6RO4

Structure of the core TFIIH-XPA-DNA complex

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0000112	cellular_component	nucleotide-excision repair factor 3 complex
A	0000166	molecular_function	nucleotide binding
A	0000439	cellular_component	transcription factor TFIIH core complex
A	0003677	molecular_function	DNA binding
A	0003678	molecular_function	DNA helicase activity
A	0003684	molecular_function	damaged DNA binding
A	0004386	molecular_function	helicase activity
A	0005515	molecular_function	protein binding
A	0005524	molecular_function	ATP binding
A	0005634	cellular_component	nucleus
A	0005654	cellular_component	nucleoplasm
A	0005669	cellular_component	transcription factor TFIID complex
A	0005675	cellular_component	transcription factor TFIIH holo complex
A	0006265	biological_process	DNA topological change
A	0006281	biological_process	DNA repair
A	0006283	biological_process	transcription-coupled nucleotide-excision repair
A	0006289	biological_process	nucleotide-excision repair
A	0006366	biological_process	transcription by RNA polymerase II
A	0006367	biological_process	transcription initiation at RNA polymerase II promoter
A	0006368	biological_process	transcription elongation by RNA polymerase II
A	0006915	biological_process	apoptotic process
A	0006974	biological_process	DNA damage response
A	0006979	biological_process	response to oxidative stress
A	0008104	biological_process	intracellular protein localization
A	0009411	biological_process	response to UV
A	0009650	biological_process	UV protection
A	0016787	molecular_function	hydrolase activity
A	0016853	molecular_function	isomerase activity
A	0016887	molecular_function	ATP hydrolysis activity
A	0035315	biological_process	hair cell differentiation
A	0043065	biological_process	positive regulation of apoptotic process
A	0043138	molecular_function	3'-5' DNA helicase activity
A	0048568	biological_process	embryonic organ development
A	0097550	cellular_component	transcription preinitiation complex
A	1901990	biological_process	regulation of mitotic cell cycle phase transition
A	1990841	molecular_function	promoter-specific chromatin binding
B	0000166	molecular_function	nucleotide binding
B	0000439	cellular_component	transcription factor TFIIH core complex
B	0000462	biological_process	maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
B	0001666	biological_process	response to hypoxia
B	0001701	biological_process	in utero embryonic development
B	0003676	molecular_function	nucleic acid binding
B	0003677	molecular_function	DNA binding
B	0003678	molecular_function	DNA helicase activity
B	0003684	molecular_function	damaged DNA binding
B	0004386	molecular_function	helicase activity
B	0005515	molecular_function	protein binding
B	0005524	molecular_function	ATP binding
B	0005634	cellular_component	nucleus
B	0005654	cellular_component	nucleoplasm
B	0005669	cellular_component	transcription factor TFIID complex
B	0005675	cellular_component	transcription factor TFIIH holo complex
B	0005737	cellular_component	cytoplasm
B	0005819	cellular_component	spindle
B	0005829	cellular_component	cytosol
B	0006139	biological_process	nucleobase-containing compound metabolic process
B	0006281	biological_process	DNA repair
B	0006283	biological_process	transcription-coupled nucleotide-excision repair
B	0006289	biological_process	nucleotide-excision repair
B	0006351	biological_process	DNA-templated transcription
B	0006357	biological_process	regulation of transcription by RNA polymerase II
B	0006362	biological_process	transcription elongation by RNA polymerase I
B	0006366	biological_process	transcription by RNA polymerase II
B	0006367	biological_process	transcription initiation at RNA polymerase II promoter
B	0006915	biological_process	apoptotic process
B	0006974	biological_process	DNA damage response
B	0006979	biological_process	response to oxidative stress
B	0007059	biological_process	chromosome segregation
B	0008340	biological_process	determination of adult lifespan
B	0009411	biological_process	response to UV
B	0009650	biological_process	UV protection
B	0009791	biological_process	post-embryonic development
B	0016787	molecular_function	hydrolase activity
B	0016818	molecular_function	hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides
B	0016853	molecular_function	isomerase activity
B	0016887	molecular_function	ATP hydrolysis activity
B	0021510	biological_process	spinal cord development
B	0022405	biological_process	hair cycle process
B	0030198	biological_process	extracellular matrix organization
B	0030282	biological_process	bone mineralization
B	0030674	molecular_function	protein-macromolecule adaptor activity
B	0032289	biological_process	central nervous system myelin formation
B	0035264	biological_process	multicellular organism growth
B	0035315	biological_process	hair cell differentiation
B	0040016	biological_process	embryonic cleavage
B	0042274	biological_process	ribosomal small subunit biogenesis
B	0043139	molecular_function	5'-3' DNA helicase activity
B	0043249	biological_process	erythrocyte maturation
B	0043588	biological_process	skin development
B	0045951	biological_process	positive regulation of mitotic recombination
B	0046872	molecular_function	metal ion binding
B	0048009	biological_process	insulin-like growth factor receptor signaling pathway
B	0048568	biological_process	embryonic organ development
B	0048820	biological_process	hair follicle maturation
B	0051536	molecular_function	iron-sulfur cluster binding
B	0051539	molecular_function	4 iron, 4 sulfur cluster binding
B	0060218	biological_process	hematopoietic stem cell differentiation
B	0070516	cellular_component	CAK-ERCC2 complex
B	0071425	biological_process	hematopoietic stem cell proliferation
B	0071817	cellular_component	MMXD complex
B	0072332	biological_process	intrinsic apoptotic signaling pathway by p53 class mediator
