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SMTL ID : 8fvw.1

CryoEM structure of E.coli transcription elongation complex bound to ppGpp

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-1-1-1-mer

Ligands

1 x G4P: GUANOSINE-5',3'-TETRAPHOSPHATE(Non-covalent)

G4P.1:

14 residues within 4Å:

Chain D: R.362, L.363, H.364, R.417, K.615, V.618, D.622, Q.623
Chain E: A.2, R.3, V.4, T.5
Ligands: MG.5, NA.6

20 PLIP interactions:

8 interactions with chain E, 12 interactions with chain D

Hydrogen bonds: E:A.2, E:R.3, E:V.4, E:T.5, E:T.5, D:R.362, D:L.363, D:H.364, D:K.615, D:Q.623
Water bridges: E:R.3, E:R.3, D:R.362, D:R.417
Salt bridges: E:R.3, D:R.417, D:K.615, D:K.615, D:D.622
pi-Cation interactions: D:R.362

2 x ZN: ZINC ION(Non-covalent)

ZN.2:	4 residues within 4Å: Chain D: C.70, C.72, 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:	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

2 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.4:	4 residues within 4Å: Chain D: D.460, D.462, D.464 Chain G: A.16 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.460, D:D.462, D:D.464, H₂O.5, H₂O.6
MG.5:	1 residues within 4Å: Ligands: G4P.1 No protein-ligand interaction detected (PLIP)

1 x NA: SODIUM ION(Non-functional Binders)

NA.6:

1 residues within 4Å:

Ligands: G4P.1

No protein-ligand interaction detected (PLIP)

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Weaver, J.W. et al., Control of transcription elongation and DNA repair by alarmone ppGpp. Nat.Struct.Mol.Biol. (2023)

Release Date

2023-04-05

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
D

B
E

C
F

D
G

E
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

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