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Cryo-EM structure of E. COLI rnap-promoter initial transcribing complex with 5-nt RNA transcript (rpitc-5NT)

Analyse Cryo-EM structure of E. COLI rnap-promoter initial transcribing complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6XLL
Type: protein + DNA + RNA
Length: 3,786 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 0.85

Structure

electron microscopy · 9 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	22% helix, 40% strand	P0A7Z6
B	DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6)	protein	222	19% helix, 42% strand	P0A7Z6
C	DNA-directed RNA polymerase subunit beta (EC 2.7.7.6)	protein	1339	29% helix, 25% 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	66% helix, 1% strand	P00579
N	Synthetic non-template strand DNA (54-mer)	dna	50	—	—
T	Synthetic template strand DNA (54-mer)	dna	48	—	—
R	RNA transcript (5-mer)	rna	5	—	—

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	741	0.85	0.89	74	empty
2	776	0.84	0.88	101	empty
3	883	0.82	0.84	80	empty
4	1093	0.81	0.82	99	1N7
5	1135	0.78	0.80	102	empty

Interfaces

20 interfaces between chains.

C–D · 8080 Å² buried · 115 hydrogen bonds · protein-protein
D–F · 2770 Å² buried · 28 hydrogen bonds · protein-protein
C–F · 2400 Å² buried · 17 hydrogen bonds · protein-protein
A–B · 2164 Å² buried · 18 hydrogen bonds · protein-protein
A–C · 1907 Å² buried · 19 hydrogen bonds · protein-protein

Modifications

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

Compared structures

6XLL · Cryo-EM structure of E. coli RNAP-promoter initial transcribing complex with 5-nt RNA… · 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 6XLL · PDBe 6XLL · UniProt P0A7Z6 · UniProt B7MIX3 · UniProt P0A8T8 · UniProt B7MFL0 · UniProt P00579

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