6ro4

Structure of the core TFIIH-XPA-DNA complex

Method: ELECTRON MICROSCOPY

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

General transcription and DNA repair factor IIH helicase subunit XPB

Homo sapiens

UniProt P19447

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 7 DNA 2	DNA1 × 1 DNA2 × 1 General transcription factor IIH subunit 5 × 1 （Q6ZYL4） TFIIH basal transcription factor complex helicase XPD subunit × 1 （P18074） General transcription factor IIH subunit 3 × 1 （Q13889） General transcription factor IIH subunit 2 × 1 （Q13888） General transcription factor IIH subunit 4 × 1 （Q92759） DNA repair protein complementing XP-A cells × 1 （P23025） IRON/SULFUR CLUSTER × 1 ZINC ION × 6	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ERCC3_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain A； PDBConstruct 1–782； UniProt 1–782

General transcription factor IIH subunit 5

Homo sapiens

UniProt Q6ZYL4

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 7 DNA 2	DNA1 × 1 DNA2 × 1 General transcription and DNA repair factor IIH helicase subunit XPB × 1 （P19447） TFIIH basal transcription factor complex helicase XPD subunit × 1 （P18074） General transcription factor IIH subunit 3 × 1 （Q13889） General transcription factor IIH subunit 2 × 1 （Q13888） General transcription factor IIH subunit 4 × 1 （Q92759） DNA repair protein complementing XP-A cells × 1 （P23025） IRON/SULFUR CLUSTER × 1 ZINC ION × 6	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TF2H5_HUMAN
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain F； PDBConstruct 1–71； UniProt 1–71

TFIIH basal transcription factor complex helicase XPD subunit

Homo sapiens

UniProt P18074

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 7 DNA 2	DNA1 × 1 DNA2 × 1 General transcription and DNA repair factor IIH helicase subunit XPB × 1 （P19447） General transcription factor IIH subunit 5 × 1 （Q6ZYL4） General transcription factor IIH subunit 3 × 1 （Q13889） General transcription factor IIH subunit 2 × 1 （Q13888） General transcription factor IIH subunit 4 × 1 （Q92759） DNA repair protein complementing XP-A cells × 1 （P23025） IRON/SULFUR CLUSTER × 1 ZINC ION × 6	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ERCC2_HUMAN
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain B； PDBConstruct 1–760； UniProt 1–760

General transcription factor IIH subunit 3

Homo sapiens

UniProt Q13889

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 7 DNA 2	DNA1 × 1 DNA2 × 1 General transcription and DNA repair factor IIH helicase subunit XPB × 1 （P19447） General transcription factor IIH subunit 5 × 1 （Q6ZYL4） TFIIH basal transcription factor complex helicase XPD subunit × 1 （P18074） General transcription factor IIH subunit 2 × 1 （Q13888） General transcription factor IIH subunit 4 × 1 （Q92759） DNA repair protein complementing XP-A cells × 1 （P23025） IRON/SULFUR CLUSTER × 1 ZINC ION × 6	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TF2H3_HUMAN
Isoform	—
PDB entities	6
Chains and sequence ranges	Author chain E； PDBConstruct 1–308； UniProt 1–308

General transcription factor IIH subunit 2

Homo sapiens

UniProt Q13888

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 7 DNA 2	DNA1 × 1 DNA2 × 1 General transcription and DNA repair factor IIH helicase subunit XPB × 1 （P19447） General transcription factor IIH subunit 5 × 1 （Q6ZYL4） TFIIH basal transcription factor complex helicase XPD subunit × 1 （P18074） General transcription factor IIH subunit 3 × 1 （Q13889） General transcription factor IIH subunit 4 × 1 （Q92759） DNA repair protein complementing XP-A cells × 1 （P23025） IRON/SULFUR CLUSTER × 1 ZINC ION × 6	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TF2H2_HUMAN
Isoform	—
PDB entities	7
Chains and sequence ranges	Author chain D； PDBConstruct 1–395； UniProt 1–395

