6uu6.1 | SWISS-MODEL Template Library

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SMTL ID : 6uu6.1

E. coli sigma-S transcription initiation complex with a 4-nt RNA and a UTP ("Old" crystal soaked with UTP, ddCTP, and dinucleotide ApG for 30 minutes)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 4.20 Å

Oligo State

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

Ligands

1 x A- G- U- DOC: RNA 4-mer (dinucleotide ApG primed synthesis)(Non-covalent)

A-G-U-DOC.1:

17 residues within 4Å:

Chain C: Q.513, R.529, P.564, E.565, N.568, Q.688, K.1065, K.1073, H.1237
Chain D: A.426
Chain H: G.10, A.11, C.12, T.13, C.14
Ligands: UTP.2, MG.5

2 PLIP interactions:

2 interactions with chain C

Salt bridges: C:K.1065, C:K.1073

1 x UTP: URIDINE 5'-TRIPHOSPHATE(Covalent)

UTP.2:

15 residues within 4Å:

Chain C: R.678, R.1106
Chain D: R.425, P.427, N.458, D.460, D.462, Q.929, M.932, R.933, H.936
Chain H: G.10
Ligands: A-G-U-DOC.1, MG.5, MG.6

9 PLIP interactions:

7 interactions with chain D, 2 interactions with chain C

Hydrogen bonds: D:R.425, D:R.425, D:N.458, C:R.678
Salt bridges: D:R.933, D:H.936, D:H.936, D:H.936, C:R.1106

2 x ZN: ZINC ION(Non-covalent)

ZN.3:	4 residues within 4Å: Chain D: C.70, C.72, C.85, C.88 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:C.72, D:C.85, D:C.88
ZN.4:	6 residues within 4Å: Chain D: C.814, R.883, 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

2 x MG: MAGNESIUM ION(Non-covalent)

MG.5:	6 residues within 4Å: Chain D: D.460, D.462, D.464 Ligands: A-G-U-DOC.1, UTP.2, MG.6 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:D.460, D:D.462, D:D.464, D:D.464
MG.6:	4 residues within 4Å: Chain D: D.460, D.462 Ligands: UTP.2, MG.5 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:D.460, D:D.460

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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