Research workbench

Human Mediator with RNA Polymerase II Pre-initiation complex

Analyse Human Mediator with RNA Polymerase II Pre-initiation complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7NVR
Type: protein + DNA
Length: 11,813 residues
Chains: 58
Method: electron microscopy
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 4.5
Source: Homo sapiens; Sus scrofa; Trichoplusia ni; SYNTHETIC CONSTRUCT
Molecule: TFIIH basal transcription factor complex helicase XPD subunit; General transcription…
EC: 3.6.4.12, 2.7.11.22, 2.7.11.23, 2.7.7.6, 2.3.1.48
UniProt: P18074, P32780, Q92759, P51948, Q13889, Q6ZYL4, Q13888, P19447, P50613, P51946, I3LGP4, I3LCH3, A0A287ADR4, I3LSI7, F1SKN8, I3LJZ9, A0A4X1ULF2, P60899, A0A4X1VYD0, A0A4X1UK25, I3LN51, Q00403, P20226, P35269, P13984, P52655, P52657, P29083, P29084, O75586, Q96G25, Q9P086, Q9NVC6, Q9BUE0, Q9H944, Q15528, Q9NPJ6, O43513, Q9NWA0, Q9BTT4, O60244, A0JLT2, Q13503, Q9Y3C7, Q6P2C8, Q9H204, Q96HR3
Ligands: SF4, ZN, MG
Pockets: 20 · best druggability 0.87

