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SMTL ID : 8u3b.1

Cryo-EM structure of E. coli NarL-transcription activation complex at 3.2A

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

1 x GTP- A- A: RNA (5'-D(*(GTP))-R(P*AP*A)-3')(Non-covalent)

GTP-A-A.1:

18 residues within 4Å:

Chain C: P.564, E.565, N.568, Q.688, K.1065, K.1073, H.1237
Chain D: R.425, D.460, D.462, D.464
Chain J: A.13, T.14, T.15, C.16, C.17, G.18
Ligands: MG.4

1 PLIP interactions:

1 interactions with chain C

Hydrogen bonds: C:N.568

2 x ZN: ZINC ION(Non-covalent)

ZN.2:	5 residues within 4Å: Chain D: C.70, C.72, G.73, 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: GTP-A-A.1

3 PLIP interactions:

3 interactions with chain D

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

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Kompaniiets, D. et al., Structural basis for transcription activation by the nitrate-responsive regulator NarL. Nucleic Acids Res. (2024)

Release Date

2024-01-17

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
Nitrate/nitrite response regulator protein NarL: GH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

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

Nitrate/nitrite response regulator protein NarL

Toggle Identical (GH)

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