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SMTL ID : 8sy7.1

E. coli DNA-directed RNA polymerase transcription elongation complex bound the unnatural dB-STP base pair in the active site

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-1-1-1-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:

21 residues within 4Å:

Chain C: Q.510, Q.513, R.540, Q.688, K.1065, K.1073, H.1237
Chain D: R.425, G.463, D.464
Chain G: C.20, C.21, T.22, C.23, T.24, C.25, G.26, A.27, T.28, G.29
Ligands: X0O.5

No protein-ligand interaction detected (PLIP)

2 x ZN: ZINC ION(Non-covalent)

ZN.2:	4 residues within 4Å: Chain D: C.70, C.85, C.88, V.90 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:C.70, D:C.85, D:C.88
ZN.3:	5 residues within 4Å: Chain D: C.814, R.883, 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: X0O.5

5 PLIP interactions:

5 interactions with chain D

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

1 x X0O: [[(2~{R},3~{S},4~{R},5~{S})-5-(4-azanyl-1-methyl-2-oxidanylidene-pyrimidin-5-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate(Non-covalent)

X0O.5:

12 residues within 4Å:

Chain C: R.678, D.814, K.1073, R.1106
Chain D: R.425, N.458, D.460, D.462, M.932
Chain G: G.19
Ligands: A-U-C-G-A-G-A-G-G.1, MG.4

8 PLIP interactions:

4 interactions with chain D, 4 interactions with chain C

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

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Oh, J. et al., A unified Watson-Crick geometry drives transcription of six-letter expanded DNA alphabets by E. coli RNA polymerase. Nat Commun (2023)

Release Date

2023-12-27

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
G

C
I

D
J

E
K

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

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