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- PDB-9gzn: Cryo-EM structure of the human mitochondrial RNA polymerase trans... -
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Open data
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Basic information
Entry | Database: PDB / ID: 9gzn | ||||||
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Title | Cryo-EM structure of the human mitochondrial RNA polymerase transcription initiation complex (POLRMT/TFB2M/DNA/RNA) without TFAM; and with a 2-mer RNA (pppGpA) and GTP poised for catalysis (pre-IC3-TFAM) | ||||||
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![]() | TRANSCRIPTION / POLRMT / TFB2M / TFAM / transcription initiation / polymerase / h-mtRNAP / mtRNAP / human mitochondrial RNA polymerase / y-mtRNAP / MTF1 / RPO41 / DNA transcription / mitochondrial DNA / mitochondria | ||||||
Function / homology | ![]() rRNA (adenine-N6-)-methyltransferase activity / Mitochondrial transcription initiation / mitochondrial DNA-directed RNA polymerase complex / mitochondrial transcription factor activity / mitochondrial promoter sequence-specific DNA binding / transcription initiation at mitochondrial promoter / rRNA (adenine-N6,N6-)-dimethyltransferase activity / Strand-asynchronous mitochondrial DNA replication / mitochondrial DNA replication / mitochondrial transcription ...rRNA (adenine-N6-)-methyltransferase activity / Mitochondrial transcription initiation / mitochondrial DNA-directed RNA polymerase complex / mitochondrial transcription factor activity / mitochondrial promoter sequence-specific DNA binding / transcription initiation at mitochondrial promoter / rRNA (adenine-N6,N6-)-dimethyltransferase activity / Strand-asynchronous mitochondrial DNA replication / mitochondrial DNA replication / mitochondrial transcription / rRNA methylation / mitochondrial nucleoid / Transferases; Transferring one-carbon groups; Methyltransferases / Transcriptional activation of mitochondrial biogenesis / DNA-directed RNA polymerase / DNA-directed RNA polymerase activity / 3'-5'-RNA exonuclease activity / sequence-specific DNA binding / mitochondrial matrix / protein-containing complex / mitochondrion / RNA binding Similarity search - Function | ||||||
Biological species | ![]() synthetic construct (others) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å | ||||||
![]() | Goovaerts, Q. / Shen, J. / Ajjugal, Y. / De Wijngaert, B. / Patel, S.S. / Das, K. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Human mitochondrial RNA polymerase structures reveal transcription start site and slippage mechanism. Authors: Jiayu Shen / Quinten Goovaerts / Yogeeshwar Ajjugal / Brent De Wijngaert / Kalyan Das / Smita S Patel / ![]() ![]() ![]() 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 ...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. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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PDBx/mmCIF format | ![]() | 284.5 KB | Display | ![]() |
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PDB format | ![]() | 214.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 1.5 MB | Display | ![]() |
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Full document | ![]() | 1.5 MB | Display | |
Data in XML | ![]() | 46.2 KB | Display | |
Data in CIF | ![]() | 71.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 51728MC ![]() 9gzmC ![]() 9gzoC ![]() 9r95C ![]() 9r96C M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 134632.344 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#4: Protein | Mass: 38901.309 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q9H5Q4, Transferases; Transferring one-carbon groups; Methyltransferases |
-DNA chain , 2 types, 2 molecules NT
#2: DNA chain | Mass: 19652.648 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#3: DNA chain | Mass: 18867.131 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-RNA chain , 1 types, 1 molecules R
#5: RNA chain | Mass: 789.413 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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-Non-polymers , 2 types, 2 molecules 


#6: Chemical | ChemComp-GTP / |
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#7: Chemical | ChemComp-MG / |
-Details
Has ligand of interest | N |
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Has protein modification | N |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
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Buffer solution | pH: 8 Details: 30 mM Tris-HCl pH 8, 200 mM NaCl, 3 mM DTT, 10 mM MgCl2 | ||||||||||||||||||||||||||||||
Specimen | Conc.: 1.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||||||||
Specimen support | Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 | ||||||||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K Details: incubated on the grid for 5 seconds prior to double sided blotting for 3.5 seconds at force 1 |
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Electron microscopy imaging
Microscopy | Model: TFS GLACIOS |
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Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 130000 X / Nominal defocus max: 1800 nm / Nominal defocus min: 600 nm / Cs: 2.7 mm / C2 aperture diameter: 20 µm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: OTHER |
Image recording | Electron dose: 40 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 1 |
EM imaging optics | Energyfilter name: TFS Selectris / Energyfilter slit width: 20 eV |
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Processing
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CTF correction | Type: NONE | ||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 136426 / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | B value: 68 / Protocol: FLEXIBLE FIT / Target criteria: Correlation coefficient | ||||||||||||||||||||||||
Refine LS restraints |
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