6pmi.1 | SWISS-MODEL Template Library

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SMTL ID : 6pmi.1

Sigm28-transcription initiation complex with specific promoter at the state 1

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

1 x ATP- A- C: Nascent RNA(Non-covalent)

ATP-A-C.1:

22 residues within 4Å:

Chain C: R.529, P.564, E.565, N.568, N.684, R.687, Q.688, K.1065, K.1073, H.1237
Chain D: R.425, D.460, G.463, D.464
Chain F: E.151
Chain H: A.12, G.13, T.14, T.15, G.16, T.17
Ligands: MG.4

4 PLIP interactions:

4 interactions with chain C

Hydrogen bonds: C:R.529, C:N.568, C:N.568
Salt bridges: C:R.529

2 x ZN: ZINC ION(Non-covalent)

ZN.2:	8 residues within 4Å: Chain D: C.70, L.71, C.72, G.73, K.74, C.85, K.87, 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:	7 residues within 4Å: Chain D: C.814, T.816, R.883, C.888, V.894, C.895, C.898 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:C.814, D:C.888, D:C.895

1 x MG: MAGNESIUM ION(Non-covalent)

MG.4:

4 residues within 4Å:

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

3 PLIP interactions:

3 interactions with chain D

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

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Shi, W. et al., Structural basis of bacterial sigma28-mediated transcription reveals roles of the RNA polymerase zinc-binding domain. Embo J. (2020)

Release Date

2020-05-13

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 FliA: 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

RNA polymerase sigma factor FliA

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