7O4L

Yeast TFIIH in the expanded state within the pre-initiation complex

Functional Information from GO Data

Chain	GOid	namespace	contents
0	0000019	biological_process	regulation of mitotic recombination
0	0000112	cellular_component	nucleotide-excision repair factor 3 complex
0	0000166	molecular_function	nucleotide binding
0	0000439	cellular_component	transcription factor TFIIH core complex
0	0003676	molecular_function	nucleic acid binding
0	0003677	molecular_function	DNA binding
0	0003678	molecular_function	DNA helicase activity
0	0003684	molecular_function	damaged DNA binding
0	0004386	molecular_function	helicase activity
0	0005515	molecular_function	protein binding
0	0005524	molecular_function	ATP binding
0	0005634	cellular_component	nucleus
0	0005675	cellular_component	transcription factor TFIIH holo complex
0	0005829	cellular_component	cytosol
0	0006139	biological_process	nucleobase-containing compound metabolic process
0	0006281	biological_process	DNA repair
0	0006289	biological_process	nucleotide-excision repair
0	0006366	biological_process	transcription by RNA polymerase II
0	0006367	biological_process	transcription initiation at RNA polymerase II promoter
0	0006974	biological_process	DNA damage response
0	0008094	molecular_function	ATP-dependent activity, acting on DNA
0	0016787	molecular_function	hydrolase activity
0	0016818	molecular_function	hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides
0	0016853	molecular_function	isomerase activity
0	0016887	molecular_function	ATP hydrolysis activity
0	0043139	molecular_function	5'-3' DNA helicase activity
0	0045951	biological_process	positive regulation of mitotic recombination
0	0046872	molecular_function	metal ion binding
0	0051536	molecular_function	iron-sulfur cluster binding
0	0051539	molecular_function	4 iron, 4 sulfur cluster binding
1	0000112	cellular_component	nucleotide-excision repair factor 3 complex
1	0000439	cellular_component	transcription factor TFIIH core complex
1	0005515	molecular_function	protein binding
1	0005634	cellular_component	nucleus
1	0005675	cellular_component	transcription factor TFIIH holo complex
1	0005829	cellular_component	cytosol
1	0006281	biological_process	DNA repair
1	0006289	biological_process	nucleotide-excision repair
1	0006351	biological_process	DNA-templated transcription
1	0006360	biological_process	transcription by RNA polymerase I
1	0006366	biological_process	transcription by RNA polymerase II
1	0006367	biological_process	transcription initiation at RNA polymerase II promoter
1	0006974	biological_process	DNA damage response
1	0010314	molecular_function	phosphatidylinositol-5-phosphate binding
1	0032266	molecular_function	phosphatidylinositol-3-phosphate binding
2	0000112	cellular_component	nucleotide-excision repair factor 3 complex
2	0000439	cellular_component	transcription factor TFIIH core complex
2	0001671	molecular_function	ATPase activator activity
2	0003690	molecular_function	double-stranded DNA binding
2	0005515	molecular_function	protein binding
2	0005634	cellular_component	nucleus
2	0005675	cellular_component	transcription factor TFIIH holo complex
2	0006281	biological_process	DNA repair
2	0006289	biological_process	nucleotide-excision repair
2	0006366	biological_process	transcription by RNA polymerase II
2	0006367	biological_process	transcription initiation at RNA polymerase II promoter
2	0006974	biological_process	DNA damage response
3	0000993	molecular_function	RNA polymerase II complex binding
3	0001174	biological_process	transcriptional start site selection at RNA polymerase II promoter
3	0005634	cellular_component	nucleus
3	0005675	cellular_component	transcription factor TFIIH holo complex
3	0006281	biological_process	DNA repair
3	0006289	biological_process	nucleotide-excision repair
3	0006357	biological_process	regulation of transcription by RNA polymerase II
3	0006366	biological_process	transcription by RNA polymerase II
3	0006367	biological_process	transcription initiation at RNA polymerase II promoter
