5U0S

Cryo-EM structure of the Mediator-RNAPII complex

Functional Information from GO Data

Chain	GOid	namespace	contents
2	0003713	molecular_function	transcription coactivator activity
2	0005515	molecular_function	protein binding
2	0005634	cellular_component	nucleus
2	0016592	cellular_component	mediator complex
2	0060261	biological_process	positive regulation of transcription initiation by RNA polymerase II
3	0003712	molecular_function	transcription coregulator activity
3	0003713	molecular_function	transcription coactivator activity
3	0005634	cellular_component	nucleus
3	0006355	biological_process	regulation of DNA-templated transcription
3	0006357	biological_process	regulation of transcription by RNA polymerase II
3	0016592	cellular_component	mediator complex
3	0060261	biological_process	positive regulation of transcription initiation by RNA polymerase II
3	0070847	cellular_component	core mediator complex
F	0003712	molecular_function	transcription coregulator activity
F	0003713	molecular_function	transcription coactivator activity
F	0005634	cellular_component	nucleus
F	0006357	biological_process	regulation of transcription by RNA polymerase II
F	0016592	cellular_component	mediator complex
F	0060261	biological_process	positive regulation of transcription initiation by RNA polymerase II
F	0070847	cellular_component	core mediator complex
G	0000791	cellular_component	euchromatin
G	0003712	molecular_function	transcription coregulator activity
G	0003713	molecular_function	transcription coactivator activity
G	0005634	cellular_component	nucleus
G	0006357	biological_process	regulation of transcription by RNA polymerase II
G	0016592	cellular_component	mediator complex
G	0060261	biological_process	positive regulation of transcription initiation by RNA polymerase II
G	0070847	cellular_component	core mediator complex
H	0000978	molecular_function	RNA polymerase II cis-regulatory region sequence-specific DNA binding
H	0003712	molecular_function	transcription coregulator activity
H	0003713	molecular_function	transcription coactivator activity
H	0005515	molecular_function	protein binding
H	0005634	cellular_component	nucleus
H	0006357	biological_process	regulation of transcription by RNA polymerase II
H	0006367	biological_process	transcription initiation at RNA polymerase II promoter
H	0016592	cellular_component	mediator complex
H	0060261	biological_process	positive regulation of transcription initiation by RNA polymerase II
H	0070847	cellular_component	core mediator complex
I	0003713	molecular_function	transcription coactivator activity
I	0005634	cellular_component	nucleus
I	0016592	cellular_component	mediator complex
I	0060261	biological_process	positive regulation of transcription initiation by RNA polymerase II
K	0003712	molecular_function	transcription coregulator activity
K	0003713	molecular_function	transcription coactivator activity
K	0005515	molecular_function	protein binding
K	0005634	cellular_component	nucleus
K	0005737	cellular_component	cytoplasm
K	0006357	biological_process	regulation of transcription by RNA polymerase II
K	0016592	cellular_component	mediator complex
K	0060261	biological_process	positive regulation of transcription initiation by RNA polymerase II
N	0003712	molecular_function	transcription coregulator activity
N	0003713	molecular_function	transcription coactivator activity
N	0005634	cellular_component	nucleus
N	0006357	biological_process	regulation of transcription by RNA polymerase II
N	0006367	biological_process	transcription initiation at RNA polymerase II promoter
N	0016592	cellular_component	mediator complex
N	0060261	biological_process	positive regulation of transcription initiation by RNA polymerase II
N	0070847	cellular_component	core mediator complex
Q	0003712	molecular_function	transcription coregulator activity
Q	0003713	molecular_function	transcription coactivator activity
Q	0005515	molecular_function	protein binding
Q	0005634	cellular_component	nucleus
Q	0006357	biological_process	regulation of transcription by RNA polymerase II
Q	0006367	biological_process	transcription initiation at RNA polymerase II promoter
Q	0016592	cellular_component	mediator complex
Q	0060261	biological_process	positive regulation of transcription initiation by RNA polymerase II
Q	0070847	cellular_component	core mediator complex
R	0003712	molecular_function	transcription coregulator activity
R	0003713	molecular_function	transcription coactivator activity
