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- EMDB-53854: Cryo-EM structure of the human mitochondrial RNA polymerase trans... -

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Entry
Database: EMDB / ID: EMD-53854
TitleCryo-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)
Map data
Sample
  • Complex: 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)
    • Organelle or cellular component: DNA (56-mer)
      • DNA: Non-template strand DNA (56-MER)
      • DNA: template strand DNA (56-MER)
    • Organelle or cellular component: Dimethyladenosine transferase 2, mitochondrial
      • Protein or peptide: Dimethyladenosine transferase 2, mitochondrial
    • Organelle or cellular component: Transcription factor A, mitochondrial
      • Protein or peptide: Transcription factor A, mitochondrial
    • Organelle or cellular component: DNA-directed RNA polymerase, mitochondrial
      • Protein or peptide: DNA-directed RNA polymerase, mitochondrial
    • RNA: RNA (5'-D(*(GTP))-R(P*GP*(3DA))-3')
  • Ligand: GUANOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
KeywordsPOLRMT / TFB2M / TFAM / transcription / initiation / transcription initiation / polymerase / h-mtRNAP / y-mtRNAP / mtRNAP / RNA / DNA / RNAP / RNA polymerase / mitochondria / mitochondrial DNA / slippage
Function / homology
Function and homology information


rRNA (adenine-N6-)-methyltransferase activity / Mitochondrial transcription initiation / mitochondrial DNA-directed RNA polymerase complex / mitochondrial transcription factor activity / mitochondrial promoter sequence-specific DNA binding / mitochondrial respiratory chain complex assembly / transcription initiation at mitochondrial promoter / rRNA (adenine-N6,N6-)-dimethyltransferase activity / Strand-asynchronous mitochondrial DNA replication / mitochondrial DNA replication ...rRNA (adenine-N6-)-methyltransferase activity / Mitochondrial transcription initiation / mitochondrial DNA-directed RNA polymerase complex / mitochondrial transcription factor activity / mitochondrial promoter sequence-specific DNA binding / mitochondrial respiratory chain complex assembly / transcription initiation at mitochondrial promoter / rRNA (adenine-N6,N6-)-dimethyltransferase activity / Strand-asynchronous mitochondrial DNA replication / mitochondrial DNA replication / mitochondrial transcription / rRNA methylation / DNA binding, bending / mitochondrial nucleoid / heat shock protein binding / response to nutrient / Mitochondrial protein degradation / Transferases; Transferring one-carbon groups; Methyltransferases / Transcriptional activation of mitochondrial biogenesis / transcription coactivator binding / DNA-directed RNA polymerase / DNA-directed RNA polymerase activity / 3'-5'-RNA exonuclease activity / sequence-specific DNA binding / response to hypoxia / transcription cis-regulatory region binding / mitochondrial matrix / chromatin binding / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / protein-containing complex / mitochondrion / RNA binding / nucleus / cytosol
Similarity search - Function
: / DNA-directed RNA polymerase, N-terminal / DNA-directed RNA polymerase, N-terminal domain superfamily / DNA-directed RNA polymerase N-terminal / Bacteriophage-type RNA polymerase family active site signature 1. / DNA-directed RNA polymerase N-terminal / DNA-directed RNA polymerase, phage-type / : / DNA-dependent RNA polymerase / Bacteriophage-type RNA polymerase family active site signature 2. ...: / DNA-directed RNA polymerase, N-terminal / DNA-directed RNA polymerase, N-terminal domain superfamily / DNA-directed RNA polymerase N-terminal / Bacteriophage-type RNA polymerase family active site signature 1. / DNA-directed RNA polymerase N-terminal / DNA-directed RNA polymerase, phage-type / : / DNA-dependent RNA polymerase / Bacteriophage-type RNA polymerase family active site signature 2. / Ribosomal RNA adenine methylase transferase, N-terminal / Ribosomal RNA adenine dimethylases / Ribosomal RNA adenine methyltransferase KsgA/Erm / Ribosomal RNA adenine dimethylase / rRNA adenine N(6)-methyltransferase family profile. / HMG-box domain / HMG (high mobility group) box / HMG boxes A and B DNA-binding domains profile. / high mobility group / High mobility group box domain / High mobility group box domain superfamily / Tetratricopeptide-like helical domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
DNA-directed RNA polymerase, mitochondrial / Transcription factor A, mitochondrial / Dimethyladenosine transferase 2, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsGoovaerts Q / Shen J / Ajjugal Y / De Wijngaert B / Patel SS / Das K
Funding support Belgium, 1 items
OrganizationGrant numberCountry
Research Foundation - Flanders (FWO)1162825N Belgium
CitationJournal: Mol Cell / Year: 2025
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.
History
DepositionMay 19, 2025-
Header (metadata) releaseJul 30, 2025-
Map releaseJul 30, 2025-
UpdateSep 3, 2025-
Current statusSep 3, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53854.png

