7k01

Structure of TFIIH in TFIIH/Rad4-Rad23-Rad33 DNA opening complex

Method: ELECTRON MICROSCOPY

▼

1. Protein Identity and Related Structures Protein Identity & Related Structures

General transcription and DNA repair factor IIH subunit TFB1

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 7	General transcription and DNA repair factor IIH subunit TFB4 × 1 （Q12004） DNA repair helicase RAD25 × 1 （Q00578） RNA polymerase II transcription factor B subunit 5 × 1 （Q3E7C1） General transcription and DNA repair factor IIH subunit TFB2 × 1 （Q02939） DNA repair helicase RAD3 × 1 （P06839） General transcription and DNA repair factor IIH subunit SSL1 × 1 （Q04673） ZINC ION × 5 IRON/SULFUR CLUSTER × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TFB1_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain 1； PDBConstruct 1–642； UniProt 1–642

General transcription and DNA repair factor IIH subunit TFB4

OrganismNot specified

UniProt Q12004

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 7	General transcription and DNA repair factor IIH subunit TFB1 × 1 （P32776） DNA repair helicase RAD25 × 1 （Q00578） RNA polymerase II transcription factor B subunit 5 × 1 （Q3E7C1） General transcription and DNA repair factor IIH subunit TFB2 × 1 （Q02939） DNA repair helicase RAD3 × 1 （P06839） General transcription and DNA repair factor IIH subunit SSL1 × 1 （Q04673） ZINC ION × 5 IRON/SULFUR CLUSTER × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TFB4_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain 4； PDBConstruct 1–338； UniProt 1–338

DNA repair helicase RAD25

OrganismNot specified

UniProt Q00578

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 7	General transcription and DNA repair factor IIH subunit TFB1 × 1 （P32776） General transcription and DNA repair factor IIH subunit TFB4 × 1 （Q12004） RNA polymerase II transcription factor B subunit 5 × 1 （Q3E7C1） General transcription and DNA repair factor IIH subunit TFB2 × 1 （Q02939） DNA repair helicase RAD3 × 1 （P06839） General transcription and DNA repair factor IIH subunit SSL1 × 1 （Q04673） ZINC ION × 5 IRON/SULFUR CLUSTER × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RAD25_YEAST
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain 7； PDBConstruct 1–843； UniProt 1–843

RNA polymerase II transcription factor B subunit 5

OrganismNot specified

UniProt Q3E7C1

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 7	General transcription and DNA repair factor IIH subunit TFB1 × 1 （P32776） General transcription and DNA repair factor IIH subunit TFB4 × 1 （Q12004） DNA repair helicase RAD25 × 1 （Q00578） General transcription and DNA repair factor IIH subunit TFB2 × 1 （Q02939） DNA repair helicase RAD3 × 1 （P06839） General transcription and DNA repair factor IIH subunit SSL1 × 1 （Q04673） ZINC ION × 5 IRON/SULFUR CLUSTER × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TFB5_YEAST
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain 5； PDBConstruct 1–72； UniProt 1–72

General transcription and DNA repair factor IIH subunit TFB2

OrganismNot specified

UniProt Q02939

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 7	General transcription and DNA repair factor IIH subunit TFB1 × 1 （P32776） General transcription and DNA repair factor IIH subunit TFB4 × 1 （Q12004） DNA repair helicase RAD25 × 1 （Q00578） RNA polymerase II transcription factor B subunit 5 × 1 （Q3E7C1） DNA repair helicase RAD3 × 1 （P06839） General transcription and DNA repair factor IIH subunit SSL1 × 1 （Q04673） ZINC ION × 5 IRON/SULFUR CLUSTER × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TFB2_YEAST
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain 2； PDBConstruct 1–513； UniProt 1–513

DNA repair helicase RAD3

OrganismNot specified

UniProt P06839

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 7	General transcription and DNA repair factor IIH subunit TFB1 × 1 （P32776） General transcription and DNA repair factor IIH subunit TFB4 × 1 （Q12004） DNA repair helicase RAD25 × 1 （Q00578） RNA polymerase II transcription factor B subunit 5 × 1 （Q3E7C1） General transcription and DNA repair factor IIH subunit TFB2 × 1 （Q02939） General transcription and DNA repair factor IIH subunit SSL1 × 1 （Q04673） ZINC ION × 5 IRON/SULFUR CLUSTER × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RAD3_YEAST
Isoform	—
PDB entities	6
Chains and sequence ranges	Author chain 0； PDBConstruct 1–778； UniProt 1–778