3	0008270	molecular_function	zinc ion binding
3	0045737	biological_process	positive regulation of cyclin-dependent protein serine/threonine kinase activity
3	0046872	molecular_function	metal ion binding
3	0061575	molecular_function	cyclin-dependent protein serine/threonine kinase activator activity
3	0070985	cellular_component	transcription factor TFIIK complex
4	0000112	cellular_component	nucleotide-excision repair factor 3 complex
4	0000439	cellular_component	transcription factor TFIIH core complex
4	0005634	cellular_component	nucleus
4	0005675	cellular_component	transcription factor TFIIH holo complex
4	0006281	biological_process	DNA repair
4	0006289	biological_process	nucleotide-excision repair
4	0006355	biological_process	regulation of DNA-templated transcription
4	0006366	biological_process	transcription by RNA polymerase II
4	0006367	biological_process	transcription initiation at RNA polymerase II promoter
4	0006974	biological_process	DNA damage response
4	0008270	molecular_function	zinc ion binding
4	0016251	molecular_function	RNA polymerase II general transcription initiation factor activity
4	0046872	molecular_function	metal ion binding
5	0000439	cellular_component	transcription factor TFIIH core complex
5	0000993	molecular_function	RNA polymerase II complex binding
5	0005515	molecular_function	protein binding
5	0005634	cellular_component	nucleus
5	0005675	cellular_component	transcription factor TFIIH holo complex
5	0005829	cellular_component	cytosol
5	0006281	biological_process	DNA repair
5	0006289	biological_process	nucleotide-excision repair
5	0006294	biological_process	nucleotide-excision repair, preincision complex assembly
5	0006366	biological_process	transcription by RNA polymerase II
5	0006367	biological_process	transcription initiation at RNA polymerase II promoter
5	0006974	biological_process	DNA damage response
6	0000112	cellular_component	nucleotide-excision repair factor 3 complex
6	0000439	cellular_component	transcription factor TFIIH core complex
6	0005634	cellular_component	nucleus
6	0005675	cellular_component	transcription factor TFIIH holo complex
6	0006281	biological_process	DNA repair
6	0006289	biological_process	nucleotide-excision repair
6	0006351	biological_process	DNA-templated transcription
6	0006357	biological_process	regulation of transcription by RNA polymerase II
6	0006366	biological_process	transcription by RNA polymerase II
6	0006367	biological_process	transcription initiation at RNA polymerase II promoter
6	0006974	biological_process	DNA damage response
6	0008270	molecular_function	zinc ion binding
6	0046872	molecular_function	metal ion binding
6	0061630	molecular_function	ubiquitin protein ligase activity
7	0000019	biological_process	regulation of mitotic recombination
7	0000112	cellular_component	nucleotide-excision repair factor 3 complex
7	0000166	molecular_function	nucleotide binding
7	0000439	cellular_component	transcription factor TFIIH core complex
7	0001111	biological_process	RNA polymerase II promoter clearance
7	0001113	biological_process	transcription open complex formation at RNA polymerase II promoter
7	0001174	biological_process	transcriptional start site selection at RNA polymerase II promoter
7	0003677	molecular_function	DNA binding
7	0003678	molecular_function	DNA helicase activity
7	0004386	molecular_function	helicase activity
7	0005524	molecular_function	ATP binding
7	0005634	cellular_component	nucleus
7	0005675	cellular_component	transcription factor TFIIH holo complex
7	0005829	cellular_component	cytosol
7	0006281	biological_process	DNA repair
7	0006289	biological_process	nucleotide-excision repair
7	0006366	biological_process	transcription by RNA polymerase II
7	0006367	biological_process	transcription initiation at RNA polymerase II promoter
7	0006974	biological_process	DNA damage response
7	0015616	molecular_function	DNA translocase activity
7	0016787	molecular_function	hydrolase activity
7	0016853	molecular_function	isomerase activity
7	0016887	molecular_function	ATP hydrolysis activity