Downloads & links

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Map

FileDownload / File: emd_53854.map.gz / Format: CCP4 / Size: 22.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
0.9 Å/pix.
x 180 pix.
= 162. Å		0.9 Å/pix.
x 180 pix.
= 162. Å		0.9 Å/pix.
x 180 pix.
= 162. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.9 Å
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Histogram (log scale)
Contour LevelBy AUTHOR: 0.0056
Minimum - Maximum-0.057880953 - 0.12248291
Average (Standard dev.)0.0007324972 (±0.0056046783)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions180180180
Spacing180180180
CellA=B=C: 162.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_53854_msk_1.map
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Additional map: #1

Fileemd_53854_additional_1.map
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Half map: #1

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Half map: #2

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Sample components

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Entire : human mitochondrial RNA polymerase transcription initiation compl...

EntireName: 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)
Components
  • Complex: 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)
    • Organelle or cellular component: DNA (56-mer)
      • DNA: Non-template strand DNA (56-MER)
      • DNA: template strand DNA (56-MER)
    • Organelle or cellular component: Dimethyladenosine transferase 2, mitochondrial
      • Protein or peptide: Dimethyladenosine transferase 2, mitochondrial
    • Organelle or cellular component: Transcription factor A, mitochondrial
      • Protein or peptide: Transcription factor A, mitochondrial
    • Organelle or cellular component: DNA-directed RNA polymerase, mitochondrial
      • Protein or peptide: DNA-directed RNA polymerase, mitochondrial
    • RNA: RNA (5'-D(*(GTP))-R(P*GP*(3DA))-3')
  • Ligand: GUANOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION

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Supramolecule #1: human mitochondrial RNA polymerase transcription initiation compl...

SupramoleculeName: 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)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 240 KDa

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Supramolecule #2: DNA (56-mer)

SupramoleculeName: DNA (56-mer) / type: organelle_or_cellular_component / ID: 2 / Parent: 1 / Macromolecule list: #2-#3
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: Dimethyladenosine transferase 2, mitochondrial

SupramoleculeName: Dimethyladenosine transferase 2, mitochondrial / type: organelle_or_cellular_component / ID: 3 / Parent: 1 / Macromolecule list: #4
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #4: Transcription factor A, mitochondrial

SupramoleculeName: Transcription factor A, mitochondrial / type: organelle_or_cellular_component / ID: 4 / Parent: 1 / Macromolecule list: #6
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #5: DNA-directed RNA polymerase, mitochondrial

SupramoleculeName: DNA-directed RNA polymerase, mitochondrial / type: organelle_or_cellular_component / ID: 5 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: DNA-directed RNA polymerase, mitochondrial