General transcription factor IIH subunit 4

Homo sapiens

UniProt Q92759

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 7 DNA 2	DNA1 × 1 DNA2 × 1 General transcription and DNA repair factor IIH helicase subunit XPB × 1 （P19447） General transcription factor IIH subunit 5 × 1 （Q6ZYL4） TFIIH basal transcription factor complex helicase XPD subunit × 1 （P18074） General transcription factor IIH subunit 3 × 1 （Q13889） General transcription factor IIH subunit 2 × 1 （Q13888） DNA repair protein complementing XP-A cells × 1 （P23025） IRON/SULFUR CLUSTER × 1 ZINC ION × 6	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TF2H4_HUMAN
Isoform	—
PDB entities	8
Chains and sequence ranges	Author chain C； PDBConstruct 1–462； UniProt 1–462

DNA repair protein complementing XP-A cells

Homo sapiens

UniProt P23025

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 7 DNA 2	DNA1 × 1 DNA2 × 1 General transcription and DNA repair factor IIH helicase subunit XPB × 1 （P19447） General transcription factor IIH subunit 5 × 1 （Q6ZYL4） TFIIH basal transcription factor complex helicase XPD subunit × 1 （P18074） General transcription factor IIH subunit 3 × 1 （Q13889） General transcription factor IIH subunit 2 × 1 （Q13888） General transcription factor IIH subunit 4 × 1 （Q92759） IRON/SULFUR CLUSTER × 1 ZINC ION × 6	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	XPA_HUMAN
Isoform	—
PDB entities	9
Chains and sequence ranges	Author chain G； PDBConstruct 1–273； UniProt 1–273

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	6ro4
Deposition date deposition_date	2019-05-10
Structure title title	Structure of the core TFIIH-XPA-DNA complex
Keywords keywords	Complex, Helicase, Translocase, DNA repair; TRANSLOCASE
Experimental Method method	ELECTRON MICROSCOPY

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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.

6ro4__assembly_1__model_1

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

Download this curve (.dat)

6ro4__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6ro4__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	50.13 Å
Rg (electron density)	50.29 Å
Total Rg	50.41 Å
Atom count	19827
Residues	2396
Excluded volume	353240 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6ro4__assembly_1__model_1`	nonameric （9）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (11)

Entity 1 Entity 1 polymer

Description description	DNA1
Molecular weight formula_weight	15036.7 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	J
Atom count atom_count	19827

CAAAGTCACGACCTAGACACTGCGAGCTCGAATTCACTGGAGTGACCTC

Entity 2 Entity 2 polymer

Description description	DNA2
Molecular weight formula_weight	15075.7 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	K

GAGGTCACTCCAGTGAATTCGAGCTCGCAACAATGAGCACATACCTAGT

Entity 3 Entity 3 polymer

Description description	General transcription and DNA repair factor IIH helicase subunit XPB
Molecular weight formula_weight	89404.7 kDa
EC 编号 ec_number	3.6.4.12
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A

MGKRDRADRDKKKSRKRHYEDEEDDEEDAPGNDPQEAVPSAAGKQVDESGTKVDEYGAKDYRLQMPLKDDHTSRPLWVAPDGHIFLEAFSPVYKYAQDFLVAIAEPVCRPTHVHEYKLTAYSLYAAVSVGLQTSDITEYLRKLSKTGVPDGIMQFIKLCTVSYGKVKLVLKHNRYFVESCHPDVIQHLLQDPVIRECRLRNSEGEATELITETFTSKSAISKTAESSGGPSTSRVTDPQGKSDIPMDLFDFYEQMDKDEEEEEETQTVSFEVKQEMIEELQKRCIHLEYPLLAEYDFRNDSVNPDINIDLKPTAVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTAACTVRKRCLVLGNSAVSVEQWKAQFKMWSTIDDSQICRFTSDAKDKPIGCSVAISTYSMLGHTTKRSWEAERVMEWLKTQEWGLMILDEVHTIPAKMFRRVLTIVQAHCKLGLTATLVREDDKIVDLNFLIGPKLYEANWMELQNNGYIAKVQCAEVWCPMSPEFYREYVAIKTKKRILLYTMNPNKFRACQFLIKFHERRNDKIIVFADNVFALKEYAIRLNKPYIYGPTSQGERMQILQNFKHNPKINTIFISKVGDTSFDLPEANVLIQISSHGGSRRQEAQRLGRVLRAKKGMVAEEYNAFFYSLVSQDTQEMAYSTKRQRFLVDQGYSFKVITKLAGMEEEDLAFSTKEEQQQLLQKVLAATDLDAEEEVVAGEFGSRSSQASRRFGTMSSMSGADDTVYMEYHSSRSKAPSKHVHPLFKRFRK