General transcription and DNA repair factor IIH subunit SSL1

OrganismNot specified

UniProt Q04673

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 7	General transcription and DNA repair factor IIH subunit TFB1 × 1 （P32776） General transcription and DNA repair factor IIH subunit TFB4 × 1 （Q12004） DNA repair helicase RAD25 × 1 （Q00578） RNA polymerase II transcription factor B subunit 5 × 1 （Q3E7C1） General transcription and DNA repair factor IIH subunit TFB2 × 1 （Q02939） DNA repair helicase RAD3 × 1 （P06839） ZINC ION × 5 IRON/SULFUR CLUSTER × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SSL1_YEAST
Isoform	—
PDB entities	7
Chains and sequence ranges	Author chain 6； PDBConstruct 1–461； UniProt 1–461

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	7k01
Deposition date deposition_date	2020-09-02
Structure title title	Structure of TFIIH in TFIIH/Rad4-Rad23-Rad33 DNA opening complex
Keywords keywords	TFIIH, Rad4, Rad4/23, XPC, NER, Nucleotide Excision Repair, GG-NER, NUCLEAR PROTEIN, NUCLEAR PROTEIN-Transferase complex; NUCLEAR PROTEIN/Transferase
Experimental Method method	ELECTRON MICROSCOPY

▼

3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

7k01__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

7k01__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7k01__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	50.08 Å
Rg (electron density)	49.75 Å
Total Rg	49.82 Å
Atom count	21052
Residues	2916
Excluded volume	370770 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7k01__assembly_1__model_1`	heptameric （7）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (9)

Entity 1 Entity 1 polymer

Description description	General transcription and DNA repair factor IIH subunit TFB1
Molecular weight formula_weight	72993.3 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	1
Atom count atom_count	21052

MSHSGAAIFEKVSGIIAINEDVSPAELTWRSTDGDKVHTVVLSTIDKLQATPASSEKMMLRLIGKVDESKKRKDNEGNEVVPKPQRHMFSFNNRTVMDNIKMTLQQIISRYKDADIYEEKRRREESAQHTETPMSSSSVTAGTPTPHLDTPQLNNGAPLINTAKLDDSLSKEKLLTNLKLQQSLLKGNKVLMKVFQETVINAGLPPSEFWSTRIPLLRAFALSTSQKVGPYNVLSTIKPVASSENKVNVNLSREKILNIFENYPIVKKAYTDNVPKNFKEPEFWARFFSSKLFRKLRGEKIMQNDRGDVIIDRYLTLDQEFDRKDDDMLLHPVKKIIDLDGNIQDDPVVRGNRPDFTMQPGVDINGNSDGTVDILKGMNRLSEKMIMALKNEYSRTNLQNKSNITNDEEDEDNDERNELKIDDLNESYKTNYAIIHLKRNAHEKTTDNDAKSSADSIKNADLKVSNQQMLQQLSLVMDNLINKLDLNQVVPNNEVSNKINKRVITAIKINAKQAKHNNVNSALGSFVDNTSQANELEVKSTLPIDLLESCRMLHTTCCEFLKHFYIHFQSGEQKQASTVKKLYNHLKDCIEKLNELFQDVLNGDGESMSNTCTAYLKPVLNSITLATHKYDEYFNEYNNNSN

Entity 2 Entity 2 polymer

Description description	General transcription and DNA repair factor IIH subunit TFB4
Molecular weight formula_weight	37506.4 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	4

MDAISDPTFKHARSRKQVTEESPSLLTVIIEIAPKLWTTFDEEGNEKGSIIKVLEALIVFLNAHLAFNSANKVAVIAAYSQGIKYLYPESTSALKASESENKTRSDLKIINSDMYRRFRNVDETLVEEIYKLFELEKKQIEQNSQRSTLAGAMSAGLTYVNRISKESVTTSLKSRLLVLTCGSGSSKDEIFQYIPIMNCIFSATKMKCPIDVVKIGGSKESTFLQQTTDATNGVYLHVESTEGLIQYLATAMFIDPSLRPIIVKPNHGSVDFRTSCYLTGRVVAVGFICSVCLCVLSIIPPGNKCPACDSQFDEHVIAKLKRKPVVPRLKAKKKVTKP

