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SMTL ID : 8fiy.1

Cryo-EM structure of E. coli RNA polymerase Elongation complex in the Transcription-Translation Complex (RNAP in an anti-swiveled conformation)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-1-1-mer

Ligands

1 x C- C- G- G- A- C- A- A- U: RNA(Non-covalent)

C-C-G-G-A-C-A-A-U.1:

22 residues within 4Å:

Chain C: Q.510, Q.513, R.529, L.533, E.565, M.685, Q.688, K.1073
Chain D: P.251, V.253, R.322, K.325, D.460
Chain F: A.15, T.16, T.17, G.18, C.20, C.21, G.22, G.23
Ligands: MG.4

2 PLIP interactions:

2 interactions with chain C

Hydrogen bonds: C:E.541, C:R.542

2 x ZN: ZINC ION(Non-covalent)

ZN.2:	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.3:	4 residues within 4Å: Chain D: C.814, 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

1 x MG: MAGNESIUM ION(Non-covalent)

MG.4:

4 residues within 4Å:

Chain D: D.460, D.462, D.464
Ligands: C-C-G-G-A-C-A-A-U.1

3 PLIP interactions:

3 interactions with chain D

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

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Wee, L.M. et al., A trailing ribosome speeds up RNA polymerase at the expense of transcript fidelity via force and allostery. Cell (2023)

Release Date

2023-03-29

Peptides

DNA-directed RNA polymerase subunit alpha: AB
DNA-directed RNA polymerase subunit beta: C
DNA-directed RNA polymerase subunit beta': D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

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'

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