R	0005515	molecular_function	protein binding
R	0005634	cellular_component	nucleus
R	0006357	biological_process	regulation of transcription by RNA polymerase II
R	0006369	biological_process	termination of RNA polymerase II transcription
R	0016592	cellular_component	mediator complex
R	0060261	biological_process	positive regulation of transcription initiation by RNA polymerase II
R	0070847	cellular_component	core mediator complex
T	0003712	molecular_function	transcription coregulator activity
T	0003713	molecular_function	transcription coactivator activity
T	0005515	molecular_function	protein binding
T	0005634	cellular_component	nucleus
T	0006357	biological_process	regulation of transcription by RNA polymerase II
T	0016592	cellular_component	mediator complex
T	0032991	cellular_component	protein-containing complex
T	0060261	biological_process	positive regulation of transcription initiation by RNA polymerase II
U	0003712	molecular_function	transcription coregulator activity
U	0003713	molecular_function	transcription coactivator activity
U	0005634	cellular_component	nucleus
U	0006357	biological_process	regulation of transcription by RNA polymerase II
U	0016592	cellular_component	mediator complex
U	0060261	biological_process	positive regulation of transcription initiation by RNA polymerase II
V	0003712	molecular_function	transcription coregulator activity
V	0003713	molecular_function	transcription coactivator activity
V	0005515	molecular_function	protein binding
V	0005634	cellular_component	nucleus
V	0006357	biological_process	regulation of transcription by RNA polymerase II
V	0006367	biological_process	transcription initiation at RNA polymerase II promoter
V	0016592	cellular_component	mediator complex
V	0060261	biological_process	positive regulation of transcription initiation by RNA polymerase II
a	0000428	cellular_component	DNA-directed RNA polymerase complex
a	0000785	cellular_component	chromatin
a	0001055	molecular_function	RNA polymerase II activity
a	0003677	molecular_function	DNA binding
a	0003899	molecular_function	DNA-directed 5'-3' RNA polymerase activity
a	0005515	molecular_function	protein binding
a	0005634	cellular_component	nucleus
a	0005665	cellular_component	RNA polymerase II, core complex
a	0005829	cellular_component	cytosol
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	0006369	biological_process	termination of RNA polymerase II transcription
a	0016591	cellular_component	RNA polymerase II, holoenzyme
a	0016740	molecular_function	transferase activity
a	0016779	molecular_function	nucleotidyltransferase activity
a	0030674	molecular_function	protein-macromolecule adaptor activity
a	0030846	biological_process	termination of RNA polymerase II transcription, poly(A)-coupled
a	0034062	molecular_function	5'-3' RNA polymerase activity
a	0046872	molecular_function	metal ion binding
b	0000428	cellular_component	DNA-directed RNA polymerase complex
b	0001055	molecular_function	RNA polymerase II activity
b	0003677	molecular_function	DNA binding
b	0003723	molecular_function	RNA binding
b	0003899	molecular_function	DNA-directed 5'-3' RNA polymerase activity
b	0005515	molecular_function	protein binding
b	0005634	cellular_component	nucleus
b	0005665	cellular_component	RNA polymerase II, core complex
b	0005721	cellular_component	pericentric heterochromatin
b	0005829	cellular_component	cytosol
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	0016591	cellular_component	RNA polymerase II, holoenzyme
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
b	0140727	biological_process	siRNA-mediated pericentric heterochromatin formation
c	0000428	cellular_component	DNA-directed RNA polymerase complex
c	0000785	cellular_component	chromatin
c	0001055	molecular_function	RNA polymerase II activity
c	0003677	molecular_function	DNA binding
c	0003899	molecular_function	DNA-directed 5'-3' RNA polymerase activity
c	0005515	molecular_function	protein binding
c	0005634	cellular_component	nucleus
c	0005665	cellular_component	RNA polymerase II, core complex
c	0005829	cellular_component	cytosol
c	0006351	biological_process	DNA-templated transcription
c	0006366	biological_process	transcription by RNA polymerase II
c	0016591	cellular_component	RNA polymerase II, holoenzyme
c	0046983	molecular_function	protein dimerization activity
c	0055029	cellular_component	nuclear DNA-directed RNA polymerase complex
d	0000166	molecular_function	nucleotide binding
d	0000428	cellular_component	DNA-directed RNA polymerase complex