Entity 3 Entity 3 polymer

Description description	DNA repair helicase RAD25
Molecular weight formula_weight	95461.7 kDa
EC 编号 ec_number	3.6.4.12
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	7

MTDVEGYQPKSKGKIFPDMGESFFSSDEDSPATDAEIDENYDDNRETSEGRGERDTGAMVTGLKKPRKKTKSSRHTAADSSMNQMDAKDKALLQDTNSDIPADFVPDSVSGMFRSHDFSYLRLRPDHASRPLWISPSDGRIILESFSPLAEQAQDFLVTIAEPISRPSHIHEYKITAYSLYAAVSVGLETDDIISVLDRLSKVPVAESIINFIKGATISYGKVKLVIKHNRYFVETTQADILQMLLNDSVIGPLRIDSDHQVQPPEDVLQQQLQQTAGKPATNVNPNDVEAVFSAVIGGDNEREEEDDDIDAVHSFEIANESVEVVKKRCQEIDYPVLEEYDFRNDHRNPDLDIDLKPSTQIRPYQEKSLSKMFGNGRARSGIIVLPCGAGKTLVGITAACTIKKSVIVLCTSSVSVMQWRQQFLQWCTLQPENCAVFTSDNKEMFQTESGLVVSTYSMVANTRNRSHDSQKVMDFLTGREWGFIILDEVHVVPAAMFRRVVSTIAAHAKLGLTATLVREDDKIGDLNFLIGPKLYEANWMELSQKGHIANVQCAEVWCPMTAEFYQEYLRETARKRMLLYIMNPTKFQACQFLIQYHERRGDKIIVFSDNVYALQEYALKMGKPFIYGSTPQQERMNILQNFQYNDQINTIFLSKVGDTSIDLPEATCLIQISSHYGSRRQEAQRLGRILRAKRRNDEGFNAFFYSLVSKDTQEMYYSTKRQAFLVDQGYAFKVITHLHGMENIPNLAYASPRERRELLQEVLLKNEEAAGIEVGDDADNSVGRGSNGHKRFKSKAVRGEGSLSGLAGGEDMAYMEYSTNKNKELKEHHPLIRKMYYKNLKK

Entity 4 Entity 4 polymer

Description description	RNA polymerase II transcription factor B subunit 5
Molecular weight formula_weight	8243.5 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	5

MARARKGALVQCDPSIKALILQIDAKMSDIVLEELDDTHLLVNPSKVEFVKHELNRLLSKNIYNPMDEEENQ

Entity 5 Entity 5 polymer

Description description	General transcription and DNA repair factor IIH subunit TFB2
Molecular weight formula_weight	58602.3 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	2

MSDYSLKHSVTQYLEEIPQQVQNRLYTSPATCLAIYRILPPLAKFFIMAMVFNENEVPLLDLDKWVNSNGKLQFQNAIKSMKSLHLLIPNKSSGTLMINLNPTFKISLRNALTGGEVQNSFGVVVEENVVSLDLLDEYSANKWETILHFMVGTPLAKIPSEKVLNLLKHSKLMEEVNSTGEFKITNEGFQFLLQEINSQLWTLLLQYLKMIETSKMDLVDVLHFIFMLGALEVGKAYKIDALSETQRIMLQDMRDYGLVFQKHSNDSIFYPTKLALMLTSDTKTIRSASNAMDSVLRQNREEPSVNEDGANGKSTTDITTSDDLNKAGLKNQDIPDGSLIVETNFKIYSYSNSPLQIAVLSLFVHLKARFVNMVLGQITRESIRRALTNGITADQIIAYLETHAHPQMRRLAEEKLEKKLELDPNCKEPLQVLPPTVVDQIRLWQLELDRVITYEGSLYSDFETSQEYNLLSKYAQDIGVLLWKDDKKKKFFISKEGNSQVLDFAKRKLKKKQ

Entity 6 Entity 6 polymer

Description description	DNA repair helicase RAD3
Molecular weight formula_weight	89899.0 kDa
EC 编号 ec_number	3.6.4.12
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	0

