Research workbench

TFIID-based PIC-Mediator holo-complex in pre-assembled state (pre-hPIC-MED)

Analyse TFIID-based PIC-Mediator holo-complex in pre-assembled state (pre-hPIC-MED) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7ENA
Type: protein + DNA
Length: 21,733 residues
Chains: 76
Method: electron microscopy
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 4.07
Source: Homo sapiens; Sus scrofa; SYNTHETIC CONSTRUCT
Molecule: CDK-activating kinase assembly factor MAT1; Cyclin-dependent kinase 7; Cyclin-H…
EC: 2.7.11.22, 2.7.11.23, 2.3.1.48, 3.6.4.12, 2.7.7.6, 2.7.11.1
UniProt: P51948, P50613, P51946, P52657, P20226, Q00403, P35269, P13984, A0A4X1TVZ5, I3LCH3, A0A481BYI6, A0A4X1VTX4, A0A4X1VEK9, A0A4X1VKG7, A0A4X1ULF2, P60899, A0A4X1UK25, A0A4X1TRS6, P21675, Q6P1X5, O00268, Q15542, P49848, Q15545, Q7Z7C8, Q16594, Q12962, Q16514, Q5VWG9, Q15544, Q15543, P29083, P29084, P32780, Q13888, Q13889, Q92759, Q6ZYL4, P19447, P18074, Q6P2C8, Q9H204, Q9NX70, Q96HR3, Q9Y3C7, Q15648, Q9NPJ6, O75586, O43513, Q96G25, Q9NWA0, Q9BTT4, Q9P086, O60244, Q96RN5, Q9NVC6, Q9BUE0, A0JLT2, Q9H944, Q13503, Q15528, O95402, O75448, Q9ULK4, Q9Y2X0
Ligands: SF4, ZN, MG
Pockets: 20 · best druggability 0.89