d	0003899	molecular_function	DNA-directed 5'-3' RNA polymerase activity
d	0005515	molecular_function	protein binding
d	0005634	cellular_component	nucleus
d	0005665	cellular_component	RNA polymerase II, core complex
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	0016591	cellular_component	RNA polymerase II, holoenzyme
d	0030880	cellular_component	RNA polymerase complex
d	0031369	molecular_function	translation initiation factor binding
d	0034402	biological_process	obsolete recruitment of 3'-end processing factors to RNA polymerase II holoenzyme complex
d	0044237	biological_process	cellular metabolic process
e	0000428	cellular_component	DNA-directed RNA polymerase complex
e	0001054	molecular_function	RNA polymerase I activity
e	0001055	molecular_function	RNA polymerase II activity
e	0001056	molecular_function	RNA polymerase III activity
e	0003677	molecular_function	DNA binding
e	0003899	molecular_function	DNA-directed 5'-3' RNA polymerase activity
e	0005515	molecular_function	protein binding
e	0005634	cellular_component	nucleus
e	0005665	cellular_component	RNA polymerase II, core complex
e	0005666	cellular_component	RNA polymerase III complex
e	0005736	cellular_component	RNA polymerase I complex
e	0005829	cellular_component	cytosol
e	0006351	biological_process	DNA-templated transcription
e	0006360	biological_process	transcription by RNA polymerase I
e	0006362	biological_process	transcription elongation by RNA polymerase I
e	0006366	biological_process	transcription by RNA polymerase II
e	0006367	biological_process	transcription initiation at RNA polymerase II promoter
e	0006383	biological_process	transcription by RNA polymerase III
e	0016591	cellular_component	RNA polymerase II, holoenzyme
e	0042797	biological_process	tRNA transcription by RNA polymerase III
e	0055029	cellular_component	nuclear DNA-directed RNA polymerase complex
f	0000428	cellular_component	DNA-directed RNA polymerase complex
f	0001054	molecular_function	RNA polymerase I activity
f	0001055	molecular_function	RNA polymerase II activity
f	0001056	molecular_function	RNA polymerase III activity
f	0003677	molecular_function	DNA binding
f	0003899	molecular_function	DNA-directed 5'-3' RNA polymerase activity
f	0005515	molecular_function	protein binding
f	0005634	cellular_component	nucleus
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	0005829	cellular_component	cytosol
f	0006351	biological_process	DNA-templated transcription
f	0006354	biological_process	DNA-templated transcription elongation
f	0006360	biological_process	transcription by RNA polymerase I
f	0006362	biological_process	transcription elongation by RNA polymerase I
f	0006366	biological_process	transcription by RNA polymerase II
f	0016591	cellular_component	RNA polymerase II, holoenzyme
f	0042797	biological_process	tRNA transcription by RNA polymerase III
g	0000291	biological_process	obsolete nuclear-transcribed mRNA catabolic process, exonucleolytic
g	0000428	cellular_component	DNA-directed RNA polymerase complex
g	0000932	cellular_component	P-body
g	0003676	molecular_function	nucleic acid binding
g	0003697	molecular_function	single-stranded DNA binding
g	0003727	molecular_function	single-stranded RNA binding
g	0005515	molecular_function	protein binding
g	0005634	cellular_component	nucleus
g	0005665	cellular_component	RNA polymerase II, core complex
g	0005829	cellular_component	cytosol
g	0006351	biological_process	DNA-templated transcription
g	0006352	biological_process	DNA-templated transcription initiation
g	0006367	biological_process	transcription initiation at RNA polymerase II promoter
g	0010590	biological_process	regulation of septum digestion after cytokinesis
g	0016591	cellular_component	RNA polymerase II, holoenzyme
g	0031369	molecular_function	translation initiation factor binding
g	0045948	biological_process	positive regulation of translational initiation
g	0055029	cellular_component	nuclear DNA-directed RNA polymerase complex
g	0060213	biological_process	positive regulation of nuclear-transcribed mRNA poly(A) tail shortening
h	0000428	cellular_component	DNA-directed RNA polymerase complex
h	0001054	molecular_function	RNA polymerase I activity
h	0001055	molecular_function	RNA polymerase II activity
h	0001056	molecular_function	RNA polymerase III activity
h	0003677	molecular_function	DNA binding
h	0003899	molecular_function	DNA-directed 5'-3' RNA polymerase activity
h	0005634	cellular_component	nucleus
