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Cryo-EM MAP of a yeast minimal preinitiation complex interacting with the mediator head module

Analyse Cryo-EM MAP of a yeast minimal preinitiation complex interacting with the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3J1N
Type: protein
Length: 3,894 residues
Chains: 12
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
UniProt: P04050, P08518, P16370, P20433, P20434, P20435, P34087, P20436, P27999, P22139, P38902, P40422
Pockets: 20 · best druggability 0.87

Structure

electron microscopy · 12 distinct chains · 30% 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	1412	38% helix, 14% strand	P04050
B	DNA-directed RNA polymerase II subunit RPB2 (EC 2.7.7.6)	protein	1094	26% helix, 19% strand	P08518
C	DNA-directed RNA polymerase II subunit RPB3	protein	266	23% helix, 16% strand	P16370
D	DNA-directed RNA polymerase II subunit RPB4	protein	177	46% helix, 6% strand	P20433
E	DNA-directed RNA polymerase II subunit RPABC1	protein	214	35% helix, 21% strand	P20434
F	DNA-directed RNA polymerase II subunit RPABC2	protein	84	27% helix, 18% strand	P20435
G	DNA-directed RNA polymerase II subunit RPB7	protein	171	10% helix, 46% strand	P34087
H	DNA-directed RNA polymerase II subunit RPABC3	protein	133	5% helix, 43% strand	P20436
I	DNA-directed RNA polymerase II subunit RPB9	protein	118	0% helix, 20% strand	P27999
J	DNA-directed RNA polymerase II subunit RPABC5	protein	65	49% helix, 2% strand	P22139
K	DNA-directed RNA polymerase II subunit RPB11	protein	114	37% helix, 22% strand	P38902
L	DNA-directed RNA polymerase II subunit RPABC4	protein	46	0% helix, 9% strand	P40422

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	925	0.87	0.89	152	empty
2	788	0.87	0.90	153	empty
3	663	0.85	0.89	141	empty
4	843	0.84	0.87	144	empty
5	387	0.80	0.89	89	empty

Interfaces

26 interfaces between chains.

A–B · 4331 Å² buried · 117 hydrogen bonds · protein-protein
A–E · 1128 Å² buried · 4 hydrogen bonds · protein-protein
A–F · 986 Å² buried · 24 hydrogen bonds · protein-protein
A–G · 909 Å² buried · 59 hydrogen bonds · protein-protein
F–G · 845 Å² buried · 53 hydrogen bonds · protein-protein

Compared structures

3J1N · Cryo-EM map of a yeast minimal preinitiation complex interacting with the Mediator Head… · the same entry in another collection · chain H against H, TM-score 1.00

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt P04050
Every structure of UniProt P08518
Every structure of UniProt P16370
Every structure of UniProt P20433
Every structure of UniProt P20434
Every structure of UniProt P20435
Every structure of UniProt P34087
Every structure of UniProt P20436
Every structure of UniProt P27999
Every structure of UniProt P22139
Every structure of UniProt P38902
Every structure of UniProt P40422
Elsewhere: RCSB PDB 3J1N · PDBe 3J1N · UniProt P04050 · UniProt P08518 · UniProt P16370 · UniProt P20433 · UniProt P20434 · UniProt P20435 · UniProt P34087 · UniProt P20436 · UniProt P27999 · UniProt P22139 · UniProt P38902 · UniProt P40422

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