Structure

electron microscopy · resolution 4.07 · 76 distinct chains · 43% helix, 12% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
0	CDK-activating kinase assembly factor MAT1	protein	306	49% helix, 3% strand	P51948
8	Cyclin-dependent kinase 7 (EC 2.7.11.22, 2.7.11.23)	protein	299	31% helix, 11% strand	P50613
9	Cyclin-H	protein	287	66% helix, 0% strand	P51946
DO	Transcription initiation factor IIA subunit 2	protein	97	38% helix, 23% strand	P52657
DP	TATA-box-binding protein	protein	177	26% helix, 33% strand	P20226
DQ	TFIIA-a	protein	122	39% helix, 32% strand	—
BA	Transcription initiation factor IIB (EC 2.3.1.48)	protein	255	53% helix, 3% strand	Q00403
FA	General transcription factor IIF subunit 1	protein	134	17% helix, 35% strand	P35269
FB	General transcription factor IIF subunit 2 (EC 3.6.4.12)	protein	222	29% helix, 27% strand	P13984
PA	RPB1	protein	1475	39% helix, 13% strand	—
PB	DNA-directed RNA polymerase subunit beta (EC 2.7.7.6)	protein	1134	27% helix, 20% strand	A0A4X1TVZ5
PC	DNA-directed RNA polymerase II subunit RPB3	protein	257	25% helix, 19% strand	I3LCH3
PD	DNA-directed RNA polymerase II subunit RPB4	protein	129	64% helix, 0% strand	A0A481BYI6
PE	DNA-directed RNA polymerase II subunit E	protein	209	40% helix, 18% strand	A0A4X1VTX4
PF	DNA-directed RNA polymerase II subunit F	protein	79	30% helix, 16% strand	A0A4X1VEK9
PG	DNA-directed RNA polymerase II subunit RPB7	protein	171	8% helix, 39% strand	A0A4X1VKG7
PH	DNA-directed RNA polymerases I, II, and III subunit RPABC3	protein	148	3% helix, 32% strand	A0A4X1ULF2
PI	DNA-directed RNA polymerase II subunit RPB9	protein	114	8% helix, 24% strand	P60899
PJ	RPB10	protein	64	39% helix, 3% strand	—
PK	RNA_pol_L_2 domain-containing protein	protein	117	38% helix, 18% strand	A0A4X1UK25
PL	RPB12	protein	44	0% helix, 20% strand	A0A4X1TRS6
DA	Transcription initiation factor TFIID subunit 1 (EC 2.3.1.48, 2.7.11.1)	protein	600	35% helix, 13% strand	P21675
DB	Transcription initiation factor TFIID subunit 2	protein	963	40% helix, 19% strand	Q6P1X5
DD	Transcription initiation factor TFIID subunit 4	protein	159	66% helix, 2% strand	O00268
DE	Transcription initiation factor TFIID subunit 5	protein	546	23% helix, 28% strand	Q15542
DF	Transcription initiation factor TFIID subunit 6	protein	408	55% helix, 2% strand	P49848
DG	Transcription initiation factor TFIID subunit 7	protein	145	25% helix, 38% strand	Q15545
DH	Transcription initiation factor TFIID subunit 8	protein	209	43% helix, 3% strand	Q7Z7C8
DI	Transcription initiation factor TFIID subunit 9	protein	120	52% helix, 1% strand	Q16594
DJ	Transcription initiation factor TFIID subunit 10	protein	90	54% helix, 3% strand	Q12962
DL	Transcription initiation factor TFIID subunit 12	protein	75	64% helix, 4% strand	Q16514
Dc	Transcription initiation factor TFIID subunit 3	protein	127	53% helix, 3% strand	Q5VWG9
Dd	Transcription initiation factor TFIID subunit 4	protein	158	53% helix, 4% strand	O00268
De	Transcription initiation factor TFIID subunit 5	protein	539	13% helix, 26% strand	Q15542
Df	Transcription initiation factor TFIID subunit 6	protein	403	52% helix, 4% strand	P49848
Di	Transcription initiation factor TFIID subunit 9	protein	121	45% helix, 3% strand	Q16594
Dj	Transcription initiation factor TFIID subunit 10	protein	95	46% helix, 3% strand	Q12962
Dk	Transcription initiation factor TFIID subunit 11	protein	98	63% helix, 0% strand	Q15544
Dl	Transcription initiation factor TFIID subunit 12	protein	107	55% helix, 3% strand	Q16514
Dm	Transcription initiation factor TFIID subunit 13	protein	87	39% helix, 1% strand	Q15543
EA	General transcription factor IIE subunit 1	protein	179	50% helix, 6% strand	P29083
EB	Transcription initiation factor IIE subunit beta	protein	172	40% helix, 6% strand	P29084
1	General transcription factor IIH subunit 1	protein	433	56% helix, 0% strand	P32780
2	General transcription factor IIH subunit 2	protein	385	31% helix, 14% strand	Q13888
3	General transcription factor IIH subunit 3	protein	295	29% helix, 10% strand	Q13889
4	General transcription factor IIH subunit 4	protein	457	41% helix, 1% strand	Q92759
5	General transcription factor IIH subunit 5	protein	66	41% helix, 3% strand	Q6ZYL4
6	General transcription and DNA repair factor IIH helicase subunit XPB (EC 3.6.4.12)	protein	652	35% helix, 9% strand	P19447
7	General transcription and DNA repair factor IIH helicase subunit XPD (EC 3.6.4.12)	protein	732	41% helix, 7% strand	P18074
c	Mediator of RNA polymerase II transcription subunit 27	protein	263	49% helix, 13% strand	Q6P2C8
e	Mediator of RNA polymerase II transcription subunit 28	protein	102	82% helix, 0% strand	Q9H204
b	Mediator of RNA polymerase II transcription subunit 29	protein	115	84% helix, 0% strand	Q9NX70
l	Mediator of RNA polymerase II transcription subunit 30	protein	126	80% helix, 1% strand	Q96HR3
m	Mediator of RNA polymerase II transcription subunit 31	protein	112	74% helix, 0% strand	Q9Y3C7
a	Mediator of RNA polymerase II transcription subunit 1	protein	469	38% helix, 21% strand	Q15648
d	Mediator of RNA polymerase II transcription subunit 4	protein	158	80% helix, 1% strand	Q9NPJ6
f	Mediator of RNA polymerase II transcription subunit 6	protein	167	36% helix, 23% strand	O75586
g	Mediator of RNA polymerase II transcription subunit 7	protein	166	60% helix, 0% strand	O43513
h	Isoform 2 of Mediator of RNA polymerase II transcription subunit 8	protein	190	62% helix, 1% strand	Q96G25
i	Mediator of RNA polymerase II transcription subunit 9	protein	73	77% helix, 0% strand	Q9NWA0
j	Mediator of RNA polymerase II transcription subunit 10	protein	122	80% helix, 0% strand	Q9BTT4
k	Mediator of RNA polymerase II transcription subunit 11	protein	112	82% helix, 0% strand	Q9P086
n	Mediator of RNA polymerase II transcription subunit 14	protein	994	39% helix, 19% strand	O60244
o	Mediator of RNA polymerase II transcription subunit 15	protein	156	46% helix, 6% strand	Q96RN5
q	Mediator of RNA polymerase II transcription subunit 17	protein	555	36% helix, 15% strand	Q9NVC6
r	Mediator of RNA polymerase II transcription subunit 18	protein	206	17% helix, 39% strand	Q9BUE0
s	Mediator of RNA polymerase II transcription subunit 19	protein	81	48% helix, 0% strand	A0JLT2
t	Mediator of RNA polymerase II transcription subunit 20	protein	193	26% helix, 32% strand	Q9H944
u	Mediator of RNA polymerase II transcription subunit 21	protein	107	87% helix, 0% strand	Q13503
v	Mediator of RNA polymerase II transcription subunit 22	protein	134	84% helix, 0% strand	Q15528
z	Mediator of RNA polymerase II transcription subunit 26	protein	97	25% helix, 10% strand	O95402
x	Mediator of RNA polymerase II transcription subunit 24	protein	896	71% helix, 0% strand	O75448
w	Mediator of RNA polymerase II transcription subunit 23	protein	1334	62% helix, 1% strand	Q9ULK4
p	Isoform 2 of Mediator of RNA polymerase II transcription subunit 16	protein	406	5% helix, 47% strand	Q9Y2X0
X	DNA (69-mer)	dna	69	—	—
Y	DNA(69-mer)	dna	69	—	—

