MolNFT v1 · #144860 · protein + DNA + RNA

Cryoem structure of E.COLI RNA polymerase elongation complex bound with nusg

6C6U · DNA (29-mer): “Cryoem structure of E.COLI RNA polymerase elongation complex bound with nusg”. Electron microscopy, 2 ligands (ZN, MG), 20 pockets (best druggability 0.86). MolNFT v1 #144860 on GenesisL1: 3D structure, binding sites…

PDB: 6C6U
Type: protein + DNA + RNA
Length: 3,334 residues
Chains: 9
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA (29-mer); RNA (5'- R(*GP*CP*AP*UP*UP*CP*AP*AP*AP*GP*CP*CP*GP*AP*GP*AP*GP*GP*UP*A)-3')…
EC: 2.7.7.6
UniProt: P0A7Z4, P0A8V2, P0A8T7, P0A800, P0AFG1
Ligands: ZN, MG
Pockets: 20 · best druggability 0.86

Structure

electron microscopy · 9 distinct chains · 31% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA (29-mer)	dna	22	—	—
B	DNA (29-mer)	dna	29	—	—
R	RNA (5'- R(GPCPAPUPUPCPAPAPAPGPCPCPGPAPGPAPGPGPUPA)-3')	rna	10	—	—
G	DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6)	protein	221	21% helix, 35% strand	P0A7Z4
H	DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6)	protein	218	19% helix, 32% strand	P0A7Z4
I	DNA-directed RNA polymerase subunit beta (EC 2.7.7.6)	protein	1317	29% helix, 22% strand	P0A8V2
J	DNA-directed RNA polymerase beta'	protein	1337	35% helix, 16% strand	P0A8T7
K	DNA-directed RNA polymerase subunit omega (EC 2.7.7.6)	protein	82	65% helix, 0% strand	P0A800
N	Transcription TERMINATION/ANTITERMINATION protein nusg	protein	98	39% helix, 22% strand	P0AFG1

Ligands and binding sites

ZN · Zinc ion · metal · 2 copies · chains J
MG · Magnesium ion · metal · chains R, J

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	1037	0.86	0.88	110	empty
2	945	0.83	0.85	81	empty
3	860	0.82	0.85	76	empty
4	982	0.80	0.81	95	empty
5	1044	0.77	0.79	96	empty

Interfaces

20 interfaces between chains.

I–J · 8436 Å² buried · 93 hydrogen bonds · protein-protein
G–H · 1881 Å² buried · 9 hydrogen bonds · protein-protein
G–I · 1863 Å² buried · 19 hydrogen bonds · protein-protein
J–K · 1288 Å² buried · 17 hydrogen bonds · protein-protein
B–J · 1108 Å² buried · 8 hydrogen bonds · protein-nucleic

Compared structures

6C6U · CryoEM structure of E.coli RNA polymerase elongation complex bound with NusG · the same entry in another collection · chain N against N, TM-score 1.00
P0A8V2 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase subunit beta (P0A8V2) · a predicted model of the same protein · chain I against A, TM-score 0.99
P0AFG1 · AlphaFold monomer V2.0 prediction for transcription TERMINATION/ANTITERMINATION protein… · a predicted model of the same protein · chain N against A, TM-score 0.84

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 P0A7Z4
Every structure of UniProt P0A8V2
Every structure of UniProt P0A8T7
Every structure of UniProt P0A800
Every structure of UniProt P0AFG1
Elsewhere: RCSB PDB 6C6U · PDBe 6C6U · UniProt P0A7Z4 · UniProt P0A8V2 · UniProt P0A8T7 · UniProt P0A800 · UniProt P0AFG1

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