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SMTL ID : 6b6h.1

The cryo-EM structure of a bacterial class I transcription activation complex

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

1 x GTP- A- G: NASCENT RNA 3-MER(Non-covalent)

GTP-A-G.1:

24 residues within 4Å:

Chain C: Q.513, R.540, P.564, E.565, N.568, I.572, N.684, R.687, Q.688, K.1065, K.1073, H.1237
Chain D: R.425, A.426, P.427, D.460, D.462, D.464
Chain K: A.12, C.13, T.14, C.15, G.16
Ligands: MG.4

3 PLIP interactions:

3 interactions with chain C

Hydrogen bonds: C:R.540, C:N.568, C:Q.688

2 x ZN: ZINC ION(Non-covalent)

ZN.2:	7 residues within 4Å: Chain D: C.70, L.71, C.72, G.73, K.74, 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:	6 residues within 4Å: Chain D: C.814, T.816, R.883, C.888, C.895, C.898 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:C.814, D:C.888, D:C.898

1 x MG: MAGNESIUM ION(Non-covalent)

MG.4:

5 residues within 4Å:

Chain D: R.425, D.460, D.462, D.464
Ligands: GTP-A-G.1

5 PLIP interactions:

5 interactions with chain D

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

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

CMP.5:	17 residues within 4Å: Chain G: I.31, V.50, L.62, S.63, I.71, G.72, E.73, L.74, G.75, R.83, S.84, A.85, V.87, R.124, T.128 Chain H: L.125, S.129 7 PLIP interactions: 6 interactions with chain G, 1 interactions with chain H Hydrogen bonds: G:G.72, G:E.73, G:L.74, G:G.75, G:R.124, H:S.129 Salt bridges: G:R.83
CMP.6:	20 residues within 4Å: Chain G: L.125, Q.126, S.129 Chain H: I.31, A.37, V.50, L.62, L.65, G.72, E.73, L.74, G.75, E.82, R.83, S.84, A.85, V.87, R.124, T.128, K.131 12 PLIP interactions: 10 interactions with chain H, 2 interactions with chain G Hydrogen bonds: H:G.72, H:E.73, H:E.73, H:L.74, H:G.75, H:E.82, H:S.84, H:T.128, H:T.128, G:Q.126, G:S.129 Salt bridges: H:R.83

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Liu, B. et al., Structural basis of bacterial transcription activation. Science (2017)

Release Date

2017-11-15

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
DNA-directed RNA polymerase subunit alpha: I

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

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)

DNA-directed RNA polymerase subunit alpha

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