Ligands and binding sites

SF4 · Iron/sulfur cluster · ligand · chains 7
ZN · Zinc ion · metal · 16 copies · chains 0, BA, PA, PB, PC, PI, PJ, PL, EA, 2, 1, 3
MG · Magnesium ion · metal · chains PA

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1017	0.89	0.91	120	empty
2	941	0.88	0.89	124	empty
3	705	0.87	0.91	96	empty
4	1067	0.86	0.87	115	empty
5	1165	0.86	0.87	118	empty

Interfaces

258 interfaces between chains.

PA–PB · 8755 Å² buried · 98 hydrogen bonds · protein-protein
DA–DG · 5020 Å² buried · 83 hydrogen bonds · protein-protein
n–q · 4115 Å² buried · 26 hydrogen bonds · protein-protein
X–Y · 3240 Å² buried · 316 hydrogen bonds · nucleic-nucleic
1–7 · 3227 Å² buried · 33 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 disulfide, 1 isopeptide (disulfide, isopeptide).

Compared structures

Q6P1X5 · AlphaFold monomer V2.0 prediction for transcription initiation factor tfiid subunit 2… · a predicted model of the same protein · chain DB against A, TM-score 0.99
Q9ULK4 · AlphaFold monomer V2.0 prediction for mediator of RNA polymerase II transcription subunit… · a predicted model of the same protein · chain w against A, TM-score 0.97
Q9Y2X0 · AlphaFold monomer V2.0 prediction for mediator of RNA polymerase II transcription subunit… · a predicted model of the same protein · chain p against A, TM-score 0.96
P20226 · AlphaFold monomer V2.0 prediction for tata-box-binding protein (P20226) · a predicted model of the same protein · chain DP against A, TM-score 0.96
P51946 · AlphaFold monomer V2.0 prediction for cyclin-H (P51946) · a predicted model of the same protein · chain 9 against A, TM-score 0.95
P18074 · AlphaFold monomer V2.0 prediction for general transcription and DNA repair factor iih… · a predicted model of the same protein · chain 7 against A, TM-score 0.95
Q9H944 · AlphaFold monomer V2.0 prediction for mediator of RNA polymerase II transcription subunit… · a predicted model of the same protein · chain t against A, TM-score 0.95
Q15542 · AlphaFold monomer V2.0 prediction for transcription initiation factor tfiid subunit 5… · a predicted model of the same protein · chain DE against A, TM-score 0.94
P52657 · AlphaFold monomer V2.0 prediction for transcription initiation factor iia subunit 2… · a predicted model of the same protein · chain DO against A, TM-score 0.92
Q9BUE0 · AlphaFold monomer V2.0 prediction for mediator of RNA polymerase II transcription subunit… · a predicted model of the same protein · chain r against A, TM-score 0.90
Q15544 · AlphaFold monomer V2.0 prediction for transcription initiation factor tfiid subunit 11… · a predicted model of the same protein · chain Dk against A, TM-score 0.90
P19447 · AlphaFold monomer V2.0 prediction for general transcription and DNA repair factor iih… · a predicted model of the same protein · chain 6 against A, TM-score 0.90

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