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SMTL ID : 6xll.1

Cryo-EM structure of E. coli RNAP-promoter initial transcribing complex with 5-nt RNA transcript (RPitc-5nt)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

1 x GTP- C- A- G- U: RNA transcript (5-MER)(Non-covalent)

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

27 residues within 4Å:

Chain C: Q.510, Q.513, L.533, R.540, E.541, P.564, N.568, I.572, Q.688, K.1065, K.1073, H.1237
Chain D: R.425, D.460, D.462, G.463, D.464
Chain F: G.512, D.513, D.514, E.515
Chain H: A.12, C.13, T.14, G.15, C.16
Ligands: MG.4

8 PLIP interactions:

4 interactions with chain C, 4 interactions with chain F

Hydrogen bonds: C:Q.510, C:R.540, F:D.514, F:E.515, F:E.515, F:E.515
Salt bridges: C:R.540, C:R.540

2 x 1N7: CHAPSO(Non-covalent)

1N7.2:	13 residues within 4Å: Chain C: Q.46, Y.47, Y.179, D.396, S.398, A.399, V.400, R.452, E.458, E.461, R.465, E.583, Y.584 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:Q.46, 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
1N7.3:	7 residues within 4Å: Chain A: D.135 Chain C: Q.725, Y.726, R.731, E.962, Q.965, I.966 8 PLIP interactions: 7 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:Q.725, C:Y.726, C:Y.726, C:Y.726, C:E.962, C:I.966 Hydrogen bonds: C:Q.965, A:D.135

1 x MG: MAGNESIUM ION(Non-covalent)

MG.4:

4 residues within 4Å:

Chain D: D.460, D.462, D.464
Ligands: GTP-C-A-G-U.1

4 PLIP interactions:

4 interactions with chain D

Metal complexes: D:D.460, D:D.462, D:D.464, 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:	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

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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