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Cryo-EM structure of RNA polymerase-SIGMA54 holoenzyme with promoter DNA and transcription activator pspf intermedate complex

Analyse Cryo-EM structure of RNA polymerase-SIGMA54 holoenzyme with promoter DNA and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5NSS
Type: protein + DNA
Length: 5,192 residues
Chains: 14
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: P0A7Z4, P0A8V2, P0A8T7, P0A800, P37344, A0A060VKE4, A0A0J4U551, A0A1W1PRD8
Pockets: 20 · best druggability 0.86

Structure

electron microscopy · 11 distinct chains · 33% helix, 12% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6)	protein	238	22% helix, 23% strand	P0A7Z4
B	DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6)	protein	235	17% helix, 28% strand	P0A7Z4
C	DNA-directed RNA polymerase subunit beta (EC 2.7.7.6)	protein	1340	30% helix, 15% strand	P0A8V2
D	DNA-directed RNA polymerase subunit BETA',DNA-directed RNA polymerase subunit BETA',DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6)	protein	1352	33% helix, 10% strand	P0A8T7
E	DNA-directed RNA polymerase subunit omega (EC 2.7.7.6)	protein	74	61% helix, 0% strand	P0A800
F, K	Psp operon transcriptional activator	protein	248	44% helix, 9% strand	P37344
G, J, N	Psp operon transcriptional activator	protein	251	40% helix, 12% strand	P37344
L	Psp operon transcriptional activator	protein	250	40% helix, 12% strand	P37344
H	Non-template promoter DNA	dna	35	—	—
M	RNA polymerase sigma-54 FACTOR,RNA polymerase sigma-54 FACTOR,RNA polymerase sigma-54 FACTOR,RNA polymerase sigma-54 factor, RNA polymerase sigma-54 FACTOR,RNA polymerase sigma-54 FACTOR,RNA polymerase sigma-54 FACTOR,RNA polymerase sigma-54 FACTOR,RNA polymerase sigma-54 FACTOR,RNA polymerase sigma-54 FACTOR,RNA polymerase sigma-54 FACTOR,RNA polymerase sigma-54 FACTOR,RNA polymerase sigma-54 FACTOR,RNA polymerase sigma-54 FACTOR,RNA polymerase sigma-54 FACTOR,RNA polymerase sigma-54 FACTOR,RNA	protein	388	41% helix, 0% strand	A0A060VKE4, A0A0J4U551, A0A1W1PRD8
I	Template promoter DNA	dna	31	—	—

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	823	0.86	0.88	94	empty
2	1024	0.82	0.83	130	empty
3	924	0.82	0.84	167	empty
4	593	0.81	0.86	83	empty
5	474	0.80	0.88	78	empty

Interfaces

24 interfaces between chains.

C–D · 6549 Å² buried · 48 hydrogen bonds · protein-protein
A–B · 1835 Å² buried · 10 hydrogen bonds · protein-protein
A–C · 1533 Å² buried · 14 hydrogen bonds · protein-protein
H–I · 1443 Å² buried · 118 hydrogen bonds · nucleic-nucleic
D–E · 1054 Å² buried · 8 hydrogen bonds · protein-protein

Compared structures

5NSS · Cryo-EM structure of RNA polymerase-sigma54 holoenzyme with promoter DNA and… · the same entry in another collection · chain I against I, TM-score 1.00

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 P37344
Every structure of UniProt A0A060VKE4
Every structure of UniProt A0A0J4U551
Every structure of UniProt A0A1W1PRD8
Elsewhere: RCSB PDB 5NSS · PDBe 5NSS · UniProt P0A7Z4 · UniProt P0A8V2 · UniProt P0A8T7 · UniProt P0A800 · UniProt P37344 · UniProt A0A060VKE4 · UniProt A0A0J4U551 · UniProt A0A1W1PRD8

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