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Basic information

Entry
Database: EMDB / ID: EMD-48415
TitleStructure of the human mitochondrial late-stage transcription initiation complex, IC8
Map data
Sample
  • Complex: Structure of the human mitochondrial late-stage transcription initiation complex, IC8'
    • Protein or peptide: Dimethyladenosine transferase 2, mitochondrial
    • Protein or peptide: DNA-directed RNA polymerase, mitochondrial
    • DNA: Non-Template Strand DNA
    • RNA: RNA
    • DNA: Template Strand DNA
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
KeywordsMitochondrial RNA Polymerase / Transcription Initiation complex / TRANSCRIPTION / POLRMT / TRANSCRIPTION-DNA-RNA complex
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 / 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
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 ...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. / 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 / Dimethyladenosine transferase 2, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.65 Å
AuthorsHerbine KH / Nayak AR / Temiakov D
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)NIH GM131832 United States
CitationJournal: Mol Cell / Year: 2025
Title: Structural basis for promoter recognition and transcription factor binding and release in human mitochondria.
Authors: Karl Herbine / Ashok R Nayak / Angelica Zamudio-Ochoa / Dmitry Temiakov /
Abstract: Transcription in human mitochondria is driven by a core apparatus consisting of a Pol A family RNA polymerase (mtRNAP), the initiation factors TFAM and TFB2M, and the elongation factor TEFM. While ...Transcription in human mitochondria is driven by a core apparatus consisting of a Pol A family RNA polymerase (mtRNAP), the initiation factors TFAM and TFB2M, and the elongation factor TEFM. While earlier structures of initiation and elongation complexes provided valuable snapshots, they represent isolated stages of a highly dynamic and multistep process. Critical aspects of mitochondrial transcription-such as DNA recognition and melting, promoter escape, and the release of initiation factors-remain poorly understood. Here, we present a series of cryoelectron microscopy (cryo-EM) structures that capture the transcription complex as it transitions from the initial open promoter complex to the processive elongation complex through intermediate stages. Our data reveal new, previously unidentified determinants of promoter specificity: the sequential disengagement of mtRNAP from TFAM and the promoter, the release of TFB2M, and the recruitment of TEFM. Together, these findings provide a detailed molecular mechanism underlying transcription in human mitochondria.
History
DepositionDec 20, 2024-
Header (metadata) releaseAug 6, 2025-
Map releaseAug 6, 2025-
UpdateAug 6, 2025-
Current statusAug 6, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_48415.png

Downloads & links

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Map

FileDownload / File: emd_48415.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
0.73 Å/pix.
x 384 pix.
= 280.32 Å		0.73 Å/pix.
x 384 pix.
= 280.32 Å		0.73 Å/pix.
x 384 pix.
= 280.32 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.73 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.01
Minimum - Maximum-0.037600283 - 1.7613443
Average (Standard dev.)0.001019138 (±0.020869546)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 280.32 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_48415_additional_1.map
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Half map: #2

Fileemd_48415_half_map_1.map
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Half map: #1

Fileemd_48415_half_map_2.map
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Sample components

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Entire : Structure of the human mitochondrial late-stage transcription ini...

EntireName: Structure of the human mitochondrial late-stage transcription initiation complex, IC8'
Components
  • Complex: Structure of the human mitochondrial late-stage transcription initiation complex, IC8'
    • Protein or peptide: Dimethyladenosine transferase 2, mitochondrial
    • Protein or peptide: DNA-directed RNA polymerase, mitochondrial
    • DNA: Non-Template Strand DNA
    • RNA: RNA
    • DNA: Template Strand DNA
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Structure of the human mitochondrial late-stage transcription ini...

SupramoleculeName: Structure of the human mitochondrial late-stage transcription initiation complex, IC8'
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Details: Human Mitochondrial RNA polymerase (d119), TFAM (d42), and TFB2M (d20) assembled on promoter DNA containing a premelted bubble, a 3-mer primer RNA, ATP, and 3'-deoxyGTP.
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 216 KDa

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Macromolecule #1: Dimethyladenosine transferase 2, mitochondrial