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Trichoplusia ni

Entity 4 Entity 4 polymer

Description description	General transcription factor IIH subunit 5
Molecular weight formula_weight	8060.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	F

MVNVLKGVLIECDPAMKQFLLYLDESNALGKKFIIQDIDDTHVFVIAELVNVLQERVGELMDQNAFSLTQK

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Trichoplusia ni

Entity 5 Entity 5 polymer

Description description	TFIIH basal transcription factor complex helicase XPD subunit
Molecular weight formula_weight	87021.1 kDa
EC 编号 ec_number	3.6.4.12
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MKLNVDGLLVYFPYDYIYPEQFSYMRELKRTLDAKGHGVLEMPSGTGKTVSLLALIMAYQRAYPLEVTKLIYCSRTVPEIEKVIEELRKLLNFYEKQEGEKLPFLGLALSSRKNLCIHPEVTPLRFGKDVDGKCHSLTASYVRAQYQHDTSLPHCRFYEEFDAHGREVPLPAGIYNLDDLKALGRRQGWCPYFLARYSILHANVVVYSYHYLLDPKIADLVSKELARKAVVVFDEAHNIDNVCIDSMSVNLTRRTLDRCQGNLETLQKTVLRIKETDEQRLRDEYRRLVEGLREASAARETDAHLANPVLPDEVLQEAVPGSIRTAEHFLGFLRRLLEYVKWRLRVQHVVQESPPAFLSGLAQRVCIQRKPLRFCAERLRSLLHTLEITDLADFSPLTLLANFATLVSTYAKGFTIIIEPFDDRTPTIANPILHFSCMDASLAIKPVFERFQSVIITSGTLSPLDIYPKILDFHPVTMATFTMTLARVCLCPMIIGRGNDQVAISSKFETREDIAVIRNYGNLLLEMSAVVPDGIVAFFTSYQYMESTVASWYEQGILENIQRNKLLFIETQDGAETSVALEKYQEACENGRGAILLSVARGKVSEGIDFVHHYGRAVIMFGVPYVYTQSRILKARLEYLRDQFQIRENDFLTFDAMRHAAQCVGRAIRGKTDYGLMVFADKRFARGDKRGKLPRWIQEHLTDANLNLTVDEGVQVAKYFLRQMAQPFHREDQLGLSLLSLEQLESEETLKRIEQIAQQL

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Trichoplusia ni

Entity 6 Entity 6 polymer

Description description	General transcription factor IIH subunit 3
Molecular weight formula_weight	34416.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E

MVSDEDELNLLVIVVDANPIWWGKQALKESQFTLSKCIDAVMVLGNSHLFMNRSNKLAVIASHIQESRFLYPGKNGRLGDFFGDPGNPPEFNPSGSKDGKYELLTSANEVIVEEIKDLMTKSDIKGQHTETLLAGSLAKALCYIHRMNKEVKDNQEMKSRILVIKAAEDSALQYMNFMNVIFAAQKQNILIDACVLDSDSGLLQQACDITGGLYLKVPQMPSLLQYLLWVFLPDQDQRSQLILPPPVHVDYRAACFCHRNLIEIGYVCSVCLSIFCNFSPICTTCETAFKISLPPVLKAKKKKLKVSA

