SMTL ID : 8ree.1

Cryo-EM structure of bacterial RNA polymerase-sigma54 initial transcribing complex - 9nt complex

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

G-C-C-G-C-G-A-U-C.1: 29 residues within 4Å: Chain C: Q.510, Q.513, R.540, P.564, E.565, N.568, I.572, R.687, Q.688, K.1065, K.1073, H.1237 Chain D: P.248, R.319, R.422, D.457, D.459, D.461 Chain F: G.10 Chain H: G.19, A.20, T.21, C.22, G.23, C.24, G.25, G.26, C.27 Ligands: MG.2 Protein-ligand interaction information (PLIP) not available

1 x MG: MAGNESIUM ION(Non-covalent)

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

2 x ZN: ZINC ION(Non-covalent)

ZN.3: 5 residues within 4Å: Chain D: C.67, L.68, K.71, C.82, C.85 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:C.67, D:L.68, D:C.85 ZN.4: 4 residues within 4Å: Chain D: C.811, C.885, C.892, C.895 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:C.885, D: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: AB
DNA-directed RNA polymerase subunit beta: C
DNA-directed RNA polymerase subunit beta': D
DNA-directed RNA polymerase subunit omega: E
RNA polymerase sigma-54 factor: F

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
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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