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Structure of yeast transcription pre-initiation complex with tfiih and core mediator

Analyse Structure of yeast transcription pre-initiation complex with tfiih and core… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5OQM
Type: protein + DNA
Length: 10,973 residues
Chains: 46
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA-directed RNA polymerase II subunit RPB1; DNA-directed RNA polymerase II subunit RPB2…
EC: 2.7.7.6, 3.6.4.12
UniProt: P04050, P08518, P16370, P20433, P20434, P20435, P34087, P20436, P27999, P22139, P38902, P40422, P29055, P13393, P41895, A0A250WD40, P41896, P32773, P32774, A0A250WIP3, P36100, P36145, P06839, P32776, Q02939, Q03290, Q12004, Q3E7C1, Q04673, Q00578, P38782, P38304, Q99278, P32569, P32585, P34162, P32570, Q12343, Q08278, P33308, Q06213, P19263, P25046, P47822, P38633
Ligands: SF4, ZN, MG
Pockets: 20 · best druggability 0.88

Structure

electron microscopy · 46 distinct chains · 44% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA-directed RNA polymerase II subunit RPB1 (EC 2.7.7.6)	protein	1398	41% helix, 16% strand	P04050
B	DNA-directed RNA polymerase II subunit RPB2 (EC 2.7.7.6)	protein	1152	29% helix, 25% strand	P08518
C	DNA-directed RNA polymerase II subunit RPB3	protein	262	25% helix, 27% strand	P16370
D	DNA-directed RNA polymerase II subunit RPB4	protein	157	54% helix, 5% strand	P20433
E	DNA-directed RNA polymerases I, II, and III subunit RPABC1	protein	213	41% helix, 22% strand	P20434
F	DNA-directed RNA polymerases I, II, and III subunit RPABC2	protein	83	35% helix, 16% strand	P20435
G	DNA-directed RNA polymerase II subunit RPB7	protein	171	13% helix, 50% strand	P34087
H	DNA-directed RNA polymerases I, II, and III subunit RPABC3	protein	136	0% helix, 49% strand	P20436
I	DNA-directed RNA polymerase II subunit RPB9	protein	116	4% helix, 27% strand	P27999
J	DNA-directed RNA polymerases I, II, and III subunit RPABC5	protein	65	54% helix, 2% strand	P22139
K	DNA-directed RNA polymerase II subunit RPB11	protein	112	39% helix, 25% strand	P38902
L	DNA-directed RNA polymerases I, II, and III subunit RPABC4	protein	45	0% helix, 20% strand	P40422
M	Transcription initiation factor iib	protein	279	57% helix, 5% strand	P29055
N	Nontemplate DNA	dna	76	—	—
O	Tata-box-binding protein	protein	180	27% helix, 37% strand	P13393
Q	Transcription initiation factor iif subunit alpha	protein	148	18% helix, 33% strand	P41895, A0A250WD40
R	Transcription initiation factor iif subunit beta (EC 3.6.4.12)	protein	190	30% helix, 31% strand	P41896
T	Template DNA	dna	72	—	—
U	Transcription initiation factor iia large subunit	protein	92	43% helix, 42% strand	P32773
V	Transcription initiation factor iia subunit 2	protein	100	38% helix, 40% strand	P32774
W	Transcription factor tfiie subunit	protein	258	57% helix, 10% strand	A0A250WIP3, P36100
X	Transcription initiation factor iie subunit beta	protein	160	43% helix, 5% strand	P36145
0	General transcription and DNA repair factor iih helicase subunit xpd (EC 3.6.4.12)	protein	698	49% helix, 10% strand	P06839
1	General transcription and DNA repair factor iih subunit TFB1	protein	491	60% helix, 10% strand	P32776
2	General transcription and DNA repair factor iih subunit TFB2	protein	395	58% helix, 12% strand	Q02939
3	RNA polymerase II transcription factor B subunit 3	protein	138	48% helix, 6% strand	Q03290
4	General transcription and DNA repair factor iih subunit TFB4	protein	297	42% helix, 16% strand	Q12004
5	General transcription and DNA repair factor iih subunit TFB5	protein	66	50% helix, 26% strand	Q3E7C1
6	General transcription and DNA repair factor iih subunit SSL1	protein	335	33% helix, 21% strand	Q04673
7	General transcription and DNA repair factor iih helicase subunit xpb (EC 3.6.4.12)	protein	408	46% helix, 18% strand	Q00578
Z	Unknown protein	protein	43	23% helix, 44% strand	—
a	Mediator of RNA polymerase II transcription subunit 6	protein	149	46% helix, 23% strand	P38782
b	Mediator of RNA polymerase II transcription subunit 8	protein	158	67% helix, 1% strand	P38304
c	Mediator of RNA polymerase II transcription subunit 11	protein	99	81% helix, 0% strand	Q99278
d	Mediator of RNA polymerase II transcription subunit 17	protein	442	50% helix, 18% strand	P32569
e	Mediator of RNA polymerase II transcription subunit 18	protein	232	21% helix, 38% strand	P32585
f	Mediator of RNA polymerase II transcription subunit 20	protein	203	24% helix, 36% strand	P34162
g	Mediator of RNA polymerase II transcription subunit 22	protein	85	91% helix, 0% strand	P32570
h	Mediator of RNA polymerase II transcription subunit 4	protein	131	82% helix, 0% strand	Q12343
i	Mediator of RNA polymerase II transcription subunit 7	protein	136	80% helix, 0% strand	Q08278
j	Mediator of RNA polymerase II transcription subunit 9	protein	66	83% helix, 0% strand	P33308
k	Mediator of RNA polymerase II transcription subunit 10	protein	127	83% helix, 0% strand	Q06213
l	Mediator of RNA polymerase II transcription subunit 14	protein	471	50% helix, 17% strand	P19263
m	Mediator of RNA polymerase II transcription subunit 19	protein	103	29% helix, 2% strand	P25046
n	Mediator of RNA polymerase II transcription subunit 21	protein	136	75% helix, 0% strand	P47822
o	Mediator of RNA polymerase II transcription subunit 31, mediator of RNA polymerase II transcription subunit 31	protein	99	74% helix, 0% strand	P38633

Ligands and binding sites

SF4 · Iron/sulfur cluster · ligand · chains 0
ZN · Zinc ion · metal · 16 copies · chains A, B, C, I, J, L, M, W, 3, 4, 6
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	1004	0.88	0.89	112	empty
2	1090	0.84	0.85	123	empty
3	1153	0.84	0.85	88	empty
4	210	0.84	0.97	37	empty
5	891	0.84	0.85	105	empty

Interfaces

123 interfaces between chains.

A–B · 9932 Å² buried · 121 hydrogen bonds · protein-protein
N–T · 3243 Å² buried · 225 hydrogen bonds · nucleic-nucleic
A–M · 2729 Å² buried · 30 hydrogen bonds · protein-protein
U–V · 2595 Å² buried · 22 hydrogen bonds · protein-protein
Q–R · 2125 Å² buried · 38 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 covalent (covalent ligand).

Compared structures

5OQM · Structure of yeast transcription pre-initiation complex with tfiih and core mediator · the same entry in another collection · chain K against K, TM-score 1.00

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