that is orchestrated by transcription factor IIH (TFIIH) in eukaryotic cells. TFIIH is a multifunctional complex that contains two DNA ...Nucleotide excision repair (NER) is a crucial DNA repair pathway that is orchestrated by transcription factor IIH (TFIIH) in eukaryotic cells. TFIIH is a multifunctional complex that contains two DNA helicase/DNA translocase subunits and a kinase module, different subsets of which act in NER, transcription initiation, and cell cycle control. To ensure fidelity despite multifunctionality, the DNA helicase activity of TFIIH is autoinhibited in its free form or when the factor engages in transcription initiation. While the release of the kinase module has been identified as a key step in TFIIH activation, the molecular mechanisms controlling this step and concomitant structural changes in TFIIH are incompletely understood. Here, we determine high-resolution structures of three NER intermediates that visualize how TFIIH arrives at sites of DNA damage in an autoinhibited state and how autoinhibition is released via previously undescribed intermediates. These findings contribute to a mechanistic understanding of human DNA repair.
History
DepositionFeb 4, 2026-
Header (metadata) releaseMay 6, 2026-
Map releaseMay 6, 2026-
UpdateAug 5, 2026-
Current statusAug 5, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_56568.png

Downloads & links

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Map

FileDownload / File: emd_56568.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPost-processed, filtered multi-body refinement cryo-EM map used to produce composite map for coordinate refinement (body 2)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.34 Å/pix.
x 280 pix.
= 375.2 Å		1.34 Å/pix.
x 280 pix.
= 375.2 Å		1.34 Å/pix.
x 280 pix.
= 375.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.34 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0127
Minimum - Maximum-0.03583263 - 0.0730486
Average (Standard dev.)-0.000053013162 (±0.0016181503)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 375.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_56568_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Unsharpened, unfiltered multi-body refinement cryo-EM half map (body...

Fileemd_56568_half_map_1.map
AnnotationUnsharpened, unfiltered multi-body refinement cryo-EM half map (body 2)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Unsharpened, unfiltered multi-body refinement cryo-EM half map (body...

Fileemd_56568_half_map_2.map
AnnotationUnsharpened, unfiltered multi-body refinement cryo-EM half map (body 2)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Human holo-TFIIH, XPC complex, and XPA with biotinylated DNA.

EntireName: Human holo-TFIIH, XPC complex, and XPA with biotinylated DNA.
Components
  • Complex: Human holo-TFIIH, XPC complex, and XPA with biotinylated DNA.

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Supramolecule #1: Human holo-TFIIH, XPC complex, and XPA with biotinylated DNA.

SupramoleculeName: Human holo-TFIIH, XPC complex, and XPA with biotinylated DNA.
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#13 / Details: XPA is not observed in this reconstruction.
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 726.82 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

Concentration0.16 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
50.0 mMHEPES-KOHHepes
150.0 mMKClPotassium chloride
0.5 mMTCEPTris(2-carboxyethyl)phosphine hydrochloride
2.0 mMMgCl2Magnesium chloride
3.0 % (w/v)TrehaloseTrehalose
0.01 % (v/v)NP-40NP-40
GridModel: Quantifoil R2/2 / Material: GOLD / Mesh: 300 / Details: Streptavidin affinity support grid
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 293.15 K / Instrument: LEICA EM GP / Details: Leica EM GP2.

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 165000
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: cryoSPARC (ver. 4.6.2) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: EMDB MAP
EMDB ID:

27996

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 5.0.0) / Number images used: 166008
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.6.2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 5.0.0)
Final 3D classificationNumber classes: 6 / Software - Name: RELION (ver. 5.0.0)

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