9R95

Cryo-EM structure of the human mitochondrial RNA polymerase transcription initiation complex (POLRMT/TFAM/TFB2M/DNA/RNA) with a slipped 3-mer RNA, pppGpGpA (slipped IC3)

Summary for 9R95

• Entry DOI: 10.2210/pdb9r95/pdb
• Related: 9GZM 9GZN 9GZO 9R96
• EMDB information: 51727 51728 51729 53853 53854
• Descriptor: DNA-directed RNA polymerase, mitochondrial, Dimethyladenosine transferase 2, mitochondrial, Transcription factor A, mitochondrial, ... (6 entities in total)
• Functional Keywords: polrmt, tfb2m, tfam, transcription, initiation, transcription initiation, polymerase, h-mtrnap, y-mtrnap, mtrnap, rna polymerase, mitochondrial, mitochondria, mitochondrial dna, dna, rna, slippage
• Biological source: Homo sapiens (human); More
• Total number of polymer chains: 6
• Total formula weight: 236815.10

Authors

Goovaerts, Q.,Shen, J.,Ajjugal, Y.,De Wijngaert, B.,Patel, S.S.,Das, K. (deposition date: 2025-05-19, release date: 2025-07-30, Last modification date: 2025-09-03)

Primary citation

Shen, J.,Goovaerts, Q.,Ajjugal, Y.,De Wijngaert, B.,Das, K.,Patel, S.S.
Human mitochondrial RNA polymerase structures reveal transcription start site and slippage mechanism.
Mol.Cell, 85:3137-3150.e7, 2025

PubMed Abstract: Transcription of the human mitochondrial DNA is initiated by POLRMT and initiation factors mitochondrial transcription factor A (TFAM) and mitochondrial transcription factor B2 (TFB2M). We present cryo-electron microscopy (cryo-EM) structures of three transcription initiation intermediates (pre-catalytic IC3 [pre-IC3], slipped-IC3, and slipped pre-IC4) catalyzing RNA synthesis by normal and slippage pathways with fully resolved transcription bubbles and RNA transcripts starting from the +1 or -1 position. The structural and biochemical studies reveal mechanisms of promoter melting, start site selection, and slippage synthesis. Promoter melting begins at -4 with base-specific interactions of template -4 and -3 guanines with POLRMT and non-template -1 adenine with TFB2M. The NT-stabilizing loop (KLDPRSGGVIKPP) and Y209 of TFB2M and W1026 of POLRMT interact with the non-template strand to guide initiation from the +1 start site. The -1 position is not an alternative start site but supports slippage initiation by base-pairing with a slipped or rebound 2-nt RNA. Cryo-EM resolved additional apo and dimeric complexes whose populations may regulate transcription initiation.

PubMed: 40712586
DOI: 10.1016/j.molcel.2025.07.002

Experimental method

ELECTRON MICROSCOPY (3.2 Å)