SMTL ID : 8rec.1

Cryo-EM structure of bacterial RNA polymerase-sigma54 initial transcribing complex - 7nt complex

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-1-1-1-1-mer

Ligands

1 x G- C- C- G- C- G- A: RNA (5'-R(P*GP*CP*CP*GP*CP*GP*A)-3')(Non-covalent)

G-C-C-G-C-G-A.1: 28 residues within 4Å: Chain B: T.19, C.20, G.21, C.22, G.23, G.24, C.25, A.26 Chain E: Q.510, Q.513, R.540, P.564, N.568, I.572, R.687, Q.688, K.1073, H.1237 Chain F: R.319, R.349, R.422, D.457, D.459, G.460, D.461 Chain H: L.17, P.18 Ligands: MG.2 Protein-ligand interaction information (PLIP) not available

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain F: D.457, D.459, D.461 Ligands: G-C-C-G-C-G-A.1 5 PLIP interactions: 5 interactions with chain F Metal complexes: F:D.457, F:D.457, F:D.459, F:D.459, F:D.461

2 x ZN: ZINC ION(Non-covalent)

ZN.3: 4 residues within 4Å: Chain F: C.67, L.68, C.82, C.85 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:C.67, F:L.68, F:C.85 ZN.4: 4 residues within 4Å: Chain F: C.811, C.885, C.892, C.895 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:C.885, F:C.895

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gao, F. et al., Structural basis of sigma 54 displacement and promoter escape in bacterial transcription. Proc.Natl.Acad.Sci.USA (2024)

Release Date

2024-01-17

Peptides

DNA-directed RNA polymerase subunit alpha: CD
DNA-directed RNA polymerase subunit beta: E
DNA-directed RNA polymerase subunit beta': F
DNA-directed RNA polymerase subunit omega: G
RNA polymerase sigma-54 factor: H

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

C
A

D
B

E
C

F
D

G
E

H
M

DNA-directed RNA polymerase subunit alpha

DNA-directed RNA polymerase subunit beta

DNA-directed RNA polymerase subunit beta'

DNA-directed RNA polymerase subunit omega

RNA polymerase sigma-54 factor

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