MacromoleculeName: Dimethyladenosine transferase 2, mitochondrial / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
EC number: Transferases; Transferring one-carbon groups; Methyltransferases
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 45.416848 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MWIPVVGLPR RLRLSALAGA GRFCILGSEA ATRKHLPARN HCGLSDSSPQ LWPEPDFRNP PRKASKASLD FKRYVTDRRL AETLAQIYL GKPSRPPHLL LECNPGPGIL TQALLEAGAK VVALESDKTF IPHLESLGKN LDGKLRVIHC DFFKLDPRSG G VIKPPAMS ...String:
MWIPVVGLPR RLRLSALAGA GRFCILGSEA ATRKHLPARN HCGLSDSSPQ LWPEPDFRNP PRKASKASLD FKRYVTDRRL AETLAQIYL GKPSRPPHLL LECNPGPGIL TQALLEAGAK VVALESDKTF IPHLESLGKN LDGKLRVIHC DFFKLDPRSG G VIKPPAMS SRGLFKNLGI EAVPWTADIP LKVVGMFPSR GEKRALWKLA YDLYSCTSIY KFGRIEVNMF IGEKEFQKLM AD PGNPDLY HVLSVIWQLA CEIKVLHMEP WSSFDIYTRK GPLENPKRRE LLDQLQQKLY LIQMIPRQNL FTKNLTPMNY NIF FHLLKH CFGRRSATVI DHLRSLTPLD ARDILMQIGK QEDEKVVNMH PQDFKTLFET IERSKDCAYK WLYDETLEDR

UniProtKB: Dimethyladenosine transferase 2, mitochondrial

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Macromolecule #2: DNA-directed RNA polymerase, mitochondrial

MacromoleculeName: DNA-directed RNA polymerase, mitochondrial / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 138.818156 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSALCWGRGA AGLKRALRPC GRPGLPGKEG TAGGVCGPRR SSSASPQEQD QDRRKDWGHV ELLEVLQARV RQLQAESVSE VVVNRVDVA RLPECGSGDG SLQPPRKVQM GAKDATPVPC GRWAKILEKD KRTQQMRMQR LKAKLQMPFQ SGEFKALTRR L QVEPRLLS ...String:
MSALCWGRGA AGLKRALRPC GRPGLPGKEG TAGGVCGPRR SSSASPQEQD QDRRKDWGHV ELLEVLQARV RQLQAESVSE VVVNRVDVA RLPECGSGDG SLQPPRKVQM GAKDATPVPC GRWAKILEKD KRTQQMRMQR LKAKLQMPFQ SGEFKALTRR L QVEPRLLS KQMAGCLEDC TRQAPESPWE EQLARLLQEA PGKLSLDVEQ APSGQHSQAQ LSGQQQRLLA FFKCCLLTDQ LP LAHHLLV VHHGQRQKRK LLTLDMYNAV MLGWARQGAF KELVYVLFMV KDAGLTPDLL SYAAALQCMG RQDQDAGTIE RCL EQMSQE GLKLQALFTA VLLSEEDRAT VLKAVHKVKP TFSLPPQLPP PVNTSKLLRD VYAKDGRVSY PKLHLPLKTL QCLF EKQLH MELASRVCVV SVEKPTLPSK EVKHARKTLK TLRDQWEKAL CRALRETKNR LEREVYEGRF SLYPFLCLLD EREVV RMLL QVLQALPAQG ESFTTLAREL SARTFSRHVV QRQRVSGQVQ ALQNHYRKYL CLLASDAEVP EPCLPRQYWE ELGAPE ALR EQPWPLPVQM ELGKLLAEML VQATQMPCSL DKPHRSSRLV PVLYHVYSFR NVQQIGILKP HPAYVQLLEK AAEPTLT FE AVDVPMLCPP LPWTSPHSGA FLLSPTKLMR TVEGATQHQE LLETCPPTAL HGALDALTQL GNCAWRVNGR VLDLVLQL F QAKGCPQLGV PAPPSEAPQP PEAHLPHSAA PARKAELRRE LAHCQKVARE MHSLRAEALY RLSLAQHLRD RVFWLPHNM DFRGRTYPCP PHFNHLGSDV ARALLEFAQG RPLGPHGLDW LKIHLVNLTG LKKREPLRKR LAFAEEVMDD ILDSADQPLT GRKWWMGAE EPWQTLACCM EVANAVRASD PAAYVSHLPV HQDGSCNGLQ HYAALGRDSV GAASVNLEPS DVPQDVYSGV A AQVEVFRR QDAQRGMRVA QVLEGFITRK VVKQTVMTVV YGVTRYGGRL QIEKRLRELS DFPQEFVWEA SHYLVRQVFK SL QEMFSGT RAIQHWLTES ARLISHMGSV VEWVTPLGVP VIQPYRLDSK VKQIGGGIQS ITYTHNGDIS RKPNTRKQKN GFP PNFIHS LDSSHMMLTA LHCYRKGLTF VSVHDCYWTH AADVSVMNQV CREQFVRLHS EPILQDLSRF LVKRFCSEPQ KILE ASQLK ETLQAVPKPG AFDLEQVKRS TYFFS

UniProtKB: DNA-directed RNA polymerase, mitochondrial

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Macromolecule #3: Non-Template Strand DNA

