MolNFT v1 · #169734 · protein + DNA + RNA

Cryo-EM structure of ecmrr-rnap-promoter initial transcribing complex with 4-nt RNA transcript (ecmrr-rpitc-4NT)

6XLJ · DNA-directed RNA polymerase subunit alpha: “Cryo-EM structure of ecmrr-rnap-promoter initial transcribing complex with 4-nt RNA transcript…”. Electron microscopy, 4 ligands (1N7, 118, MG), 20 pockets (best druggability 0.81). MolNFT…

PDB: 6XLJ
Type: protein + DNA + RNA
Length: 4,333 residues
Chains: 11
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, 118, MG, ZN
Pockets: 20 · best druggability 0.81

Structure

electron microscopy · 10 distinct chains · 37% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6)	protein	231	20% helix, 38% strand	P0A7Z6
B	DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6)	protein	224	21% helix, 41% strand	P0A7Z6
C	DNA-directed RNA polymerase subunit beta (EC 2.7.7.6)	protein	1339	30% helix, 24% strand	B7MIX3
D	DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6)	protein	1336	37% helix, 19% 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	476	65% helix, 3% strand	P00579
G, H	Merr family transcriptional regulator ecmrr	protein	268	40% helix, 25% strand	—
N	Synthetic non-template strand DNA (54-mer)	dna	54	—	—
R	RNA (5'-D((GTP))-R(PCPAPG)-3')	rna	4	—	—
T	Synthetic template strand DNA (54-mer)	dna	54	—	—

Ligands and binding sites

1N7 · Chapso · ligand · 5 copies · chains A, C, D, F, T, G, H
118 · Tetraphenylantimonium ion · ligand · 3 copies · chains C, D, N, T, G, H
MG · Magnesium ion · metal · 2 copies · chains D, R
ZN · Zinc ion · metal · 2 copies · chains D

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	400	0.81	0.90	37	empty
2	791	0.81	0.84	70	empty
3	350	0.79	0.90	42	empty
4	444	0.78	0.87	62	empty
5	331	0.77	0.89	56	empty

Interfaces

27 interfaces between chains.

C–D · 8116 Å² buried · 108 hydrogen bonds · protein-protein
D–F · 2733 Å² buried · 27 hydrogen bonds · protein-protein
G–H · 2586 Å² buried · 12 hydrogen bonds · protein-protein
C–F · 2384 Å² buried · 16 hydrogen bonds · protein-protein
A–B · 2148 Å² buried · 17 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 modified (nucleotide modification).

Compared structures

6XLJ · Cryo-EM structure of EcmrR-RNAP-promoter initial transcribing complex with 4-nt RNA… · the same entry in another collection · chain T against T, 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

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 6XLJ · PDBe 6XLJ · UniProt P0A7Z6 · UniProt B7MIX3 · UniProt P0A8T8 · UniProt B7MFL0 · UniProt P00579

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