4BOC

Structure of mitochondrial RNA polymerase elongation complex

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.181 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history. 


Literature

Structure of Human Mitochondrial RNA Polymerase Elongation Complex

Schwinghammer, K., Cheung, A.C.M., Morozov, Y.I., Agaronyan, K., Temiakov, D., Cramer, P.

(2013) Nat Struct Mol Biol 20: 1298

  • DOI: https://doi.org/10.1038/nsmb.2683
  • Primary Citation of Related Structures:  
    4BOC

  • PubMed Abstract: 

    Here we report the crystal structure of the human mitochondrial RNA polymerase (mtRNAP) transcription elongation complex, determined at 2.65-Å resolution. The structure reveals a 9-bp hybrid formed between the DNA template and the RNA transcript and one turn of DNA both upstream and downstream of the hybrid. Comparisons with the distantly related RNA polymerase (RNAP) from bacteriophage T7 indicates conserved mechanisms for substrate binding and nucleotide incorporation but also strong mechanistic differences. Whereas T7 RNAP refolds during the transition from initiation to elongation, mtRNAP adopts an intermediary conformation that is capable of elongation without refolding. The intercalating hairpin that melts DNA during T7 RNAP initiation separates RNA from DNA during mtRNAP elongation. Newly synthesized RNA exits toward the pentatricopeptide repeat (PPR) domain, a unique feature of mtRNAP with conserved RNA-recognition motifs.

    • Organizational Affiliation: 

    Gene Center, Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany.


Macromolecules

Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-DIRECTED RNA POLYMERASE, MITOCHONDRIAL1,088Homo sapiensMutation(s): 0 
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
Sequence Annotations
Expand
  • Reference Sequence
Find similar nucleic acids by: 
(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains LengthOrganismImage
5'-D(*CP*AP*TP*GP*GP*GP*GP*TP*AP*AP*TP*TP*AP*TP *TP*TP*CP*GP*AP*CP*GP*CP*CP*AP*GP*AP*CP*G)-3'B [auth N]28synthetic construct
Sequence Annotations
Expand
  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 3
MoleculeChains LengthOrganismImage
5'-R(*AP*GP*UP*CP*UP*GP*CP*GP*GP*CP*GP*CP*GP*CP)-3'C [auth R]14synthetic construct
Sequence Annotations
Expand
  • Reference Sequence
Find similar nucleic acids by: 
(by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains LengthOrganismImage
5'-D(*CP*GP*TP*CP*TP*GP*GP*CP*GP*TP*GP*CP*GP*CP *GP*CP*CP*GP*CP*TP*AP*CP*CP*CP*CP*AP*TP*G)-3'D [auth T]28synthetic construct
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.181 
  • Space Group: I 2 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 225.19α = 90
b = 225.19β = 90
c = 225.19γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-09-25
    Type: Initial release
  • Version 1.1: 2013-10-09
    Changes: Database references
  • Version 1.2: 2013-10-16
    Changes: Database references
  • Version 1.3: 2013-11-20
    Changes: Database references
  • Version 1.4: 2023-12-20
    Changes: Data collection, Database references, Other, Refinement description