MacromoleculeName: DNA-directed RNA polymerase, mitochondrial / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 134.632344 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString: SASPQEQDQD RRKDWGHVEL LEVLQARVRQ LQAESVSEVV VNRVDVARLP ECGSGDGSLQ PPRKVQMGAK DATPVPCGRW AKILEKDKR TQQMRMQRLK AKLQMPFQSG EFKALTRRLQ VEPRLLSKQM AGCLEDCTRQ APESPWEEQL ARLLQEAPGK L SLDVEQAP ...String:
SASPQEQDQD RRKDWGHVEL LEVLQARVRQ LQAESVSEVV VNRVDVARLP ECGSGDGSLQ PPRKVQMGAK DATPVPCGRW AKILEKDKR TQQMRMQRLK AKLQMPFQSG EFKALTRRLQ VEPRLLSKQM AGCLEDCTRQ APESPWEEQL ARLLQEAPGK L SLDVEQAP SGQHSQAQLS GQQQRLLAFF KCCLLTDQLP LAHHLLVVHH GQRQKRKLLT LDMYNAVMLG WARQGAFKEL VY VLFMVKD AGLTPDLLSY AAALQCMGRQ DQDAGTIERC LEQMSQEGLK LQALFTAVLL SEEDRATVLK AVHKVKPTFS LPP QLPPPV NTSKLLRDVY AKDGRVSYPK LHLPLKTLQC LFEKQLHMEL ASRVCVVSVE KPTLPSKEVK HARKTLKTLR DQWE KALCR ALRETKNRLE REVYEGRFSL YPFLCLLDER EVVRMLLQVL QALPAQGESF TTLARELSAR TFSRHVVQRQ RVSGQ VQAL QNHYRKYLCL LASDAEVPEP CLPRQYWEEL GAPEALREQP WPLPVQMELG KLLAEMLVQA TQMPCSLDKP HRSSRL VPV LYHVYSFRNV QQIGILKPHP AYVQLLEKAA EPTLTFEAVD VPMLCPPLPW TSPHSGAFLL SPTKLMRTVE GATQHQE LL ETCPPTALHG ALDALTQLGN CAWRVNGRVL DLVLQLFQAK GCPQLGVPAP PSEAPQPPEA HLPHSAAPAR KAELRREL A HCQKVAREMH SLRAEALYRL SLAQHLRDRV FWLPHNMDFR GRTYPCPPHF NHLGSDVARA LLEFAQGRPL GPHGLDWLK IHLVNLTGLK KREPLRKRLA FAEEVMDDIL DSADQPLTGR KWWMGAEEPW QTLACCMEVA NAVRASDPAA YVSHLPVHQD GSCNGLQHY AALGRDSVGA ASVNLEPSDV PQDVYSGVAA QVEVFRRQDA QRGMRVAQVL EGFITRKVVK QTVMTVVYGV T RYGGRLQI EKRLRELSDF PQEFVWEASH YLVRQVFKSL QEMFSGTRAI QHWLTESARL ISHMGSVVEW VTPLGVPVIQ PY RLDSKVK QIGGGIQSIT YTHNGDISRK PNTRKQKNGF PPNFIHSLDS SHMMLTALHC YRKGLTFVSV HDCYWTHAAD VSV MNQVCR EQFVRLHSEP ILQDLSRFLV KRFCSEPQKI LEASQLKETL QAVPKPGAFD LEQVKRSTYF FS

UniProtKB: DNA-directed RNA polymerase, mitochondrial

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Macromolecule #4: Dimethyladenosine transferase 2, mitochondrial

MacromoleculeName: Dimethyladenosine transferase 2, mitochondrial / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
EC number: Transferases; Transferring one-carbon groups; Methyltransferases
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 38.901309 KDa
Recombinant expressionOrganism: Escherichia coli B (bacteria)
SequenceString: PPRKASKASL DFKRYVTDRR LAETLAQIYL GKPSRPPHLL LECNPGPGIL TQALLEAGAK VVALESDKTF IPHLESLGKN LDGKLRVIH CDFFKLDPRS GGVIKPPAMS SRGLFKNLGI EAVPWTADIP LKVVGMFPSR GEKRALWKLA YDLYSCTSIY K FGRIEVNM ...String:
PPRKASKASL DFKRYVTDRR LAETLAQIYL GKPSRPPHLL LECNPGPGIL TQALLEAGAK VVALESDKTF IPHLESLGKN LDGKLRVIH CDFFKLDPRS GGVIKPPAMS SRGLFKNLGI EAVPWTADIP LKVVGMFPSR GEKRALWKLA YDLYSCTSIY K FGRIEVNM FIGEKEFQKL MADPGNPDLY HVLSVIWQLA CEIKVLHMEP WSSFDIYTRK GPLENPKRRE LLDQLQQKLY LI QMIPRQN LFTKNLTPMN YNIFFHLLKH CFGRRSATVI DHLRSLTPLD ARDILMQIGK QEDEKVVNMH PQDFKTLFET IER SKDCAY KWLYDETLED R

UniProtKB: Dimethyladenosine transferase 2, mitochondrial

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Macromolecule #6: Transcription factor A, mitochondrial

MacromoleculeName: Transcription factor A, mitochondrial / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 27.637615 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString: MSYYHHHHHH DYDIPTTENL YFQGAMGSSV LASCPKKPVS SYLRFSKEQL PIFKAQNPDA KTTELIRRIA QRWRELPDSK KKIYQDAYR AEWQVYKEEI SRFKEQLTPS QIMSLEKEIM DKHLKRKAMT KKKELTLLGK PKRPRSAYNV YVAERFQEAK G DSPQEKLK ...String:
MSYYHHHHHH DYDIPTTENL YFQGAMGSSV LASCPKKPVS SYLRFSKEQL PIFKAQNPDA KTTELIRRIA QRWRELPDSK KKIYQDAYR AEWQVYKEEI SRFKEQLTPS QIMSLEKEIM DKHLKRKAMT KKKELTLLGK PKRPRSAYNV YVAERFQEAK G DSPQEKLK TVKENWKNLS DSEKELYIQH AKEDETRYHN EMKSWEEQMI EVGRKDLLRR TIKKQRKYGA EE

