SMTL ID : 7khi.1

Escherichia coli RNA polymerase and rrnBP1 promoter complex with DksA/ppGpp

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

4 x 1N7: CHAPSO(Non-covalent)

1N7.1: 6 residues within 4Å: Chain A: E.72, D.135 Chain C: Q.725, Y.726, E.962, I.966 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain C Hydrogen bonds: A:E.72, C:Q.725 Hydrophobic interactions: C:I.966, C:I.966 1N7.2: 12 residues within 4Å: Chain C: Q.46, Y.47, D.396, S.398, A.399, I.414, R.452, E.458, E.461, R.465, E.583, Y.584 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:Q.46, C:Y.47, C:Y.47, C:A.399, C:E.458, C:Y.584 Hydrogen bonds: C:S.398, C:E.583, C:Y.584 1N7.7: 8 residues within 4Å: Chain C: R.143, Q.513 Chain D: R.259 Chain F: I.505, T.509, I.511, G.512 Ligands: 1N7.8 3 PLIP interactions: 1 interactions with chain F, 2 interactions with chain D Hydrophobic interactions: F:I.511 Hydrogen bonds: D:R.259, D:R.259 1N7.8: 8 residues within 4Å: Chain C: F.514, Q.761 Chain D: L.255 Chain F: I.511, L.519, F.522, I.523 Ligands: 1N7.7 4 PLIP interactions: 1 interactions with chain F, 2 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: F:I.511, D:L.255 Hydrogen bonds: C:Q.761 pi-Cation interactions: C:F.514

1 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 3 residues within 4Å: Chain D: D.460, D.462, D.464 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:D.462, D:D.464, D:D.464

3 x ZN: ZINC ION(Non-covalent)

ZN.4: 4 residues within 4Å: Chain D: C.70, C.72, C.85, C.88 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.70, D:C.72, D:C.85, D:C.88 ZN.5: 5 residues within 4Å: Chain D: C.814, R.883, C.888, C.895, C.898 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.814, D:C.888, D:C.895, D:C.898 ZN.9: 5 residues within 4Å: Chain I: C.114, C.117, V.119, C.135, C.138 4 PLIP interactions: 4 interactions with chain I Metal complexes: I:C.114, I:C.117, I:C.135, I:C.138

2 x G4P: GUANOSINE-5',3'-TETRAPHOSPHATE(Non-covalent)

G4P.6: 10 residues within 4Å: Chain D: R.362, H.364, R.417, V.618, I.619, D.622, Q.623 Chain E: A.2, R.3, V.4 10 PLIP interactions: 6 interactions with chain D, 4 interactions with chain E Hydrogen bonds: D:R.417, D:D.622, D:Q.623, E:A.2, E:R.3 Salt bridges: D:K.615, D:D.622, E:R.3, E:R.3 pi-Cation interactions: D:R.362 G4P.10: 10 residues within 4Å: Chain D: N.680, D.684 Chain I: R.87, R.91, E.92, K.94, L.95, K.98, R.129, K.139 10 PLIP interactions: 8 interactions with chain I, 2 interactions with chain D Hydrogen bonds: I:R.91, I:R.91, I:R.91, D:N.680 Salt bridges: I:R.87, I:K.98, I:K.98, I:R.129, I:K.139, D:D.684

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shin, Y. et al., Structural basis of ribosomal RNA transcription regulation. Nat Commun (2021)

Release Date

2020-10-28

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 factor RpoD: F
RNA polymerase-binding transcription factor DksA: I

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

I
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 factor RpoD

RNA polymerase-binding transcription factor DksA

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