9PB7 | pdb_00009pb7

TFIIH of PIC-Med-SWI/SNF

PDB DOI: https://doi.org/10.2210/pdb9PB7/pdb
EM Map EMD-71456: EMDB EMDataResource

Classification: TRANSCRIPTION/DNA
Organism(s): Saccharomyces cerevisiae
Mutation(s): No

Deposited: 2025-06-26 Released: 2026-09-30
Deposition Author(s): Yang, C., Nagai, S., Chen, D.-H.
Funding Organization(s): Other private

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 4.40 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Structure of TFIIH of PIC-Med-SWI/SNF

Yang, C., Nagai, S., Chen, D.-H.

To be published.

Macromolecule Content

Total Structure Weight: 600.16 kDa
Atom Count: 26,523
Modeled Residue Count: 3,220
Deposited Residue Count: 5,169
Unique protein chains: 10
Unique nucleic acid chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
General transcription and DNA repair factor IIH subunit TFB5	A [auth 5]	72	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for Q3E7C1 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q3E7C1 Go to UniProtKB: Q3E7C1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q3E7C1
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
General transcription and DNA repair factor IIH helicase subunit XPD/RAD3	B [auth 0]	778	Saccharomyces cerevisiae	Mutation(s): 0 EC: 5.6.2.3
UniProt
Find proteins for P06839 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P06839 Go to UniProtKB: P06839
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P06839
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Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA polymerase II transcription factor B subunit 3	C [auth 3]	321	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for Q03290 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q03290 Go to UniProtKB: Q03290
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q03290
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Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
General transcription and DNA repair factor IIH helicase subunit XPB	D [auth 7]	843	Saccharomyces cerevisiae	Mutation(s): 0 EC: 3.6.4.12 (PDB Primary Data), 5.6.2.4 (UniProt)
UniProt
Find proteins for Q00578 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q00578 Go to UniProtKB: Q00578
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q00578
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Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
SWI/SNF chromatin-remodeling complex subunit SNF5	E [auth 8]	905	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P18480 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P18480 Go to UniProtKB: P18480
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P18480
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Reference Sequence

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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcription initiation factor TFIID subunit 14	F [auth 9]	244	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P35189 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P35189 Go to UniProtKB: P35189
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P35189
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Reference Sequence

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Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
General transcription and DNA repair factor IIH subunit TFB4	I [auth 4]	338	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for Q12004 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q12004 Go to UniProtKB: Q12004
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q12004
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Reference Sequence

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Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
General transcription and DNA repair factor IIH subunit SSL1	J [auth 6]	461	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for Q04673 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q04673 Go to UniProtKB: Q04673
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q04673
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Reference Sequence

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Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
General transcription and DNA repair factor IIH subunit TFB1	K [auth 1]	642	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P32776 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P32776 Go to UniProtKB: P32776
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P32776
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Reference Sequence

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Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
General transcription and DNA repair factor IIH subunit TFB2	L [auth 2]	513	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for Q02939 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q02939 Go to UniProtKB: Q02939
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q02939
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Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 7
promoter DNA	G [auth N]	26	Saccharomyces cerevisiae
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Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 8
promoter DNA	H [auth T]	26	Saccharomyces cerevisiae
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SF4 Query on SF4 Download:Ideal Coordinates CCD File SDF format, chain M [auth 0] MOL2 format, chain M [auth 0] mmCIF format, chain M [auth 0]	M [auth 0]	IRON/SULFUR CLUSTER Fe₄ S₄ LJBDFODJNLIPKO-UHFFFAOYSA-N		Interactions Focus chain M [auth 0] Interactions & Density Focus chain M [auth 0]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain O [auth 3] SDF format, chain Q [auth 6] SDF format, chain S [auth 6] SDF format, chain T [auth 6] SDF format, chain R [auth 6] SDF format, chain P [auth 4] SDF format, chain N [auth 3] MOL2 format, chain O [auth 3] MOL2 format, chain Q [auth 6] MOL2 format, chain S [auth 6] MOL2 format, chain T [auth 6] MOL2 format, chain R [auth 6] MOL2 format, chain P [auth 4] MOL2 format, chain N [auth 3] mmCIF format, chain O [auth 3] mmCIF format, chain Q [auth 6] mmCIF format, chain S [auth 6] mmCIF format, chain T [auth 6] mmCIF format, chain R [auth 6] mmCIF format, chain P [auth 4] mmCIF format, chain N [auth 3]	N [auth 3] O [auth 3] P [auth 4] Q [auth 6] R [auth 6] N [auth 3], O [auth 3], P [auth 4], Q [auth 6], R [auth 6], S [auth 6], T [auth 6]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain N [auth 3] Focus chain O [auth 3] Focus chain P [auth 4] Focus chain Q [auth 6] Focus chain R [auth 6] Focus chain S [auth 6] Focus chain T [auth 6] Interactions & Density Focus chain N [auth 3] Focus chain O [auth 3] Focus chain P [auth 4] Focus chain Q [auth 6] Focus chain R [auth 6] Focus chain S [auth 6] Focus chain T [auth 6]