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SMTL ID : 6rh3.1

Cryo-EM structure of E. coli RNA polymerase elongation complex bound to CTP substrate

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-1-1-1-mer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1:	4 residues within 4Å: Chain F: C.70, C.72, C.85, C.88 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:C.70, F:C.72, F:C.85, F:C.88
ZN.2:	5 residues within 4Å: Chain F: C.814, R.883, C.888, C.895, C.898 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:C.814, F:C.888, F:C.895, F:C.898

1 x CTP: CYTIDINE-5'-TRIPHOSPHATE(Non-covalent)

CTP.3:

14 residues within 4Å:

Chain B: G.17
Chain E: R.678, M.681, K.1073, R.1106
Chain F: R.425, P.427, N.458, D.460, D.462, M.932, H.936
Chain H: G.14
Ligands: MG.4

8 PLIP interactions:

4 interactions with chain E, 4 interactions with chain F

Salt bridges: E:R.678, E:K.1073, E:K.1073, E:R.1106
Hydrogen bonds: F:R.425, F:R.425, F:N.458, F:D.462

1 x MG: MAGNESIUM ION(Non-covalent)

MG.4:

3 residues within 4Å:

Chain F: D.460, D.462
Ligands: CTP.3

2 PLIP interactions:

2 interactions with chain F

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

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Abdelkareem, M. et al., Structural Basis of Transcription: RNA Polymerase Backtracking and Its Reactivation. Mol.Cell (2019)

Release Date

2019-07-03

Peptides

DNA-directed RNA polymerase subunit alpha: CD
DNA-directed RNA polymerase subunit beta: E
DNA-directed RNA polymerase subunit beta': F
DNA-directed RNA polymerase subunit omega: G

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

C
A

D
B

E
C

F
D

G
E

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

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3iyd.1 | 3lu0.1 | 4jk1.1 | 4jk1.2 | 4jk2.1 | 4jk2.2 | 4jkr.1 | 4jkr.2 | 4kmu.1 | 4kmu.2 | 4kn4.1 | 4kn4.2 | 4kn7.1 | 4kn7.2 | 4ljz.1 | 4ljz.2 | 4lk0.1 | 4lk0.2 | 4lk1.1 | 4lk1.2 | 4llg.1 | 4llg.2 | 4mex.1 | 4mex.2 | 4mey.1 | 4mey.2 | 4s20.1 | 4s20.2 | 4xsx.1 | 4xsx.2 more...less...

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