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SMTL ID : 6uub.1

E. coli sigma-S transcription initiation complex with a mismatching UTP ("Fresh" crystal soaked with UTP for 2 hours)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.96 Å

Oligo State

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

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1:	4 residues within 4Å: Chain C: E.813, R.1106 Chain D: R.731 Ligands: UTP.5 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:E.813
MG.4:	3 residues within 4Å: Chain D: D.460, D.462, D.464 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:D.460, D:D.460, D:D.462, D:D.462, D:D.464

2 x ZN: ZINC ION(Non-covalent)

ZN.2:	5 residues within 4Å: Chain D: C.70, C.72, G.73, C.85, C.88 3 PLIP interactions: 3 interactions with chain D Metal complexes: 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 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:C.814, D:C.895, D:C.898

1 x UTP: URIDINE 5'-TRIPHOSPHATE(Non-covalent)

UTP.5:

7 residues within 4Å:

Chain C: S.1105, R.1106
Chain D: N.458, D.460, R.731, T.786
Ligands: MG.1

7 PLIP interactions:

4 interactions with chain D, 3 interactions with chain C

Hydrophobic interactions: D:T.786
Hydrogen bonds: D:N.458, D:N.458, C:S.1105, C:R.1106
Salt bridges: D:R.731, C:R.1106

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Zuo, Y. et al., Structural Insights into Transcription Initiation from De Novo RNA Synthesis to Transitioning into Elongation. Iscience (2020)

Release Date

2020-08-26

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 RpoS: F

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
AAA

B
BBB

C
CCC

D
DDD

E
EEE

F
FFF

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 RpoS

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Background

Transparent

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