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SMTL ID : 6xl9.1

Cryo-EM structure of EcmrR-RNAP-promoter initial transcribing complex with 3-nt RNA transcript (EcmrR-RPitc-3nt)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

1 x GTP- A- G: RNA (5'-D(*(GTP))-R(P*AP*G)-3')(Non-covalent)

GTP-A-G.1:

19 residues within 4Å:

Chain C: P.564, G.566, P.567, N.568, Q.688, K.1065, K.1073, H.1237
Chain D: R.425, A.426, P.427, D.462, D.464
Chain G: C.13, T.14, C.15, G.16
Ligands: MG.4, MG.6

3 PLIP interactions:

3 interactions with chain C

Hydrogen bonds: C:G.566, C:N.568, C:Q.688

2 x ZN: ZINC ION(Non-covalent)

ZN.2:	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.3:	4 residues within 4Å: Chain D: C.814, 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

2 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.4:	4 residues within 4Å: Chain D: D.460, D.462, D.464 Ligands: GTP-A-G.1 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:D.460, D:D.462, D:D.464, D:D.464
MG.6:	1 residues within 4Å: Ligands: GTP-A-G.1 No protein-ligand interaction detected (PLIP)

3 x 118: TETRAPHENYLANTIMONIUM ION(Non-covalent)

118.5:	7 residues within 4Å: Chain E: T.432, W.433, R.436, Q.437, T.440 Chain F: T.33 Chain G: A.26 6 PLIP interactions: 6 interactions with chain E Hydrophobic interactions: E:T.432, E:W.433, E:W.433, E:W.433, E:R.436 pi-Cation interactions: E:R.436
118.7:	9 residues within 4Å: Chain H: Y.126, G.146, M.150, A.162, C.164, F.182, E.184, Y.244, W.249 5 PLIP interactions: 5 interactions with chain H Hydrophobic interactions: H:A.162, H:F.182, H:Y.244, H:W.249 pi-Stacking: H:W.249
118.8:	8 residues within 4Å: Chain I: Y.126, I.142, G.146, C.164, F.182, E.184, Y.244, W.249 8 PLIP interactions: 8 interactions with chain I Hydrophobic interactions: I:I.142, I:I.142, I:F.182, I:F.182, I:W.249 pi-Stacking: I:Y.244, I:W.249, I:W.249

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
RNA polymerase sigma factor RpoD: E
MerR family transcriptional regulator EcmrR: HI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
F

H
G

I
H

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'

RNA polymerase sigma factor RpoD

MerR family transcriptional regulator EcmrR

Toggle Identical (HI)

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