B	1901990	biological_process	regulation of mitotic cell cycle phase transition
C	0000438	cellular_component	core TFIIH complex portion of holo TFIIH complex
C	0000439	cellular_component	transcription factor TFIIH core complex
C	0001671	molecular_function	ATPase activator activity
C	0003690	molecular_function	double-stranded DNA binding
C	0005515	molecular_function	protein binding
C	0005634	cellular_component	nucleus
C	0005654	cellular_component	nucleoplasm
C	0005669	cellular_component	transcription factor TFIID complex
C	0005675	cellular_component	transcription factor TFIIH holo complex
C	0006281	biological_process	DNA repair
C	0006289	biological_process	nucleotide-excision repair
C	0006366	biological_process	transcription by RNA polymerase II
C	0006974	biological_process	DNA damage response
C	0016251	molecular_function	RNA polymerase II general transcription initiation factor activity
C	0016607	cellular_component	nuclear speck
D	0000438	cellular_component	core TFIIH complex portion of holo TFIIH complex
D	0000439	cellular_component	transcription factor TFIIH core complex
D	0002031	biological_process	G protein-coupled receptor internalization
D	0005515	molecular_function	protein binding
D	0005634	cellular_component	nucleus
D	0005654	cellular_component	nucleoplasm
D	0005669	cellular_component	transcription factor TFIID complex
D	0005675	cellular_component	transcription factor TFIIH holo complex
D	0006281	biological_process	DNA repair
D	0006289	biological_process	nucleotide-excision repair
D	0006351	biological_process	DNA-templated transcription
D	0006357	biological_process	regulation of transcription by RNA polymerase II
D	0006366	biological_process	transcription by RNA polymerase II
D	0006367	biological_process	transcription initiation at RNA polymerase II promoter
D	0006974	biological_process	DNA damage response
D	0008270	molecular_function	zinc ion binding
D	0009411	biological_process	response to UV
D	0016251	molecular_function	RNA polymerase II general transcription initiation factor activity
D	0016607	cellular_component	nuclear speck
D	0046872	molecular_function	metal ion binding
E	0000438	cellular_component	core TFIIH complex portion of holo TFIIH complex
E	0000439	cellular_component	transcription factor TFIIH core complex
E	0005515	molecular_function	protein binding
E	0005634	cellular_component	nucleus
E	0005654	cellular_component	nucleoplasm
E	0005669	cellular_component	transcription factor TFIID complex
E	0005675	cellular_component	transcription factor TFIIH holo complex
E	0006281	biological_process	DNA repair
E	0006289	biological_process	nucleotide-excision repair
E	0006355	biological_process	regulation of DNA-templated transcription
E	0006366	biological_process	transcription by RNA polymerase II
E	0006974	biological_process	DNA damage response
E	0008270	molecular_function	zinc ion binding
E	0016251	molecular_function	RNA polymerase II general transcription initiation factor activity
E	0046872	molecular_function	metal ion binding
E	0097550	cellular_component	transcription preinitiation complex
F	0000439	cellular_component	transcription factor TFIIH core complex
F	0000462	biological_process	maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
F	0005515	molecular_function	protein binding
F	0005634	cellular_component	nucleus
F	0005654	cellular_component	nucleoplasm
F	0005669	cellular_component	transcription factor TFIID complex
F	0005675	cellular_component	transcription factor TFIIH holo complex
F	0005730	cellular_component	nucleolus
F	0005737	cellular_component	cytoplasm
F	0006281	biological_process	DNA repair
F	0006289	biological_process	nucleotide-excision repair
F	0006294	biological_process	nucleotide-excision repair, preincision complex assembly
F	0006362	biological_process	transcription elongation by RNA polymerase I
F	0006366	biological_process	transcription by RNA polymerase II
F	0006367	biological_process	transcription initiation at RNA polymerase II promoter
F	0006974	biological_process	DNA damage response
F	0071480	biological_process	cellular response to gamma radiation
G	0000110	cellular_component	nucleotide-excision repair factor 1 complex
G	0000715	biological_process	nucleotide-excision repair, DNA damage recognition
G	0003677	molecular_function	DNA binding
G	0003684	molecular_function	damaged DNA binding
G	0005515	molecular_function	protein binding
G	0005634	cellular_component	nucleus
G	0005654	cellular_component	nucleoplasm
G	0005662	cellular_component	DNA replication factor A complex
G	0005829	cellular_component	cytosol
G	0006281	biological_process	DNA repair
G	0006284	biological_process	base-excision repair
G	0006289	biological_process	nucleotide-excision repair
G	0006974	biological_process	DNA damage response
G	0006979	biological_process	response to oxidative stress
G	0008270	molecular_function	zinc ion binding
G	0008630	biological_process	intrinsic apoptotic signaling pathway in response to DNA damage
G	0009411	biological_process	response to UV
G	0009636	biological_process	response to toxic substance
G	0009650	biological_process	UV protection
G	0010506	biological_process	regulation of autophagy
G	0016604	cellular_component	nuclear body
G	0019904	molecular_function	protein domain specific binding
G	0034504	biological_process	protein localization to nucleus
G	0035264	biological_process	multicellular organism growth
G	0042803	molecular_function	protein homodimerization activity
G	0046872	molecular_function	metal ion binding
G	0060261	biological_process	positive regulation of transcription initiation by RNA polymerase II
G	0070914	biological_process	UV-damage excision repair
G	1901255	biological_process	nucleotide-excision repair involved in interstrand cross-link repair
G	1990837	molecular_function	sequence-specific double-stranded DNA binding