7	0016973	biological_process	poly(A)+ mRNA export from nucleus
7	0043138	molecular_function	3'-5' DNA helicase activity
7	0097550	cellular_component	transcription preinitiation complex
A	0000428	cellular_component	DNA-directed RNA polymerase complex
A	0001172	biological_process	RNA-templated transcription
A	0003677	molecular_function	DNA binding
A	0003899	molecular_function	DNA-directed RNA polymerase activity
A	0003968	molecular_function	RNA-directed RNA polymerase activity
A	0005515	molecular_function	protein binding
A	0005634	cellular_component	nucleus
A	0005665	cellular_component	RNA polymerase II, core complex
A	0005739	cellular_component	mitochondrion
A	0006351	biological_process	DNA-templated transcription
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	0008270	molecular_function	zinc ion binding
A	0010494	cellular_component	cytoplasmic stress granule
A	0016740	molecular_function	transferase activity
A	0016779	molecular_function	nucleotidyltransferase activity
A	0019985	biological_process	translesion synthesis
A	0034062	molecular_function	5'-3' RNA polymerase activity
A	0042789	biological_process	mRNA transcription by RNA polymerase II
A	0046872	molecular_function	metal ion binding
B	0000428	cellular_component	DNA-directed RNA polymerase complex
B	0001172	biological_process	RNA-templated transcription
B	0003676	molecular_function	nucleic acid binding
B	0003677	molecular_function	DNA binding
B	0003729	molecular_function	mRNA binding
B	0003899	molecular_function	DNA-directed RNA polymerase activity
B	0003968	molecular_function	RNA-directed RNA polymerase activity
B	0005515	molecular_function	protein binding
B	0005634	cellular_component	nucleus
B	0005665	cellular_component	RNA polymerase II, core complex
B	0005739	cellular_component	mitochondrion
B	0006351	biological_process	DNA-templated transcription
B	0006366	biological_process	transcription by RNA polymerase II
B	0006367	biological_process	transcription initiation at RNA polymerase II promoter
B	0006368	biological_process	transcription elongation by RNA polymerase II
B	0008270	molecular_function	zinc ion binding
B	0010494	cellular_component	cytoplasmic stress granule
B	0016740	molecular_function	transferase activity
B	0016779	molecular_function	nucleotidyltransferase activity
B	0032549	molecular_function	ribonucleoside binding
B	0034062	molecular_function	5'-3' RNA polymerase activity
B	0046872	molecular_function	metal ion binding
D	0000166	molecular_function	nucleotide binding
D	0000288	biological_process	nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay
D	0000428	cellular_component	DNA-directed RNA polymerase complex
D	0000932	cellular_component	P-body
D	0001172	biological_process	RNA-templated transcription
D	0003697	molecular_function	single-stranded DNA binding
D	0003727	molecular_function	single-stranded RNA binding
D	0003968	molecular_function	RNA-directed RNA polymerase activity
D	0005515	molecular_function	protein binding
D	0005634	cellular_component	nucleus
D	0005665	cellular_component	RNA polymerase II, core complex
D	0005737	cellular_component	cytoplasm
D	0006352	biological_process	DNA-templated transcription initiation
D	0006366	biological_process	transcription by RNA polymerase II
D	0006367	biological_process	transcription initiation at RNA polymerase II promoter
D	0006368	biological_process	transcription elongation by RNA polymerase II
D	0006397	biological_process	mRNA processing
D	0030880	cellular_component	RNA polymerase complex
D	0031369	molecular_function	translation initiation factor binding
D	0045948	biological_process	positive regulation of translational initiation
D	1990328	cellular_component	RPB4-RPB7 complex
F	0000428	cellular_component	DNA-directed RNA polymerase complex
F	0001172	biological_process	RNA-templated transcription
F	0003677	molecular_function	DNA binding
F	0003899	molecular_function	DNA-directed RNA polymerase activity
F	0003968	molecular_function	RNA-directed RNA polymerase activity
F	0005515	molecular_function	protein binding
F	0005634	cellular_component	nucleus