MacromoleculeName: Non-Template Strand DNA / type: dna / ID: 3 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 20.524199 KDa
SequenceString: (DG)(DT)(DG)(DT)(DT)(DA)(DG)(DT)(DT)(DA) (DG)(DG)(DG)(DA)(DG)(DT)(DG)(DA)(DC)(DT) (DG)(DT)(DT)(DA)(DA)(DA)(DA)(DG)(DT) (DG)(DC)(DA)(DT)(DA)(DC)(DC)(DG)(DC)(DC) (DA) (DA)(DG)(DA)(DG)(DA)(DA) ...String:
(DG)(DT)(DG)(DT)(DT)(DA)(DG)(DT)(DT)(DA) (DG)(DG)(DG)(DA)(DG)(DT)(DG)(DA)(DC)(DT) (DG)(DT)(DT)(DA)(DA)(DA)(DA)(DG)(DT) (DG)(DC)(DA)(DT)(DA)(DC)(DC)(DG)(DC)(DC) (DA) (DA)(DG)(DA)(DG)(DA)(DA)(DA)(DA) (DG)(DA)(DA)(DA)(DA)(DC)(DC)(DC)(DA)(DA) (DT)(DT) (DG)(DT)(DG)(DG)(DC)(DC)

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Macromolecule #5: Template Strand DNA

MacromoleculeName: Template Strand DNA / type: dna / ID: 5 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 20.162908 KDa
SequenceString: (DG)(DG)(DC)(DC)(DA)(DC)(DA)(DA)(DT)(DT) (DG)(DG)(DG)(DT)(DT)(DT)(DT)(DC)(DT)(DT) (DT)(DT)(DC)(DT)(DC)(DT)(DT)(DG)(DG) (DC)(DG)(DG)(DT)(DA)(DT)(DG)(DC)(DA)(DC) (DT) (DT)(DT)(DT)(DA)(DA)(DC) ...String:
(DG)(DG)(DC)(DC)(DA)(DC)(DA)(DA)(DT)(DT) (DG)(DG)(DG)(DT)(DT)(DT)(DT)(DC)(DT)(DT) (DT)(DT)(DC)(DT)(DC)(DT)(DT)(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)(DT)(DC)(DC)(DC)(DT)(DA) (DA)(DC) (DT)(DA)(DA)(DC)(DA)(DC)

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Macromolecule #4: RNA

MacromoleculeName: RNA / type: rna / ID: 4 / Number of copies: 1
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 1.962277 KDa
SequenceString:
GAAAAG

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Macromolecule #6: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 6 / Number of copies: 1 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

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Macromolecule #7: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 7 / 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

Concentration0.75 mg/mL
BufferpH: 7.9
Details: 20 mM Tris Buffer, pH 7.9, 150 mM NaCl, 10 mM DTT, and 10 mM MgCl2
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 90 sec. / Pretreatment - Atmosphere: AIR / Details: 15
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
Details5 uM mtRNAP (D119) was mixed with TFAM (D42), TFB2M (D20) and promoter DNA at a 1:3:2:1 molar ratio in buffer containing 20 mM Tris-HCl, pH 7.9, 150 mM NaCl, 10 mM DTT, and 10 mM MgCl2 and incubated for 10 minutes on ice prior to overnight dialysis at 4C in the same buffer. Following overnight dialysis, 5 uM IC was incubated with GAG RNA primer, ATP, and 3' deoxy GTP at a molar ratio of 1:10:25:50.

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: TFS Selectris / Energy filter - Slit width: 10 eV
SoftwareName: Leginon
DetailsPreliminary grid screening performed manually using TFS Glacios.
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 2 / Number real images: 17559 / Average electron dose: 45.44 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.2 µm / Nominal defocus min: 0.4 µm / Nominal magnification: 165000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 5354890
Details: Automated particle picking (Blob picker, CryoSPARC) with manual inspection (Inspect Particle Picks).
CTF correctionSoftware - Name: cryoSPARC (ver. 4.6.0) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: Ab-initio reconstruction in cryoSPARC
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.65 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.6.0) / Number images used: 163170
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.6.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.6.0)
Final 3D classificationNumber classes: 6 / Software - Name: cryoSPARC (ver. 4.6.0)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

6erp


Chain - Source name: PDB / Chain - Initial model type: experimental model
SoftwareName: Coot (ver. 0.9.8.2)
DetailsInitial docking of the starting model was done in Chimera and flexible/refined fitting done with Coot, and Phenix Real-Space Refinement.
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Target criteria: Cross-correlation Coefficient
Output model

PDB-9mn7:
Structure of the human mitochondrial late-stage transcription initiation complex, IC8

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