Research workbench

Cryo-EM structure of human RNA polymerase I in complex with RRN3

Analyse Cryo-EM structure of human RNA polymerase I in complex with RRN3 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7OBA
Type: protein
Length: 4,477 residues
Chains: 14
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA-directed RNA polymerase I subunit RPA1; DNA-directed RNA polymerase I subunit RPA2…
EC: 2.7.7.6
UniProt: O95602, Q9H9Y6, O15160, P19388, P61218, Q3B726, P52434, Q9P1U0, P62875, P0DPB6, P53803, Q9GZS1, O15446, Q9NYV6
Ligands: ZN
Pockets: 20 · best druggability 0.81

Structure

electron microscopy · 14 distinct chains · 26% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA-directed RNA polymerase I subunit RPA1 (EC 2.7.7.6)	protein	1522	30% helix, 11% strand	O95602
B	DNA-directed RNA polymerase I subunit RPA2 (EC 2.7.7.6)	protein	1127	21% helix, 24% strand	Q9H9Y6
C	DNA-directed RNA polymerases I and III subunit RPAC1	protein	309	27% helix, 29% strand	O15160
E	DNA-directed RNA polymerases I, II, and III subunit RPABC1	protein	210	26% helix, 20% strand	P19388
F	DNA-directed RNA polymerases I, II, and III subunit RPABC2	protein	78	29% helix, 15% strand	P61218
G	DNA-directed RNA polymerase I subunit RPA43	protein	159	9% helix, 28% strand	Q3B726
H	DNA-directed RNA polymerases I, II, and III subunit RPABC3	protein	149	0% helix, 42% strand	P52434
I	DNA-directed RNA polymerase I subunit RPA12	protein	105	5% helix, 30% strand	Q9P1U0
J	DNA-directed RNA polymerases I, II, and III subunit RPABC5	protein	64	27% helix, 5% strand	P62875
K	DNA-directed RNA polymerases I and III subunit RPAC2	protein	107	33% helix, 22% strand	P0DPB6
L	DNA-directed RNA polymerases I, II, and III subunit RPABC4	protein	46	0% helix, 33% strand	P53803
M	DNA-directed RNA polymerase I subunit RPA49	protein	105	4% helix, 44% strand	Q9GZS1
N	DNA-directed RNA polymerase I subunit RPA34	protein	149	3% helix, 13% strand	O15446
O	RNA polymerase I-specific transcription initiation factor RRN3	protein	347	67% helix, 0% strand	Q9NYV6

Ligands and binding sites

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	1157	0.81	0.83	148	empty
2	765	0.80	0.84	69	empty
3	887	0.80	0.82	84	empty
4	929	0.79	0.82	116	empty
5	861	0.79	0.82	95	empty

Interfaces

33 interfaces between chains.

A–B · 9888 Å² buried · 105 hydrogen bonds · protein-protein
A–E · 3709 Å² buried · 47 hydrogen bonds · protein-protein
M–N · 2490 Å² buried · 37 hydrogen bonds · protein-protein
A–F · 2299 Å² buried · 17 hydrogen bonds · protein-protein
A–H · 2223 Å² buried · 31 hydrogen bonds · protein-protein

Compared structures

7OBA · Cryo-EM structure of human RNA Polymerase I in complex with RRN3 · 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 O95602
Every structure of UniProt Q9H9Y6
Every structure of UniProt O15160
Every structure of UniProt P19388
Every structure of UniProt P61218
Every structure of UniProt Q3B726
Every structure of UniProt P52434
Every structure of UniProt Q9P1U0
Every structure of UniProt P62875
Every structure of UniProt P0DPB6
Every structure of UniProt P53803
Every structure of UniProt Q9GZS1
Every structure of UniProt O15446
Every structure of UniProt Q9NYV6
Elsewhere: RCSB PDB 7OBA · PDBe 7OBA · UniProt O95602 · UniProt Q9H9Y6 · UniProt O15160 · UniProt P19388 · UniProt P61218 · UniProt Q3B726 · UniProt P52434 · UniProt Q9P1U0 · UniProt P62875 · UniProt P0DPB6 · UniProt P53803 · UniProt Q9GZS1 · UniProt O15446 · UniProt Q9NYV6

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