Functional Information from PDB Data

site_id	AC1
Number of Residues	6
Details	binding site for residue SF4 B 1000

Chain	Residue
B	LEU115
B	CYS116
B	CYS134
B	CYS155
B	PHE157
B	CYS190

---

site_id	AC2
Number of Residues	6
Details	binding site for residue ZN E 401

Chain	Residue
E	CYS282
E	THR284
E	CYS285
E	CYS268
E	VAL270
E	CYS271

---

site_id	AC3
Number of Residues	4
Details	binding site for residue ZN E 402

Chain	Residue
E	CYS255
E	CYS257
E	HIS258
E	CYS276

---

site_id	AC4
Number of Residues	4
Details	binding site for residue ZN D 401

Chain	Residue
D	CYS291
D	CYS294
D	CYS305
D	CYS308

---

site_id	AC5
Number of Residues	4
Details	binding site for residue ZN D 402

Chain	Residue
D	CYS345
D	CYS348
D	CYS368
D	CYS371

---

site_id	AC6
Number of Residues	4
Details	binding site for residue ZN D 403

Chain	Residue
D	CYS360
D	CYS363
D	CYS382
D	CYS385

---

site_id	AC7
Number of Residues	4
Details	binding site for residue ZN G 301

Chain	Residue
G	CYS105
G	CYS108
G	CYS126
G	CYS129

---

Functional Information from PROSITE/UniProt

site_id	PS00028
Number of Residues	21
Details	ZINC_FINGER_C2H2_1 Zinc finger C2H2 type domain signature. Cav..CqnvFcvdcdvfvHdsl..H

