MolNFT v1 · #169737 · protein + DNA + RNA

Cryo-EM structure of E.COLI rnap-DNA elongation complex 1 (RDE1) in ecmrr-dependent transcription

6XLM · DNA-directed RNA polymerase subunit alpha: “Cryo-EM structure of E.COLI rnap-DNA elongation complex 1 (RDE1) in ecmrr-dependent transcription”. Electron microscopy, 3 ligands (1N7, ZN, MG), 20 pockets (best druggability 0.84).…

PDB: 6XLM
Type: protein + DNA + RNA
Length: 3,525 residues
Chains: 9
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA-directed RNA polymerase subunit alpha; DNA-directed RNA polymerase subunit beta…
EC: 2.7.7.6
UniProt: P0A7Z6, B7MIX3, P0A8T8, B7MFL0, P00579
Ligands: 1N7, ZN, MG
Pockets: 20 · best druggability 0.84

Structure

electron microscopy · 9 distinct chains · 37% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6)	protein	231	23% helix, 40% strand	P0A7Z6
B	DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6)	protein	222	20% helix, 44% strand	P0A7Z6
C	DNA-directed RNA polymerase subunit beta (EC 2.7.7.6)	protein	1339	31% helix, 24% strand	B7MIX3
D	DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6)	protein	1336	38% helix, 20% strand	P0A8T8
E	DNA-directed RNA polymerase subunit omega (EC 2.7.7.6)	protein	79	59% helix, 0% strand	B7MFL0
F	RNA polymerase sigma factor rpod	protein	278	79% helix, 3% strand	P00579
N	Synthetic non-template strand DNA (54-mer)	dna	14	—	—
T	Synthetic template strand DNA (54-mer)	dna	17	—	—
R	9-nt RNA transcript	rna	9	—	—

Ligands and binding sites

1N7 · Chapso · ligand · 2 copies · chains C, A
ZN · Zinc ion · metal · 2 copies · chains D
MG · Magnesium ion · metal · chains D, R

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	1126	0.84	0.85	110	empty
2	413	0.80	0.89	45	empty
3	837	0.79	0.82	86	empty
4	453	0.76	0.85	39	empty
5	269	0.75	0.89	49	empty

Interfaces

16 interfaces between chains.

C–D · 8262 Å² buried · 105 hydrogen bonds · protein-protein
A–B · 2164 Å² buried · 16 hydrogen bonds · protein-protein
A–C · 1884 Å² buried · 22 hydrogen bonds · protein-protein
D–E · 1233 Å² buried · 10 hydrogen bonds · protein-protein
D–F · 1111 Å² buried · 16 hydrogen bonds · protein-protein

Compared structures

6XLM · Cryo-EM structure of E.coli RNAP-DNA elongation complex 1 (RDe1) in EcmrR-dependent… · the same entry in another collection · chain R against R, TM-score 1.00
B7MIX3 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase subunit beta (B7MIX3) · a predicted model of the same protein · chain C against A, TM-score 0.99
P0A7Z6 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase subunit alpha (P0A7Z6) · a predicted model of the same protein · chain B against A, TM-score 0.96
B7MFL0 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase subunit omega (B7MFL0) · a predicted model of the same protein · chain E against A, TM-score 0.95

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 P0A7Z6
Every structure of UniProt B7MIX3
Every structure of UniProt P0A8T8
Every structure of UniProt B7MFL0
Every structure of UniProt P00579
Elsewhere: RCSB PDB 6XLM · PDBe 6XLM · UniProt P0A7Z6 · UniProt B7MIX3 · UniProt P0A8T8 · UniProt B7MFL0 · UniProt P00579

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