8txo.1 | SWISS-MODEL Template Library

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SMTL ID : 8txo.1

E. coli DNA-directed RNA polymerase transcription elongation complex bound to the unnatural dZ-PTP base pair in the active site

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-1-1-mer

Ligands

1 x A- U- C- G- A- G- A- G- G: RNA oligomer(Non-covalent)

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

26 residues within 4Å:

Chain C: Q.510, Q.513, R.540, P.564, I.572, R.687, Q.688, K.1065, K.1073, H.1237
Chain D: V.253, A.261, R.425, A.426, D.462, D.464
Chain F: C.11, C.12, T.13, C.14, T.15, C.16, G.17, A.18, T.19
Ligands: S9F.5

No protein-ligand interaction detected (PLIP)

2 x ZN: ZINC ION(Non-covalent)

ZN.2:	6 residues within 4Å: Chain D: C.70, C.72, G.73, K.74, Y.75, C.85 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:C.70, D:C.72, D:C.85
ZN.3:	5 residues within 4Å: Chain D: C.814, C.888, T.890, 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: S9F.5

4 PLIP interactions:

4 interactions with chain D

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

1 x S9F: [[(2~{R},3~{S},4~{R},5~{R})-5-(4-azanyl-2-oxidanylidene-1$l^{4},3,5,7-tetrazabicyclo[4.3.0]nona-1(6),3,8-trien-7-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate

S9F.5:

19 residues within 4Å:

Chain C: R.678, D.814, K.1073, R.1106
Chain D: R.425, P.427, N.458, D.460, D.462, D.464, T.786, Q.929, M.932, F.935, H.936
Chain F: X.10, C.11
Ligands: A-U-C-G-A-G-A-G-G.1, MG.4

10 PLIP interactions:

6 interactions with chain D, 4 interactions with chain C

Hydrogen bonds: D:R.425, D:R.425, D:N.458, D:D.462, D:D.462
Salt bridges: D:H.936, C:R.678, C:K.1073, C:K.1073, C:R.1106

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Aiyer, S. et al., Overcoming resolution attenuation during tilted cryo-EM data collection. Nat Commun (2024)

Release Date

2024-01-24

Peptides

DNA-directed RNA polymerase subunit alpha: AB
DNA-directed RNA polymerase subunit beta: C
DNA-directed RNA polymerase subunit beta': D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
G

C
I

D
J

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'

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