Chain	Residue	Details
D	CYS360-HIS380

---

site_id	PS00690
Number of Residues	10
Details	DEAH_ATP_HELICASE DEAH-box subfamily ATP-dependent helicases signature. AvVVFDEAHN

Chain	Residue	Details
B	ALA229-ASN238

---

site_id	PS00752
Number of Residues	25
Details	XPA_1 XPA protein signature 1. CeECgkeFm.DsyLmnhFdlptCdnC

Chain	Residue	Details
G	CYS105-CYS129

---

site_id	PS00753
Number of Residues	17
Details	XPA_2 XPA protein signature 2. LITKTEaKqEYLLkDcD

Chain	Residue	Details
G	LEU138-ASP154

---

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	161
Details	Domain: {"description":"Helicase ATP-binding","evidences":[{"source":"PROSITE-ProRule","id":"PRU00541","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI2
Number of Residues	3
Details	Motif: {"description":"DEVH box"}

Chain

Residue

Details

---

site_id	SWS_FT_FI3
Number of Residues	7
Details	Binding site: {"evidences":[{"source":"PROSITE-ProRule","id":"PRU00541","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"33902107","evidenceCode":"ECO:0000305"},{"source":"PDB","id":"7NVV","evidenceCode":"ECO:0000312"},{"source":"PDB","id":"7NVX","evidenceCode":"ECO:0000312"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI4
Number of Residues	2
Details	Binding site: {"evidences":[{"source":"PubMed","id":"33902107","evidenceCode":"ECO:0000305"},{"source":"PDB","id":"7NVV","evidenceCode":"ECO:0000312"},{"source":"PDB","id":"7NVX","evidenceCode":"ECO:0000312"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI5
Number of Residues	1
Details	Modified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"23186163","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI6
Number of Residues	199
Details	Region: {"description":"Mediates interaction with MMS19"}

Chain

Residue

Details

---

site_id	SWS_FT_FI7
Number of Residues	3
Details	Motif: {"description":"DEAH box"}

Chain

Residue

Details

---

site_id	SWS_FT_FI8
Number of Residues	13
Details	Motif: {"description":"Nuclear localization signal","evidences":[{"evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI9
Number of Residues	7
Details	Binding site: {"evidences":[{"source":"PROSITE-ProRule","id":"PRU00541","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI10
Number of Residues	4
Details	Binding site: {"evidences":[{"source":"PubMed","id":"31253769","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"6RO4","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI11
Number of Residues	34
Details	Zinc finger: {"description":"C4-type"}

Chain

Residue

Details

---

site_id	SWS_FT_FI12
Number of Residues	176
Details	Domain: {"description":"VWFA","evidences":[{"source":"PROSITE-ProRule","id":"PRU00219","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI13
Number of Residues	1
Details	Modified residue: {"description":"Phosphotyrosine","evidences":[{"source":"UniProtKB","id":"A0JN27","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI14
Number of Residues	24
Details	Zinc finger: {"evidences":[{"source":"PubMed","id":"2234061","evidenceCode":"ECO:0000305"},{"source":"PubMed","id":"31253769","evidenceCode":"ECO:0000305"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI15
Number of Residues	4
Details	Binding site: {"evidences":[{"source":"PubMed","id":"31253769","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1D4U","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1XPA","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"6RO4","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI16
Number of Residues	1
Details	Modified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"16540648","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"23186163","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI17
Number of Residues	2
Details	Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)","evidences":[{"source":"PubMed","id":"25218447","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---