7khe.1 | SWISS-MODEL Template Library

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SMTL ID : 7khe.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

4 x 1N7: CHAPSO(Non-covalent)

1N7.1:	7 residues within 4Å: Chain A: D.135 Chain C: Q.725, Y.726, E.962, I.966, A.969, R.976 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:I.966, C:I.966, C:A.969 Hydrogen bonds: C:E.962 Salt bridges: C:R.976
1N7.2:	12 residues within 4Å: Chain C: Q.46, Y.47, Y.179, S.398, A.399, V.400, R.452, E.458, E.461, R.465, E.583, Y.584 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:Q.46, C:Y.179, C:A.399, C:Y.584 Hydrogen bonds: C:E.583 Salt bridges: C:E.583
1N7.7:	7 residues within 4Å: Chain C: F.514, Q.761 Chain D: L.255, D.256 Chain F: I.511, F.522 Ligands: 1N7.8 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain F Hydrophobic interactions: D:L.255, F:F.522
1N7.8:	9 residues within 4Å: Chain C: R.143 Chain D: L.255, D.256, G.257, G.258, R.259 Chain F: I.505, P.510 Ligands: 1N7.7 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain F Hydrophobic interactions: D:R.259, F:I.505 Hydrogen bonds: D:G.257, D:R.259

1 x MG: MAGNESIUM ION(Non-covalent)

MG.3:

3 residues within 4Å:

Chain D: D.460, D.462, D.464

4 PLIP interactions:

4 interactions with chain D

Metal complexes: D:D.462, D:D.462, D:D.464, D:D.464

3 x ZN: ZINC ION(Non-covalent)

ZN.4:	5 residues within 4Å: Chain D: C.70, C.72, G.73, 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:	12 residues within 4Å: Chain D: R.362, R.417, K.615, V.618, I.619, D.622, Q.623 Chain E: A.2, R.3, V.4, E.42, R.52 15 PLIP interactions: 9 interactions with chain D, 6 interactions with chain E Hydrogen bonds: D:R.362, D:L.363, D:K.615, D:Q.623, E:A.2, E:A.2, E:R.3, E:E.42, E:R.52 Salt bridges: D:K.615, D:K.615, D:D.622, E:R.3 pi-Cation interactions: D:R.362, 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 11 PLIP interactions: 9 interactions with chain I, 2 interactions with chain D Hydrogen bonds: I:R.91, I:R.91, I:R.129, I:R.129, 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

2020-12-09

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

Export Alignment

Secondary Structure
NoneDSSPPSIPREDSSpro

Colour Scheme

Fade MismatchesEnhance Mismatches

ChainUnique ChainRainbow2° StructureBfactorBfactor RangeSOAEntropyClustalHydrophobicSizeChargedPolarProlineSer/ThrCysteineAliphaticAromaticNo Colour

Background

3D Viewer
NGLPV2D

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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