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SMTL ID : 7mke.1

Cryo-EM structure of Escherichia coli RNA polymerase bound to lambda PR promoter DNA (class 2)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

4 x 1N7: CHAPSO(Non-covalent)

1N7.1:	10 residues within 4Å: Chain C: Q.46, Y.47, Y.179, S.398, A.399, V.400, E.458, E.461, E.583, Y.584 12 PLIP interactions: 12 interactions with chain C Hydrophobic interactions: C:Q.46, C:Y.47, C:Y.47, C:Y.179, C:A.399, C:V.400, C:Y.584, C:Y.584 Hydrogen bonds: C:Q.46, C:S.398, C:A.399, C:V.400
1N7.2:	7 residues within 4Å: Chain A: D.135 Chain C: Q.725, Y.726, E.962, Q.965, I.966, A.969 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:Y.726, C:Y.726, C:E.962, C:I.966, C:I.966, C:A.969 Hydrogen bonds: C:E.962
1N7.6:	7 residues within 4Å: Chain C: Q.1264 Chain D: L.255, D.256 Chain F: I.511, L.519, F.522 Ligands: 1N7.7 5 PLIP interactions: 4 interactions with chain F, 1 interactions with chain D Hydrophobic interactions: F:I.511, F:L.519, F:F.522, F:F.522, D:L.255
1N7.7:	5 residues within 4Å: Chain F: I.505, T.509, P.510, I.511 Ligands: 1N7.6 3 PLIP interactions: 3 interactions with chain F Hydrophobic interactions: F:I.505, F:T.509, F:I.511

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

2 x ZN: ZINC ION(Non-covalent)

ZN.4:	6 residues within 4Å: Chain D: C.70, C.72, C.85, K.87, C.88, G.89 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

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Saecker, R.M. et al., Structural origins of Escherichia coli RNA polymerase open promoter complex stability. Proc.Natl.Acad.Sci.USA (2021)

Release Date

2021-09-29

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

B
H

C
I

D
J

E
K

F
L

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

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