6uu7.1 | SWISS-MODEL Template Library

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SMTL ID : 6uu7.1

E. coli sigma-S transcription initiation complex with a 6-nt RNA and an NTP ("Old" crystal soaked with UTP, CTP, ddGTP, and dinucleotide ApG for 30 minutes)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 4.40 Å

Oligo State

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

Ligands

1 x A- G- U- C- U- DDG: DNA/RNA (5'-R(*AP*GP*UP*CP*U)-D(P*(DDG))-3')(Non-covalent)

A-G-U-C-U-DDG.1:

20 residues within 4Å:

Chain C: Q.510, Q.513, R.529, R.540, P.564, N.568, I.572, Q.688, K.1065, K.1073, H.1237
Chain H: C.8, A.9, G.10, A.11, C.12, T.13, C.14
Ligands: MG.4, DG3.6

2 PLIP interactions:

2 interactions with chain C

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

2 x ZN: ZINC ION(Non-covalent)

ZN.2:	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.3:	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.4:	6 residues within 4Å: Chain D: D.460, D.462, D.464 Ligands: A-G-U-C-U-DDG.1, MG.5, DG3.6 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:D.460, D:D.462
MG.5:	5 residues within 4Å: Chain C: R.1106 Chain D: D.460, D.462 Ligands: MG.4, DG3.6 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:D.460

1 x DG3: 2'-3'-DIDEOXYGUANOSINE-5'-TRIPHOSPHATE(Non-covalent)

DG3.6:

15 residues within 4Å:

Chain C: R.1106
Chain D: R.425, P.427, N.458, D.460, R.731, Q.929, M.932, R.933, H.936, I.937
Chain H: T.7
Ligands: A-G-U-C-U-DDG.1, MG.4, MG.5

7 PLIP interactions:

1 interactions with chain C, 6 interactions with chain D

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

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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