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SMTL ID : 6pb5.1

The E. coli class-II CAP-dependent transcription activation complex at the state 1 architecture

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1:	8 residues within 4Å: Chain D: C.70, L.71, C.72, G.73, K.74, C.85, K.87, C.88 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:C.70, D:C.72, D:C.88
ZN.2:	6 residues within 4Å: Chain D: C.814, R.883, S.884, 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.3:

4 residues within 4Å:

Chain D: R.425, D.460, D.462, D.464

3 PLIP interactions:

3 interactions with chain D

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

2 x CMP: ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE(Non-covalent)

CMP.4:	15 residues within 4Å: Chain G: V.50, L.62, S.63, L.65, I.71, G.72, E.73, L.74, S.84, A.85, V.87, R.124, T.128 Chain H: L.125, S.129 5 PLIP interactions: 3 interactions with chain G, 2 interactions with chain H Hydrogen bonds: G:G.72, G:E.73, G:T.128, H:S.129, H:S.129
CMP.5:	19 residues within 4Å: Chain G: L.125, S.129 Chain H: I.31, V.50, L.62, S.63, L.65, F.70, I.71, G.72, E.73, L.74, R.83, S.84, A.85, W.86, V.87, R.124, T.128 9 PLIP interactions: 7 interactions with chain H, 2 interactions with chain G Hydrogen bonds: H:S.63, H:G.72, H:E.73, H:E.73, H:S.84, H:A.85, G:S.129, G:S.129 Salt bridges: H:R.83

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Shi, W. et al., Visualization of two architectures in class-II CAP-dependent transcription activation. Plos Biol. (2020)

Release Date

2020-03-18

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
cAMP-activated global transcriptional regulator CRP: 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

cAMP-activated global transcriptional regulator CRP

Toggle Identical (GH)

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