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SMTL ID : 6utw.1

E. coli sigma-S transcription initiation complex with a 4-nt RNA ("Fresh" crystal)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.85 Å

Oligo State

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

Ligands

1 x GTP- A- G- U: RNA 4-mer (de novo synthesized)(Non-covalent)

GTP-A-G-U.1:

24 residues within 4Å:

Chain C: R.529, P.564, E.565, N.568, I.572, Q.688, K.1065, K.1073, H.1237
Chain D: R.425, A.426, P.427, N.458, D.462, D.464, M.932, H.936
Chain H: A.11, C.12, T.13, C.14, G.15
Ligands: MG.5, DPO.6

2 PLIP interactions:

2 interactions with chain C

Hydrogen bonds: C:N.568, C:Q.688

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2:	6 residues within 4Å: Chain C: E.813, D.814, R.1106 Chain D: D.460, D.462 Ligands: DPO.6 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:D.814
MG.5:	4 residues within 4Å: Chain D: D.460, D.462, D.464 Ligands: GTP-A-G-U.1 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:D.460, D:D.460, D:D.462, D:D.464

2 x ZN: ZINC ION(Non-covalent)

ZN.3:	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.4:	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 DPO: DIPHOSPHATE(Non-covalent)

DPO.6:

9 residues within 4Å:

Chain C: E.813, R.1106
Chain D: D.460, R.731, R.933, H.936, I.937
Ligands: GTP-A-G-U.1, MG.2

6 PLIP interactions:

2 interactions with chain C, 4 interactions with chain D

Hydrogen bonds: C:S.1105, D:D.460, D:R.933
Salt bridges: C:R.1106, D:R.731, D:H.936

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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