MKFYIDDLPVLFPYPKIYPEQYNYMCDIKKTLDVGGNSILEMPSGTGKTVSLLSLTIAYQMHYPEHRKIIYCSRTMSEIEKALVELENLMDYRTKELGYQEDFRGLGLTSRKNLCLHPEVSKERKGTVVDEKCRRMTNGQAKRKLEEDPEANVELCEYHENLYNIEVEDYLPKGVFSFEKLLKYCEEKTLCPYFIVRRMISLCNIIIYSYHYLLDPKIAERVSNEVSKDSIVIFDEAHNIDNVCIESLSLDLTTDALRRATRGANALDERISEVRKVDSQKLQDEYEKLVQGLHSADILTDQEEPFVETPVLPQDLLTEAIPGNIRRAEHFVSFLKRLIEYLKTRMKVLHVISETPKSFLQHLKQLTFIERKPLRFCSERLSLLVRTLEVTEVEDFTALKDIATFATLISTYEEGFLLIIEPYEIENAAVPNPIMRFTCLDASIAIKPVFERFSSVIITSGTISPLDMYPRMLNFKTVLQKSYAMTLAKKSFLPMIITKGSDQVAISSRFEIRNDPSIVRNYGSMLVEFAKITPDGMVVFFPSYLYMESIVSMWQTMGILDEVWKHKLILVETPDAQETSLALETYRKACSNGRGAILLSVARGKVSEGIDFDHQYGRTVLMIGIPFQYTESRILKARLEFMRENYRIRENDFLSFDAMRHAAQCLGRVLRGKDDYGVMVLADRRFSRKRSQLPKWIAQGLSDADLNLSTDMAISNTKQFLRTMAQPTDPKDQEGVSVWSYEDLIKHQNSRKDQGGFIENENKEGEQDEDEDEDIEMQ

Entity 7 Entity 7 polymer

Description description	General transcription and DNA repair factor IIH subunit SSL1
Molecular weight formula_weight	52370.0 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	6

MAPVVISESEEDEDRVAITRRTKRQVHFDGEGDDRVDQQQQQHSSSHRDRDKHVQRKKKKRLSNRNLQGSNGGYAWEDEIKRSWDLVKVDDEGDMASLVASIVEARKKRTAKKNITPYQRGIIRSLILTLDCSEAMLEKDLRPNRHAMIIQYAIDFVHEFFDQNPISQMGIIIMRNGLAQLVSQVSGNPQDHIDALKSIRKQEPKGNPSLQNALEMARGLLLPVPAHCTREVLIVFGSLSTTDPGDIHQTIDSLVSEKIRVKVLGLSAQVAICKELCKATNYGDESFYKILLDETHLKELFNEAVTPLPVNKINKGFTLVKMGFPTRIFEDTPTFCSCHSKLVYGGYFCPNCHSKVCSLPTVCPCCDLMLILSTHLARSYHHLMPLKTFAEVPTTEKFRSEDCFSCQSRFPILKNHKNGKLLTSSRYRCEDCKQEFCVDCDVFIHEILHNCPGCESKPVIT

Entity 8 Entity 8 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 9 Entity 9 non-polymer

Description description	IRON/SULFUR CLUSTER
Molecular weight formula_weight	351.6 kDa
Source method src_method	syn
Copy count entity_count	1

▼

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	7k01001
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	7k01401
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	410 — von Willebrand factor, type A domain

▶

Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	—

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	3.90 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	56101

Structure of TFIIH in TFIIH/Rad4-Rad23-Rad33 DNA opening complex

1. Protein Identity and Related Structures Protein Identity & Related Structures

General transcription and DNA repair factor IIH subunit TFB1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

General transcription and DNA repair factor IIH subunit TFB4

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

DNA repair helicase RAD25

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

RNA polymerase II transcription factor B subunit 5

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

General transcription and DNA repair factor IIH subunit TFB2

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

DNA repair helicase RAD3

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

General transcription and DNA repair factor IIH subunit SSL1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

7k01__assembly_1__model_1

7k01__assembly_1__model_1 | I(q)

7k01__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (9)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 polymer

Polymer Polymer

Entity 5 Entity 5 polymer

Polymer Polymer

Entity 6 Entity 6 polymer

Polymer Polymer