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SMTL ID : 6jbq.1

CryoEM structure of Escherichia coli sigmaE transcription initiation complex containing 5nt of RNA

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

1 x C- U- C- G- A: RNA (5'-R(*CP*UP*CP*GP*A)-3')(Non-covalent)

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

24 residues within 4Å:

Chain C: Q.510, Q.513, L.533, R.540, P.564, E.565, N.568, I.572, M.681, N.684, R.687, Q.688, K.1073, H.1237
Chain D: R.425, D.462, D.464
Chain G: T.14, C.15, G.16, A.17, G.18, G.19
Ligands: MG.2

Protein-ligand interaction information (PLIP) not available

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2:

4 residues within 4Å:

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

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.3:	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.4:	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

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Fang, C. et al., Structures and mechanism of transcription initiation by bacterial ECF factors. Nucleic Acids Res. (2019)

Release Date

2019-05-29

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
ECF RNA polymerase sigma-E factor: F

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

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

ECF RNA polymerase sigma-E factor

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