9MN4 | pdb_00009mn4

Structure of the human mitochondrial initially transcribing complex, IC3


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.05 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural basis for promoter recognition and transcription factor binding and release in human mitochondria.

Herbine, K.Nayak, A.R.Zamudio-Ochoa, A.Temiakov, D.

(2025) Mol Cell 85: 3123-3136.e7

  • DOI: https://doi.org/10.1016/j.molcel.2025.06.016
  • Primary Citation of Related Structures:  
    9MN4, 9MN5, 9MN6, 9MN7, 9MN8, 9MN9, 9MNA

  • PubMed 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 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.


  • Organizational Affiliation
    • Department of Biochemistry and Molecular Biology, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA 19107, USA.

Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription factor A, mitochondrial246Homo sapiensMutation(s): 0 
Gene Names: TFAMTCF6TCF6L2
UniProt & NIH Common Fund Data Resources
Find proteins for Q00059 (Homo sapiens)
Explore Q00059 
Go to UniProtKB:  Q00059
PHAROS:  Q00059
GTEx:  ENSG00000108064 
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UniProt GroupQ00059
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Dimethyladenosine transferase 2, mitochondrial396Homo sapiensMutation(s): 0 
Gene Names: TFB2MNS5ATP5
EC: 2.1.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H5Q4 (Homo sapiens)
Explore Q9H5Q4 
Go to UniProtKB:  Q9H5Q4
PHAROS:  Q9H5Q4
GTEx:  ENSG00000162851 
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Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9H5Q4
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase, mitochondrialC [auth E]1,230Homo sapiensMutation(s): 0 
Gene Names: POLRMT
EC: 2.7.7.6
UniProt & NIH Common Fund Data Resources
Find proteins for O00411 (Homo sapiens)
Explore O00411 
Go to UniProtKB:  O00411
PHAROS:  O00411
GTEx:  ENSG00000099821 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO00411
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  • Reference Sequence
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Entity ID: 4
MoleculeChains LengthOrganismImage
Non-Template Strand DNAD [auth N]60synthetic construct
Sequence Annotations
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  • Reference Sequence

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Entity ID: 5
MoleculeChains LengthOrganismImage
RNA (RNA3mt)E [auth R]3synthetic construct
Sequence Annotations
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Entity ID: 6
MoleculeChains LengthOrganismImage
Template Strand DNAF [auth T]60synthetic construct
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.05 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21rc1_5015
RECONSTRUCTIONcryoSPARC4.6.0

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesNIH GM131832

Revision History  (Full details and data files)

  • Version 1.0: 2025-08-06
    Type: Initial release
  • Version 1.1: 2025-09-03
    Changes: Data collection, Database references