Research workbench

CryoEM structure of E.coli RNA polymerase elongation complex bound with RfaH

Analyse CryoEM structure of E.coli RNA polymerase elongation complex bound with RfaH in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6C6S
Type: protein + DNA + RNA
Length: 3,428 residues
Chains: 9
Method: electron microscopy
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 3.7
Source: Escherichia coli; Escherichia coli (strain K12); SYNTHETIC CONSTRUCT
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, P0AFW0
Ligands: ZN, MG
Pockets: 20 · best druggability 0.82

Structure

electron microscopy · resolution 3.7 · 9 distinct chains · 31% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA (29-mer)	dna	29	—	—
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	22% helix, 36% strand	P0A7Z4
H	DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6)	protein	219	19% helix, 37% strand	P0A7Z4
I	DNA-directed RNA polymerase subunit beta (EC 2.7.7.6)	protein	1341	29% helix, 21% strand	P0A8V2
J	DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6)	protein	1335	36% helix, 17% strand	P0A8T7
K	DNA-directed RNA polymerase subunit omega (EC 2.7.7.6)	protein	83	63% helix, 0% strand	P0A800
D	Transcription antitermination protein RfaH	protein	161	15% helix, 34% strand	P0AFW0

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	688	0.82	0.87	71	empty
2	837	0.82	0.85	75	empty
3	387	0.80	0.90	50	empty
4	1040	0.80	0.82	97	empty
5	572	0.80	0.86	65	empty

Interfaces

19 interfaces between chains.

I–J · 8478 Å² buried · 97 hydrogen bonds · protein-protein
G–I · 1915 Å² buried · 26 hydrogen bonds · protein-protein
G–H · 1857 Å² buried · 11 hydrogen bonds · protein-protein
J–K · 1284 Å² buried · 16 hydrogen bonds · protein-protein
J–D · 1062 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

6C6S · Cryoem structure of E.COLI RNA polymerase elongation complex bound with rfah · the same entry in another collection · chain R against R, 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 0.98
P0A8T7 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase subunit beta' (P0A8T7) · a predicted model of the same protein · chain J against A, TM-score 0.94
P0A800 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase subunit omega (P0A800) · a predicted model of the same protein · chain K against A, TM-score 0.93

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 P0AFW0
Elsewhere: RCSB PDB 6C6S · PDBe 6C6S · UniProt P0A7Z4 · UniProt P0A8V2 · UniProt P0A8T7 · UniProt P0A800 · UniProt P0AFW0

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.