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Trichoplusia ni

Entity 7 Entity 7 polymer

Description description	General transcription factor IIH subunit 2
Molecular weight formula_weight	44482.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

MDEEPERTKRWEGGYERTWEILKEDESGSLKATIEDILFKAKRKRVFEHHGQVRLGMMRHLYVVVDGSRTMEDQDLKPNRLTCTLKLLEYFVEEYFDQNPISQIGIIVTKSKRAEKLTELSGNPRKHITSLKKAVDMTCHGEPSLYNSLSIAMQTLKHMPGHTSREVLIIFSSLTTCDPSNIYDLIKTLKAAKIRVSVIGLSAEVRVCTVLARETGGTYHVILDESHYKELLTHHVSPPPASSSSECSLIRMGFPQHTIASLSDQDAKPSFSMAHLDGNTEPGLTLGGYFCPQCRAKYCELPVECKICGLTLVSAPHLARSYHHLFPLDAFQEIPLEEYNGERFCYGCQGELKDQHVYVCAVCQNVFCVDCDVFVHDSLHCCPGCIHKIPAPSGV

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Trichoplusia ni

Entity 8 Entity 8 polymer

Description description	General transcription factor IIH subunit 4
Molecular weight formula_weight	52245.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

MESTPSRGLNRVHLQCRNLQEFLGGLSPGVLDRLYGHPATCLAVFRELPSLAKNWVMRMLFLEQPLPQAAVALWVKKEFSKAQEESTGLLSGLRIWHTQLLPGGLQGLILNPIFRQNLRIALLGGGKAWSDDTSQLGPDKHARDVPSLDKYAEERWEVVLHFMVGSPSAAVSQDLAQLLSQAGLMKSTEPGEPPCITSAGFQFLLLDTPAQLWYFMLQYLQTAQSRGMDLVEILSFLFQLSFSTLGKDYSVEGMSDSLLNFLQHLREFGLVFQRKRKSRRYYPTRLAINLSSGVSGAGGTVHQPGFIVVETNYRLYAYTESELQIALIALFSEMLYRFPNMVVAQVTRESVQQAIASGITAQQIIHFLRTRAHPVMLKQTPVLPPTITDQIRLWELERDRLRFTEGVLYNQFLSQVDFELLLAHARELGVLVFENSAKRLMVVTPAGHSDVKRFWKRQKHSS

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Trichoplusia ni

Entity 9 Entity 9 polymer

Description description	DNA repair protein complementing XP-A cells
Molecular weight formula_weight	31422.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G

MAAADGALPEAAALEQPAELPASVRASIERKRQRALMLRQARLAARPYSATAAAATGGMANVKAAPKIIDTGGGFILEEEEEEEQKIGKVVHQPGPVMEFDYVICEECGKEFMDSYLMNHFDLPTCDNCRDADDKHKLITKTEAKQEYLLKDCDLEKREPPLKFIVKKNPHHSQWGDMKLYLKLQIVKRSLEVWGSQEALEEAKEVRQENREKMKQKKFDKKVKELRRAVRSSVWKRETIVHQHEYGPEENLEDDMYRKTCTMCGHELTYEKM

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Trichoplusia ni

Entity 10 Entity 10 non-polymer

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

Entity 11 Entity 11 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	6

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6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	6ro4F00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	1220 — TFB5-like

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Resolution resolution	3.50 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	227776

Structure of the core TFIIH-XPA-DNA complex

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

General transcription and DNA repair factor IIH helicase subunit XPB

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 factor IIH 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

TFIIH basal transcription factor complex helicase XPD subunit

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 factor IIH subunit 3

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 factor IIH subunit 2

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 factor IIH subunit 4

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 protein complementing XP-A cells

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

6ro4__assembly_1__model_1

6ro4__assembly_1__model_1 | I(q)

6ro4__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (11)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 polymer

Polymer Polymer

Source Source

Entity 6 Entity 6 polymer