SMTL ID : 6ymw.1

Cryo-EM structure of yeast mitochondrial RNA polymerase transcription initiation complex

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-mer

Ligands

1 x GTP- G: RNA (pppGpG)(Non-covalent)

GTP-G.1: 16 residues within 4Å: Chain B: R.740, Y.742, L.751, G.752, N.753, R.757, K.946, H.1074, V.1098, H.1099, D.1100 Chain D: A.10, C.11, C.12, G.13 Ligands: P5E.2 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Y.742, B:Y.742, B:R.757 Salt bridges: B:K.946, B:K.946

1 x P5E: [[(2~{R},3~{S},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-sulfanyl-phosphoryl] phosphono hydrogen phosphate(Non-covalent)

P5E.2: 17 residues within 4Å: Chain B: R.740, G.857, T.858, C.859, N.860, Y.890, R.921, K.925, Q.926, M.929, Y.933, H.1074, D.1077, D.1100 Chain D: A.10 Ligands: GTP-G.1, MG.3 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:R.740, B:R.740, B:C.859, B:N.860, B:Q.926, B:Y.933, B:D.1077 Salt bridges: B:R.921, B:K.925, B:K.925

1 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 3 residues within 4Å: Chain B: G.857, D.1100 Ligands: P5E.2 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:G.857, B:D.1100

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

De Wijngaert, B. et al., Cryo-EM Structures Reveal Transcription Initiation Steps by Yeast Mitochondrial RNA Polymerase. Mol.Cell (2021)

Release Date

2020-12-09

Peptides

Mitochondrial transcription factor 1: A
DNA-directed RNA polymerase, mitochondrial: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
A

Mitochondrial transcription factor 1

DNA-directed RNA polymerase, mitochondrial

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