Research workbench

Cryo-EM structure of human RNA polymerase III in apo state

Analyse Cryo-EM structure of human RNA polymerase III in apo state in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7D59
Type: protein
Length: 5,010 residues
Chains: 17
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA-directed RNA polymerase III subunit RPC1; DNA-directed RNA polymerase III subunit…
EC: 2.7.7.6
UniProt: O14802, Q9NW08, O15160, O75575, P19388, P61218, Q9Y535, P52434, Q9Y2Y1, P0DPB6, P53803, Q9NVU0, P05423, Q9BUI4, Q9H1D9, O15318
Ligands: SF4, ZN
Pockets: 20 · best druggability 0.86

Structure

electron microscopy · 17 distinct chains · 32% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA-directed RNA polymerase III subunit RPC1 (EC 2.7.7.6)	protein	1386	37% helix, 14% strand	O14802
B	DNA-directed RNA polymerase III subunit RPC2 (EC 2.7.7.6)	protein	1095	27% helix, 24% strand	Q9NW08
C	DNA-directed RNA polymerases I and III subunit RPAC1	protein	345	24% helix, 31% strand	O15160
D	DNA-directed RNA polymerase III subunit RPC9	protein	126	59% helix, 2% strand	O75575
E	DNA-directed RNA polymerases I, II, and III subunit RPABC1	protein	210	34% helix, 22% strand	P19388
F	DNA-directed RNA polymerases I, II, and III subunit RPABC2	protein	79	32% helix, 16% strand	P61218
G	DNA-directed RNA polymerase III subunit RPC8	protein	183	7% helix, 48% strand	Q9Y535
H	DNA-directed RNA polymerases I, II, and III subunit RPABC3	protein	149	0% helix, 46% strand	P52434
I	DNA-directed RNA polymerase III subunit RPC10	protein	108	4% helix, 43% strand	Q9Y2Y1
J	DNA-directed RNA polymerases I, II, and III subunit RPABC5	protein	67	36% helix, 4% strand	—
K	DNA-directed RNA polymerases I and III subunit RPAC2	protein	107	47% helix, 26% strand	P0DPB6
L	DNA-directed RNA polymerases I, II, and III subunit RPABC4	protein	47	0% helix, 23% strand	P53803
M	DNA-directed RNA polymerase III subunit RPC5	protein	222	25% helix, 27% strand	Q9NVU0
N	DNA-directed RNA polymerase III subunit RPC4	protein	136	14% helix, 35% strand	P05423
O	DNA-directed RNA polymerase III subunit RPC3	protein	490	60% helix, 9% strand	Q9BUI4
P	DNA-directed RNA polymerase III subunit RPC6	protein	139	48% helix, 12% strand	Q9H1D9
Q	DNA-directed RNA polymerase III subunit RPC7	protein	121	21% helix, 1% strand	O15318

Ligands and binding sites

SF4 · Iron/sulfur cluster · ligand · chains O, P
ZN · Zinc ion · metal · 7 copies · chains A, B, I, J, L

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	767	0.86	0.89	106	empty
2	1016	0.84	0.85	98	empty
3	1136	0.84	0.85	130	empty
4	1122	0.83	0.84	104	empty
5	804	0.82	0.85	76	empty

Interfaces

41 interfaces between chains.

A–B · 9211 Å² buried · 83 hydrogen bonds · protein-protein
M–N · 3912 Å² buried · 45 hydrogen bonds · protein-protein
A–I · 2656 Å² buried · 18 hydrogen bonds · protein-protein
A–O · 2264 Å² buried · 18 hydrogen bonds · protein-protein
C–K · 2213 Å² buried · 13 hydrogen bonds · protein-protein

Compared structures

7D59 · cryo-EM structure of human RNA polymerase III in apo state · the same entry in another collection · chain K against K, 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 O14802
Every structure of UniProt Q9NW08
Every structure of UniProt O15160
Every structure of UniProt O75575
Every structure of UniProt P19388
Every structure of UniProt P61218
Every structure of UniProt Q9Y535
Every structure of UniProt P52434
Every structure of UniProt Q9Y2Y1
Every structure of UniProt P0DPB6
Every structure of UniProt P53803
Every structure of UniProt Q9NVU0
Every structure of UniProt P05423
Every structure of UniProt Q9BUI4
Every structure of UniProt Q9H1D9
Every structure of UniProt O15318
Elsewhere: RCSB PDB 7D59 · PDBe 7D59 · UniProt O14802 · UniProt Q9NW08 · UniProt O15160 · UniProt O75575 · UniProt P19388 · UniProt P61218 · UniProt Q9Y535 · UniProt P52434 · UniProt Q9Y2Y1 · UniProt P0DPB6 · UniProt P53803 · UniProt Q9NVU0 · UniProt P05423 · UniProt Q9BUI4 · UniProt Q9H1D9 · UniProt O15318

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