F	0005654	cellular_component	nucleoplasm
F	0005665	cellular_component	RNA polymerase II, core complex
F	0005666	cellular_component	RNA polymerase III complex
F	0005736	cellular_component	RNA polymerase I complex
F	0005737	cellular_component	cytoplasm
F	0006351	biological_process	DNA-templated transcription
F	0006360	biological_process	transcription by RNA polymerase I
F	0006361	biological_process	transcription initiation at RNA polymerase I promoter
F	0006362	biological_process	transcription elongation by RNA polymerase I
F	0006363	biological_process	termination of RNA polymerase I transcription
F	0006366	biological_process	transcription by RNA polymerase II
F	0006367	biological_process	transcription initiation at RNA polymerase II promoter
F	0006368	biological_process	transcription elongation by RNA polymerase II
F	0006383	biological_process	transcription by RNA polymerase III
F	0006384	biological_process	transcription initiation at RNA polymerase III promoter
F	0006386	biological_process	termination of RNA polymerase III transcription
F	0042254	biological_process	ribosome biogenesis
F	0042790	biological_process	nucleolar large rRNA transcription by RNA polymerase I
F	0042797	biological_process	tRNA transcription by RNA polymerase III
G	0000288	biological_process	nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay
G	0000428	cellular_component	DNA-directed RNA polymerase complex
G	0000932	cellular_component	P-body
G	0000956	biological_process	nuclear-transcribed mRNA catabolic process
G	0001172	biological_process	RNA-templated transcription
G	0003676	molecular_function	nucleic acid binding
G	0003697	molecular_function	single-stranded DNA binding
G	0003727	molecular_function	single-stranded RNA binding
G	0003968	molecular_function	RNA-directed RNA polymerase activity
G	0005515	molecular_function	protein binding
G	0005634	cellular_component	nucleus
G	0005665	cellular_component	RNA polymerase II, core complex
G	0005737	cellular_component	cytoplasm
G	0006351	biological_process	DNA-templated transcription
G	0006352	biological_process	DNA-templated transcription initiation
G	0006366	biological_process	transcription by RNA polymerase II
G	0006367	biological_process	transcription initiation at RNA polymerase II promoter
G	0006368	biological_process	transcription elongation by RNA polymerase II
G	0031369	molecular_function	translation initiation factor binding
G	0045948	biological_process	positive regulation of translational initiation
G	0060213	biological_process	positive regulation of nuclear-transcribed mRNA poly(A) tail shortening
G	1990328	cellular_component	RPB4-RPB7 complex
W	0000993	molecular_function	RNA polymerase II complex binding
W	0001097	molecular_function	TFIIH-class transcription factor complex binding
W	0001113	biological_process	transcription open complex formation at RNA polymerase II promoter
W	0003697	molecular_function	single-stranded DNA binding
W	0005515	molecular_function	protein binding
W	0005634	cellular_component	nucleus
W	0005673	cellular_component	transcription factor TFIIE complex
W	0005739	cellular_component	mitochondrion
W	0006366	biological_process	transcription by RNA polymerase II
W	0006367	biological_process	transcription initiation at RNA polymerase II promoter
W	0008270	molecular_function	zinc ion binding
W	0046872	molecular_function	metal ion binding
W	0097550	cellular_component	transcription preinitiation complex
X	0000993	molecular_function	RNA polymerase II complex binding
X	0001097	molecular_function	TFIIH-class transcription factor complex binding
X	0003677	molecular_function	DNA binding
X	0003697	molecular_function	single-stranded DNA binding
X	0005515	molecular_function	protein binding
X	0005634	cellular_component	nucleus
X	0005673	cellular_component	transcription factor TFIIE complex
X	0006366	biological_process	transcription by RNA polymerase II
X	0006367	biological_process	transcription initiation at RNA polymerase II promoter
X	0097550	cellular_component	transcription preinitiation complex