h	0005665	cellular_component	RNA polymerase II, core complex
h	0005666	cellular_component	RNA polymerase III complex
h	0005736	cellular_component	RNA polymerase I complex
h	0005829	cellular_component	cytosol
h	0006351	biological_process	DNA-templated transcription
h	0006362	biological_process	transcription elongation by RNA polymerase I
h	0006366	biological_process	transcription by RNA polymerase II
h	0006383	biological_process	transcription by RNA polymerase III
h	0016591	cellular_component	RNA polymerase II, holoenzyme
i	0000428	cellular_component	DNA-directed RNA polymerase complex
i	0001193	biological_process	maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II
i	0003676	molecular_function	nucleic acid binding
i	0003899	molecular_function	DNA-directed 5'-3' RNA polymerase activity
i	0005634	cellular_component	nucleus
i	0005665	cellular_component	RNA polymerase II, core complex
i	0005730	cellular_component	nucleolus
i	0005829	cellular_component	cytosol
i	0006283	biological_process	transcription-coupled nucleotide-excision repair
i	0006351	biological_process	DNA-templated transcription
i	0006367	biological_process	transcription initiation at RNA polymerase II promoter
i	0008270	molecular_function	zinc ion binding
i	0016591	cellular_component	RNA polymerase II, holoenzyme
i	0046872	molecular_function	metal ion binding
j	0000428	cellular_component	DNA-directed RNA polymerase complex
j	0001054	molecular_function	RNA polymerase I activity
j	0001055	molecular_function	RNA polymerase II activity
j	0001056	molecular_function	RNA polymerase III activity
j	0003677	molecular_function	DNA binding
j	0003899	molecular_function	DNA-directed 5'-3' RNA polymerase activity
j	0005634	cellular_component	nucleus
j	0005665	cellular_component	RNA polymerase II, core complex
j	0005666	cellular_component	RNA polymerase III complex
j	0005730	cellular_component	nucleolus
j	0005736	cellular_component	RNA polymerase I complex
j	0005829	cellular_component	cytosol
j	0006351	biological_process	DNA-templated transcription
j	0006360	biological_process	transcription by RNA polymerase I
j	0006362	biological_process	transcription elongation by RNA polymerase I
j	0006366	biological_process	transcription by RNA polymerase II
j	0006367	biological_process	transcription initiation at RNA polymerase II promoter
j	0006383	biological_process	transcription by RNA polymerase III
j	0008270	molecular_function	zinc ion binding
j	0016591	cellular_component	RNA polymerase II, holoenzyme
j	0042797	biological_process	tRNA transcription by RNA polymerase III
j	0046872	molecular_function	metal ion binding
k	0000428	cellular_component	DNA-directed RNA polymerase complex
k	0001055	molecular_function	RNA polymerase II activity
k	0003677	molecular_function	DNA binding
k	0003899	molecular_function	DNA-directed 5'-3' RNA polymerase activity
k	0005515	molecular_function	protein binding
k	0005634	cellular_component	nucleus
k	0005665	cellular_component	RNA polymerase II, core complex
k	0005829	cellular_component	cytosol
k	0006351	biological_process	DNA-templated transcription
k	0006366	biological_process	transcription by RNA polymerase II
k	0006367	biological_process	transcription initiation at RNA polymerase II promoter
k	0016591	cellular_component	RNA polymerase II, holoenzyme
k	0046983	molecular_function	protein dimerization activity
l	0000428	cellular_component	DNA-directed RNA polymerase complex
l	0001054	molecular_function	RNA polymerase I activity
l	0001055	molecular_function	RNA polymerase II activity
l	0001056	molecular_function	RNA polymerase III activity
l	0003677	molecular_function	DNA binding
l	0003899	molecular_function	DNA-directed 5'-3' RNA polymerase activity
l	0005515	molecular_function	protein binding
l	0005634	cellular_component	nucleus
l	0005665	cellular_component	RNA polymerase II, core complex
l	0005666	cellular_component	RNA polymerase III complex
l	0005730	cellular_component	nucleolus
l	0005736	cellular_component	RNA polymerase I complex
l	0005829	cellular_component	cytosol
l	0006351	biological_process	DNA-templated transcription
l	0006360	biological_process	transcription by RNA polymerase I
l	0006362	biological_process	transcription elongation by RNA polymerase I
l	0006366	biological_process	transcription by RNA polymerase II
l	0006383	biological_process	transcription by RNA polymerase III
l	0008270	molecular_function	zinc ion binding
l	0046872	molecular_function	metal ion binding

