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SMTL ID : 7mki.1

Cryo-EM structure of Escherichia coli RNA polymerase bound to lambda PR (-5G to C) promoter DNA

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

3 x 1N7: CHAPSO(Non-covalent)

1N7.1:	12 residues within 4Å: Chain D: Q.46, Y.47, Y.179, D.396, S.398, A.399, V.400, R.452, E.458, E.461, E.583, Y.584 10 PLIP interactions: 10 interactions with chain D Hydrophobic interactions: D:Y.47, D:Y.47, D:A.399, D:Y.584, D:Y.584 Hydrogen bonds: D:Q.46, D:D.396, D:S.398, D:A.399, D:V.400
1N7.2:	7 residues within 4Å: Chain B: D.135 Chain D: Q.725, Y.726, E.962, Q.965, I.966, A.969 9 PLIP interactions: 8 interactions with chain D, 1 interactions with chain B Hydrophobic interactions: D:Q.725, D:Y.726, D:Y.726, D:Y.726, D:I.966, D:I.966, D:A.969 Hydrogen bonds: D:Q.965, B:D.135
1N7.6:	4 residues within 4Å: Chain E: D.256 Chain G: I.511, L.519, F.522 5 PLIP interactions: 3 interactions with chain G, 2 interactions with chain E Hydrophobic interactions: G:I.511, G:L.519, G:F.522 Hydrogen bonds: E:D.256, E:D.256

1 x MG: MAGNESIUM ION(Non-covalent)

MG.3:

3 residues within 4Å:

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

4 PLIP interactions:

4 interactions with chain E

Metal complexes: E:D.460, E:D.462, E:D.464, E:D.464

2 x ZN: ZINC ION(Non-covalent)

ZN.4:	4 residues within 4Å: Chain E: C.70, C.72, C.85, C.88 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:C.70, E:C.72, E:C.85, E:C.88
ZN.5:	4 residues within 4Å: Chain E: C.814, C.888, C.895, C.898 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:C.814, E:C.888, E:C.895, E: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: BC
DNA-directed RNA polymerase subunit beta: D
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:

B
G

C
H

D
I

E
J

F
K

G
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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