Functional Information from PROSITE/UniProt

site_id	PS00014
Number of Residues	4
Details	ER_TARGET Endoplasmic reticulum targeting sequence. SEEL

Chain	Residue	Details
3	SER318-LEU321

---

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

Chain	Residue	Details
6	CYS429-HIS449

---

site_id	PS00115
Number of Residues	7
Details	RNA_POL_II_REPEAT Eukaryotic RNA polymerase II heptapeptide repeat. YSPTSPA

Chain	Residue	Details
A	TYR1549-ALA1555
A	TYR1612-SER1618
A	TYR1619-SER1625
A	TYR1626-SER1632
A	TYR1633-SER1639
A	TYR1640-SER1646
A	TYR1647-SER1653
A	TYR1654-ALA1660
A	TYR1661-SER1667
A	TYR1668-SER1674
A	TYR1675-SER1681
A	TYR1556-SER1562
A	TYR1682-SER1688
A	TYR1689-ASN1695
A	TYR1696-SER1702
A	TYR1563-SER1569
A	TYR1570-SER1576
A	TYR1577-SER1583
A	TYR1584-SER1590
A	TYR1591-SER1597
A	TYR1598-SER1604
A	TYR1605-SER1611

---

site_id	PS00387
Number of Residues	7
Details	PPASE Inorganic pyrophosphatase signature. DDDEMDI

Chain	Residue	Details
W	ASP471-ILE477

---

site_id	PS00518
Number of Residues	10
Details	ZF_RING_1 Zinc finger RING-type signature. CyHrICesCV

Chain	Residue	Details
3	CYS34-VAL43

---

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

Chain	Residue	Details
0	SER230-ASN239

---

site_id	PS01111
Number of Residues	15
Details	RNA_POL_K_14KD RNA polymerases K / 14 to 18 Kd subunits signature. TkYErARiLGtRAlQ

Chain	Residue	Details
F	THR86-GLN100

---

site_id	PS01166
Number of Residues	13
Details	RNA_POL_BETA RNA polymerases beta chain signature. GdKFASrHGQKGT

Chain	Residue	Details
B	GLY977-THR989

---

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	440
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":"DEAH box"}

Chain

Residue

Details

---

site_id	SWS_FT_FI3
Number of Residues	14
Details	Binding site: {"evidences":[{"source":"PROSITE-ProRule","id":"PRU00541","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI4
Number of Residues	4
Details	Binding site: {"evidences":[{"source":"UniProtKB","id":"P18074","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI5
Number of Residues	47
Details	Zinc finger: {"description":"RING-type","evidences":[{"source":"PROSITE-ProRule","id":"PRU00175","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI6
Number of Residues	58
Details	Zinc finger: {"description":"C4-type"}

Chain

Residue

Details

---

site_id	SWS_FT_FI7
Number of Residues	179
Details	Domain: {"description":"VWFA","evidences":[{"source":"PROSITE-ProRule","id":"PRU00219","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI8
Number of Residues	154
Details	Domain: {"description":"Helicase C-terminal","evidences":[{"source":"PROSITE-ProRule","id":"PRU00542","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI9
Number of Residues	3
Details	Motif: {"description":"DEAH box","evidences":[{"source":"PROSITE-ProRule","id":"PRU00541","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI10
Number of Residues	1
Details	Modified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"17330950","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI11
Number of Residues	8
Details	Binding site: {"evidences":[{"source":"PubMed","id":"23151482","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"25652824","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"4BBR","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4V1M","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI12
Number of Residues	4
Details	Binding site: {}

Chain

Residue

Details

---

site_id	SWS_FT_FI13
Number of Residues	90
Details	Domain: {"description":"HTH TFE/IIEalpha-type","evidences":[{"source":"PROSITE-ProRule","id":"PRU00676","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI14
Number of Residues	28
Details	Zinc finger: {"description":"C4-type","evidences":[{"evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI15
Number of Residues	21
Details	Region: {"description":"Disordered","evidences":[{"source":"SAM","id":"MobiDB-lite","evidenceCode":"ECO:0000256"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI16
Number of Residues	12
Details	Compositional bias: {"description":"Basic and acidic residues","evidences":[{"source":"SAM","id":"MobiDB-lite","evidenceCode":"ECO:0000256"}]}

Chain

Residue

Details

---

Catalytic Information from CSA

site_id	MCSA1
Number of Residues
Details	M-CSA 788

Chain

Residue

Details

---