Functional Information from PROSITE/UniProt

site_id	PS00018
Number of Residues	13
Details	EF_HAND_1 EF-hand calcium-binding domain. DENKNQSIEnaDY

Chain	Residue	Details
F	ASP177-TYR189

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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	THR76-GLN90

---

site_id	PS00446
Number of Residues	41
Details	RNA_POL_D_30KD RNA polymerases D / 30 to 40 Kd subunits signature. NSLRRvvlaeiptvAidlVeinvNtSvmpDEfLAhRLGMIP

Chain	Residue	Details
c	ASN30-PRO70

---

site_id	PS01154
Number of Residues	32
Details	RNA_POL_L_13KD RNA polymerases L / 13 to 16 Kd subunits signature. LekEdHTLaNmLanqLlsderVlfagYkvpHP

Chain	Residue	Details
k	LEU34-PRO65

---

site_id	PS01112
Number of Residues	10
Details	RNA_POL_N_8KD RNA polymerases N / 8 Kd subunits signature. IIPIrCFSCG

Chain	Residue	Details
j	ILE2-GLY11

---

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

Chain	Residue	Details
b	GLY966-THR978

---

site_id	PS01110
Number of Residues	14
Details	RNA_POL_H_23KD RNA polymerases H / 23 Kd subunits signature. HELVPKHilLspDE

Chain	Residue	Details
e	HIS142-GLU155

---

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

Chain	Residue	Details
a	TYR1578-SER1584
a	TYR1648-SER1654
a	TYR1655-SER1661
a	TYR1662-SER1668
a	TYR1669-SER1675
a	TYR1676-SER1682
a	TYR1683-SER1689
a	TYR1690-SER1696
a	TYR1697-SER1703
a	TYR1704-SER1710
a	TYR1711-SER1717
a	TYR1585-SER1591
a	TYR1718-SER1724
a	TYR1725-SER1731
a	TYR1732-SER1738
a	TYR1739-SER1745
a	TYR1746-SER1752
a	TYR1592-SER1598
a	TYR1599-SER1605
a	TYR1613-SER1619
a	TYR1620-SER1626
a	TYR1627-SER1633
a	TYR1634-SER1640
a	TYR1641-SER1647

---

site_id	PS00466
Number of Residues	36
Details	ZF_TFIIS_1 Zinc finger TFIIS-type signature. CprChqheavfyqTHSRRgDTMmtliyvCvh...CgfaF

Chain	Residue	Details
i	CYS75-PHE110

---

site_id	PS01030
Number of Residues	27
Details	RNA_POL_M_15KD RNA polymerases M / 15 Kd subunits signature. YCiECNNMLypredkvdrvlrlaCrnC

Chain	Residue	Details
i	TYR6-CYS32

---

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	20
Details	ZN_FING: C4-type => ECO:0000255

Chain	Residue	Details
l	CYS24-CYS44
a	CYS109
a	CYS112
a	CYS150
a	CYS175
a	ASP487
a	ASP489
a	ASP491
j	CYS10
j	CYS44
j	CYS45

---

site_id	SWS_FT_FI2
Number of Residues	4
Details	BINDING: BINDING => ECO:0000250

Chain	Residue	Details
b	CYS1173
l	CYS24
l	CYS27
l	CYS41
l	CYS44

---

site_id	SWS_FT_FI3
Number of Residues	4
Details	BINDING: BINDING => ECO:0000250|UniProtKB:P27999

Chain	Residue	Details
i	CYS7
i	CYS10
i	CYS29
i	CYS32

---

site_id	SWS_FT_FI4
Number of Residues	4
Details	BINDING: BINDING => ECO:0000255|PROSITE-ProRule:PRU00472

Chain	Residue	Details
i	CYS75
i	CYS78
i	CYS103
i	CYS106

---