6uu9.1 | SWISS-MODEL Template Library

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SMTL ID : 6uu9.1

E. coli mutant sigma-S transcription initiation complex with an 8-nt RNA ("Fresh" mutant crystal soaked with GTP, UTP, CTP, and ddATP for 30 minutes)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 5.40 Å

Oligo State

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

Ligands

1 x GTP- A- G- U- C- U- G: RNA 8-mer(Non-covalent)

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

34 residues within 4Å:

Chain C: Q.510, Q.513, R.529, L.533, R.540, P.564, N.568, I.572, Q.688, K.1065, K.1073, H.1237
Chain D: R.322, Q.335, R.425, A.426, P.427, D.460, D.462, G.463, D.464
Chain F: D.223, T.224, P.225
Chain H: C.8, A.9, G.10, A.11, C.12, T.13, C.14, G.15
Ligands: MG.4, 2DA.6

6 PLIP interactions:

2 interactions with chain F, 4 interactions with chain D

Hydrogen bonds: F:T.224, F:T.224, D:R.322, D:Q.335, D:Q.335
Salt bridges: D:K.325

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:	7 residues within 4Å: Chain D: C.814, R.883, C.888, D.889, 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: GTP-A-G-U-C-U-G.1, MG.5, 2DA.6 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:D.460, D:D.462, D:D.464
MG.5:	6 residues within 4Å: Chain C: R.1106 Chain D: D.460, D.462 Ligands: MG.4, 2DA.6, DPO.7 No protein-ligand interaction detected (PLIP)

1 x 2DA: 2',3'-DIDEOXYADENOSINE-5'-MONOPHOSPHATE(Non-covalent)

2DA.6:

12 residues within 4Å:

Chain D: R.425, P.427, N.458, D.460, D.464, Q.929, M.932
Chain H: T.7
Ligands: GTP-A-G-U-C-U-G.1, MG.4, MG.5, DPO.7

3 PLIP interactions:

3 interactions with chain D

Hydrophobic interactions: D:N.458
Hydrogen bonds: D:R.425, D:R.425

1 x DPO: DIPHOSPHATE(Non-covalent)

DPO.7:

7 residues within 4Å:

Chain C: R.1106
Chain D: D.460, R.933, H.936, I.937
Ligands: MG.5, 2DA.6

6 PLIP interactions:

1 interactions with chain C, 5 interactions with chain D

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