4BOC | pdb_00004boc

Structure of mitochondrial RNA polymerase elongation complex

• PDB DOI: https://doi.org/10.2210/pdb4BOC/pdb
• NAKB: 4BOC

• Classification: TRANSCRIPTION
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-05-18 Released: 2013-09-25 
• Deposition Author(s): Schwinghammer, K., Cheung, A., Morozov, Y., Agaronyan, K., Temiakov, D., Cramer, P.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å
• R-Value Free: 
  0.209 (Depositor), 0.214 (DCC) 
• R-Value Work: 
  0.179 (Depositor), 0.186 (DCC) 
• R-Value Observed: 
  0.181 (Depositor) 

Starting Model: experimental

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

• PubMed: 24096365 
• DOI: https://doi.org/10.1038/nsmb.2683
• Primary Citation 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.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 145.06 kDa 
• Atom Count: 9,302 
• Modeled Residue Count: 1,046 
• Deposited Residue Count: 1,158 
• Unique protein chains: 1
• Unique nucleic acid chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-DIRECTED RNA POLYMERASE, MITOCHONDRIAL	A	1,088	Homo sapiens	Mutation(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 ID: 2
Molecule	Chains	Length	Organism	Image
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]	28	synthetic construct

Entity ID: 3
Molecule	Chains	Length	Organism	Image
5'-R(*AP*GP*UP*CP*UP*GP*CP*GP*GP*CP*GP*CP*GP*CP)-3'	C [auth R]	14	synthetic construct

Entity ID: 4
Molecule	Chains	Length	Organism	Image
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]	28	synthetic construct

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å
• R-Value Free:  0.209 (Depositor), 0.214 (DCC) 
• R-Value Work:  0.179 (Depositor), 0.186 (DCC) 
• R-Value Observed: 0.181 (Depositor) 

Space Group: I 2 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 225.19	α = 90
b = 225.19	β = 90
c = 225.19	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
MOSFLM	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-09-25 
Deposition Author(s): Schwinghammer, K., Cheung, A., Morozov, Y., Agaronyan, K., Temiakov, D., Cramer, P.

Revision History  

• 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