SMTL ID : 6psq.1

Escherichia coli RNA polymerase closed complex (TRPc) with TraR and rpsT P2 promoter

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-3-1-1-1-mer

Ligands

1 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: D.460, D.462, D.464 Chain B: S.1 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.460, A:D.462, A:D.464, A:D.464

3 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: C.70, C.72, C.85, C.88 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.70, A:C.72, A:C.85, A:C.88 ZN.3: 6 residues within 4Å: Chain A: C.814, T.816, C.888, D.889, C.895, C.898 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.814, A:C.888, A:C.895, A:C.898 ZN.7: 4 residues within 4Å: Chain B: C.36, C.39, C.57, C.60 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.36, B:C.39, B:C.57, B:C.60

4 x 1N7: CHAPSO(Non-covalent)

1N7.4: 6 residues within 4Å: Chain A: L.255, D.256 Chain G: I.514, L.522, F.525 Ligands: 1N7.5 2 PLIP interactions: 2 interactions with chain G Hydrophobic interactions: G:F.525, G:F.525 1N7.5: 7 residues within 4Å: Chain A: L.255, D.256, R.259 Chain G: I.508, I.514, L.522 Ligands: 1N7.4 5 PLIP interactions: 3 interactions with chain G, 2 interactions with chain A Hydrophobic interactions: G:I.508, G:I.514, G:L.522, A:L.255 Hydrogen bonds: A:D.256 1N7.6: 11 residues within 4Å: Chain A: F.935, H.936, I.937, L.1243, Q.1244 Chain B: S.9, E.12, Q.13, M.16, T.17, N.20 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:Q.13, B:Q.13, B:M.16, A:I.937, A:L.1243 1N7.8: 7 residues within 4Å: Chain C: D.135 Chain E: Q.725, Y.726, E.962, Q.965, I.966, A.969 5 PLIP interactions: 5 interactions with chain E Hydrophobic interactions: E:Y.726, E:Y.726, E:I.966, E:A.969 Hydrogen bonds: E:Q.965

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chen, J. et al., Stepwise Promoter Melting by Bacterial RNA Polymerase. Mol.Cell (2020)

Release Date

2020-03-25

Peptides

DNA-directed RNA polymerase subunit beta': A
Protein TraR: B
DNA-directed RNA polymerase subunit alpha: CDH
DNA-directed RNA polymerase subunit beta: E
DNA-directed RNA polymerase subunit omega: F
RNA polymerase sigma factor RpoD: G

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
J

B
N

C
G

D
H

H
M

E
I

F
K

G
L

DNA-directed RNA polymerase subunit beta'

Protein TraR

DNA-directed RNA polymerase subunit alpha

DNA-directed RNA polymerase subunit beta

DNA-directed RNA polymerase subunit omega

RNA polymerase sigma factor RpoD

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