UniProtKB: Transcription factor A, mitochondrial

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Macromolecule #2: Non-template strand DNA (56-MER)

MacromoleculeName: Non-template strand DNA (56-MER) / type: dna / ID: 2 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 17.486254 KDa
SequenceString: (DA)(DT)(DG)(DT)(DG)(DT)(DT)(DA)(DG)(DT) (DT)(DG)(DG)(DG)(DG)(DG)(DG)(DT)(DG)(DA) (DC)(DT)(DG)(DT)(DT)(DA)(DA)(DA)(DA) (DG)(DT)(DG)(DC)(DA)(DT)(DA)(DC)(DC)(DG) (DA) (DA)(DC)(DA)(DA)(DA)(DG) ...String:
(DA)(DT)(DG)(DT)(DG)(DT)(DT)(DA)(DG)(DT) (DT)(DG)(DG)(DG)(DG)(DG)(DG)(DT)(DG)(DA) (DC)(DT)(DG)(DT)(DT)(DA)(DA)(DA)(DA) (DG)(DT)(DG)(DC)(DA)(DT)(DA)(DC)(DC)(DG) (DA) (DA)(DC)(DA)(DA)(DA)(DG)(DA)(DT) (DA)(DA)(DA)(DA)(DT)(DT)(DT)(DG)

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Macromolecule #3: template strand DNA (56-MER)

MacromoleculeName: template strand DNA (56-MER) / type: dna / ID: 3 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 17.022959 KDa
SequenceString: (DC)(DA)(DA)(DA)(DT)(DT)(DT)(DT)(DA)(DT) (DC)(DT)(DC)(DC)(DA)(DG)(DG)(DC)(DG)(DG) (DT)(DA)(DT)(DG)(DC)(DA)(DC)(DT)(DT) (DT)(DT)(DA)(DA)(DC)(DA)(DG)(DT)(DC)(DA) (DC) (DC)(DC)(DC)(DC)(DC)(DA) ...String:
(DC)(DA)(DA)(DA)(DT)(DT)(DT)(DT)(DA)(DT) (DC)(DT)(DC)(DC)(DA)(DG)(DG)(DC)(DG)(DG) (DT)(DA)(DT)(DG)(DC)(DA)(DC)(DT)(DT) (DT)(DT)(DA)(DA)(DC)(DA)(DG)(DT)(DC)(DA) (DC) (DC)(DC)(DC)(DC)(DC)(DA)(DA)(DC) (DT)(DA)(DA)(DC)(DA)(DC)(DA)(DT)

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Macromolecule #5: RNA (5'-D(*(GTP))-R(P*GP*(3DA))-3')

MacromoleculeName: RNA (5'-D(*(GTP))-R(P*GP*(3DA))-3') / type: rna / ID: 5 / Number of copies: 1
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 1.11862 KDa
SequenceString:
(GTP)G(3DA)

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Macromolecule #7: GUANOSINE-5'-TRIPHOSPHATE

MacromoleculeName: GUANOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 7 / Number of copies: 1 / Formula: GTP
Molecular weightTheoretical: 523.18 Da
Chemical component information

ChemComp-GTP:
GUANOSINE-5'-TRIPHOSPHATE / GTP, energy-carrying molecule*YM

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Macromolecule #8: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 8 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1.2 mg/mL
BufferpH: 8
Details: 30 mM Tris-HCl pH8, 200 mM NaCl, 3 mM DTT, 10 mM MgCl2
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 45 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.03 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV
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

MicroscopeTFS GLACIOS
Specialist opticsEnergy filter - Name: TFS Selectris / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 1 / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 20.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 130000
Sample stageSpecimen holder model: OTHER / Cooling holder cryogen: NITROGEN

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Image processing

CTF correctionSoftware - Name: CTFFIND / Type: NONE
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6erp

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: Coot / Number images used: 155000
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Overall B value: 102 / Target criteria: Correlation Coefficient
Output model

PDB-9r96:
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)

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