SMTL ID : 9r96.1

Cryo-EM structure of the human mitochondrial RNA polymerase transcription initiation complex (POLRMT/TFAM/TFB2M/DNA/RNA) with a slipped 3-mer RNA (pppGpGpA) and GTP poised for catalysis (slipped pre-IC4)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-mer

Ligands

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

GTP-G-3DA.1: 11 residues within 4Å: Chain A: R.763, L.774, G.775, R.780, K.970, V.1107, H.1108 Chain C: T.12, C.13, C.14 Ligands: GTP.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.763, A:H.1108 Salt bridges: A:R.780, A:K.970

1 x GTP: GUANOSINE-5'-TRIPHOSPHATE(Non-covalent)

GTP.2: 19 residues within 4Å: Chain A: D.880, G.881, S.882, C.883, N.884, G.885, Y.914, R.945, K.949, Q.950, M.953, T.954, Y.957, H.1083, D.1109 Chain C: C.11, T.12 Ligands: GTP-G-3DA.1, MG.3 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:G.881, A:C.883, A:N.884, A:G.885, A:Y.914, A:Q.950, A:Y.957 Salt bridges: A:R.945, A:K.949, A:K.949, A:K.949

1 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain A: D.880, G.881, D.1109 Ligands: GTP.2 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.880, A:G.881, A:D.1109

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shen, J. et al., Human mitochondrial RNA polymerase structures reveal transcription start site and slippage mechanism. Mol.Cell (2025)

Release Date

2025-07-30

Peptides

DNA-directed RNA polymerase, mitochondrial: A
Dimethyladenosine transferase 2, mitochondrial: D
Transcription factor A, mitochondrial: E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
B

E
C

DNA-directed RNA polymerase, mitochondrial

Dimethyladenosine transferase 2, mitochondrial

Transcription factor A, mitochondrial

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