Structure

electron microscopy · resolution 4.5 · 58 distinct chains · 45% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
0	TFIIH basal transcription factor complex helicase XPD subunit (EC 3.6.4.12)	protein	714	51% helix, 12% strand	P18074
1	General transcription factor IIH subunit 1	protein	265	66% helix, 0% strand	P32780
2	General transcription factor IIH subunit 4	protein	390	55% helix, 12% strand	Q92759
3	CDK-activating kinase assembly factor MAT1	protein	214	49% helix, 5% strand	P51948
4	General transcription factor IIH subunit 3	protein	263	41% helix, 13% strand	Q13889
5	General transcription factor IIH subunit 5	protein	66	47% helix, 21% strand	Q6ZYL4
6	General transcription factor IIH subunit 2	protein	347	32% helix, 19% strand	Q13888
7	General transcription and DNA repair factor IIH helicase subunit XPB (EC 3.6.4.12)	protein	605	41% helix, 17% strand	P19447
8	Cyclin-dependent kinase 7 (EC 2.7.11.22, 2.7.11.23)	protein	298	34% helix, 18% strand	P50613
9	Cyclin-H	protein	281	69% helix, 0% strand	P51946
A	DNA-directed RNA polymerase subunit (EC 2.7.7.6)	protein	1423	44% helix, 15% strand	—
B	DNA-directed RNA polymerase subunit beta (EC 2.7.7.6)	protein	1136	31% helix, 25% strand	I3LGP4
C	DNA-directed RNA polymerase II subunit RPB3	protein	257	25% helix, 28% strand	I3LCH3
D	RPOL4c domain-containing protein	protein	128	59% helix, 3% strand	A0A287ADR4
E	DNA-directed RNA polymerase II subunit E	protein	209	40% helix, 22% strand	I3LSI7
F	DNA-directed RNA polymerase II subunit F	protein	79	34% helix, 16% strand	F1SKN8
G	DNA-directed RNA polymerase II subunit RPB7	protein	171	9% helix, 48% strand	I3LJZ9
H	DNA-directed RNA polymerases I, II, and III subunit RPABC3	protein	148	3% helix, 49% strand	A0A4X1ULF2
I	DNA-directed RNA polymerase II subunit RPB9	protein	114	8% helix, 32% strand	P60899
J	DNA-directed RNA polymerases I, II, and III subunit RPABC5	protein	64	47% helix, 5% strand	A0A4X1VYD0
K	RNA_pol_L_2 domain-containing protein	protein	115	42% helix, 23% strand	A0A4X1UK25
L	RNA polymerase II subunit K	protein	44	0% helix, 27% strand	I3LN51
M	Transcription initiation factor IIB (EC 2.3.1.48)	protein	252	60% helix, 3% strand	Q00403
N	Nt	dna	64	—	—
O	TATA-box-binding protein	protein	179	26% helix, 38% strand	P20226
Q	General transcription factor IIF subunit 1	protein	138	16% helix, 37% strand	P35269
R	General transcription factor IIF subunit 2 (EC 3.6.4.12)	protein	222	36% helix, 27% strand	P13984
T	Template	dna	64	—	—
U	Transcription initiation factor IIA subunit 1	protein	113	36% helix, 32% strand	P52655
V	Transcription initiation factor IIA subunit 2	protein	99	41% helix, 35% strand	P52657
W	General transcription factor IIE subunit 1	protein	202	59% helix, 10% strand	P29083
X	Transcription initiation factor IIE subunit beta	protein	171	54% helix, 10% strand	P29084
Y	Unassigned peptide, likely TFIIE-beta	protein	19	16% helix, 0% strand	—
Z	Unassigned peptide, likely XPB	protein	8	0% helix, 25% strand	—
a	Mediator of RNA polymerase II transcription subunit 6	protein	143	35% helix, 27% strand	O75586
b	Mediator of RNA polymerase II transcription subunit 8	protein	136	76% helix, 0% strand	Q96G25
c	Mediator of RNA polymerase II transcription subunit 11	protein	109	78% helix, 0% strand	Q9P086
d	Mediator of RNA polymerase II transcription subunit 17	protein	439	43% helix, 15% strand	Q9NVC6
e	Mediator of RNA polymerase II transcription subunit 18	protein	167	22% helix, 46% strand	Q9BUE0
f	Mediator of RNA polymerase II transcription subunit 20	protein	186	29% helix, 22% strand	Q9H944
g	Mediator of RNA polymerase II transcription subunit 22	protein	130	88% helix, 0% strand	Q15528
h	Mediator of RNA polymerase II transcription subunit 4	protein	138	78% helix, 0% strand	Q9NPJ6
i	Mediator of RNA polymerase II transcription subunit 7	protein	113	77% helix, 0% strand	O43513
j	Mediator of RNA polymerase II transcription subunit 9	protein	72	64% helix, 0% strand	Q9NWA0
k	Mediator of RNA polymerase II transcription subunit 10	protein	133	76% helix, 2% strand	Q9BTT4
l	Mediator of RNA polymerase II transcription subunit 14	protein	501	53% helix, 15% strand	O60244
m	Mediator of RNA polymerase II transcription subunit 19	protein	84	33% helix, 0% strand	A0JLT2
n	Mediator of RNA polymerase II transcription subunit 21	protein	132	73% helix, 0% strand	Q13503
o	Mediator of RNA polymerase II transcription subunit 31	protein	91	79% helix, 0% strand	Q9Y3C7
p	Mediator of RNA polymerase II transcription subunit 27	protein	154	31% helix, 10% strand	Q6P2C8
q	Mediator of RNA polymerase II transcription subunit 28	protein	69	93% helix, 0% strand	Q9H204
r	unassigned peptide (MED29 or MED30)	protein	20	90% helix, 0% strand	—
s	Mediator of RNA polymerase II transcription subunit 30	protein	44	91% helix, 0% strand	Q96HR3
v	unassigned peptide (MED14)	protein	22	0% helix, 9% strand	—
w	unassigned peptide (MED6)	protein	16	88% helix, 0% strand	—
x	unassigned peptide (MED17)	protein	11	82% helix, 0% strand	—
y	unassigned peptide (MED29 or MED30)	protein	18	89% helix, 0% strand	—
z	unassigned peptide (MED29 or MED30)	protein	23	91% helix, 0% strand	—

Ligands and binding sites

SF4 · Iron/sulfur cluster · ligand · chains 0
ZN · Zinc ion · metal · 18 copies · chains 3, 4, 6, A, B, C, I, J, L, M, W, p
MG · Magnesium ion · metal · chains A

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	1154	0.87	0.88	131	empty
2	621	0.81	0.86	68	empty
3	189	0.81	0.96	33	empty
4	893	0.80	0.83	119	empty
5	644	0.80	0.86	51	empty

Interfaces

157 interfaces between chains.

A–B · 9143 Å² buried · 125 hydrogen bonds · protein-protein
N–T · 2875 Å² buried · 213 hydrogen bonds · nucleic-nucleic
U–V · 2815 Å² buried · 39 hydrogen bonds · protein-protein
4–6 · 2480 Å² buried · 19 hydrogen bonds · protein-protein
Q–R · 2423 Å² buried · 41 hydrogen bonds · protein-protein

Compared structures

7NVR · Human mediator with RNA polymerase II pre-initiation complex · the same entry in another collection · chain 9 against 9, TM-score 1.00

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