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SMTL ID : 6xlm.1

Cryo-EM structure of E.coli RNAP-DNA elongation complex 1 (RDe1) in EcmrR-dependent transcription

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

1 x G- C- A- G- U- C- U- G- A: 9-nt RNA transcript(Non-covalent)

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

29 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, R.425, A.426, D.460, D.462, D.464
Chain H: T.8, C.9, A.10, G.11, A.12, C.13, T.14, G.15, C.16, A.17
Ligands: MG.4

Protein-ligand interaction information (PLIP) not available

2 x 1N7: CHAPSO(Non-covalent)

1N7.2:	12 residues within 4Å: Chain C: Q.46, Y.47, D.396, S.398, A.399, V.400, R.452, E.458, E.461, R.465, E.583, Y.584 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:Q.46, C:Y.47, C:Y.47, C:A.399, C:Y.584, C:Y.584 Hydrogen bonds: C:Q.46, C:S.398, C:A.399, C:V.400, C:R.465
1N7.3:	9 residues within 4Å: Chain A: E.72, D.135, N.137 Chain C: Q.725, Y.726, E.962, Q.965, I.966, A.969 11 PLIP interactions: 7 interactions with chain C, 4 interactions with chain A Hydrophobic interactions: C:Q.725, C:Y.726, C:Y.726, C:Y.726, C:I.966, C:A.969 Hydrogen bonds: C:Q.965, A:E.72, A:D.135, A:D.135, A:N.137

1 x MG: MAGNESIUM ION(Non-covalent)

MG.4:

4 residues within 4Å:

Chain D: D.460, D.462, D.464
Ligands: G-C-A-G-U-C-U-G-A.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.5:	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.6:	6 residues within 4Å: Chain D: C.814, R.883, C.888, D.889, 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

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Yang, Y. et al., Structural visualization of transcription activated by a multidrug-sensing MerR family regulator. Nat Commun (2021)

Release Date

2021-04-07

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 RpoD: F

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

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 RpoD

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