Primary Citation PubMed: 24096365
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Yeast mitochondrial RNAP conformational changes are regulated by interactions with the mitochondrial transcription factor.
(2014) Nucleic Acids Res 42
PubMed: 25183523 | PubMedCentral: PMC4176174 | DOI: 10.1093/nar/gku795
The difference in the positions of both the upstream and downstream DNA termini as modeled from the human MtRNAP EC structure and as experimentally determined by positions of the streptavidin molecule... is ∼15 Å (in the case of upstream DNA termini this discrepancy is even smaller as the 5′NT end of DNA used in this study is in the single stranded form, comparing to the corresponding nucleotide at position −10 of DNA in 4BOC).
The narrowness of this cleft in the quasi-IC seems to correspond to the ‘clenched’ conformation with a constricted central binding cleft observed in human MtRNAP ( 23 ) (Figure 1A ), and this notion is strengthened by a better docking correlation value with this atomic structure (PDB ID: 3SPA; 0.85) than with that of mtRNAP EC (PDB ID: 4BOC; 0.84) (Figure 1B ), but specially by a 3D reconstruction of quasi-IC with DNA labeled with streptavidin at its upstream end (‘upstream streptavidin quasi-IC’), generated from 16514 particles (Supplementary Figure S3B; 18 Å resolution) in which the streptavidin molecule (and therefore the 5′-end of the NT-strand DNA) is located closer to the polymerase domain.
Right: docking of the human MtRNAPEC (PDB ID: 4BOC) in the cryo-EM map of yeast MtRNAPEC, obtained in this study.
Right: docking of the human MtRNAPEC (PDB ID: 4BOC) in the cryo-EM map, obtained in this study.
( B ) As in (A), but with the atomic structure of human MtRNAP EC (PDB ID: 4BOC ( 24 )) docked in; the DNA is not shown) ( C ) The quasi-IC 3D reconstruction rotated as indicated and cut at the plane indicated by the red line.
ACCESSION NUMBERS PDB IDs: 3SPA, 4BOC, 1I4W, 1N43, 3E2E and 1QLN.
This would be consistent with what is observed with both human MtRNAP structures (PDB IDs: 4BOC ( 24 ) and 3SPA ( 9 )), in which residues 1–105 were deleted to enhance crystallization, and in which residues 106–217 are disordered and invisible in the electron density map ( 23 ).
The docked atomic structure of human MtRNAPEC (PDB ID: 4BOC, DNA not shown) and the DNA of aligned T7RNAPIC (3E2E) are shown and labeled as in Figure 5 .
The atomic structure of human EC (PDB ID: 4BOC ( 24 )) is fitted into the 3D reconstruction (correlation coefficient 0.74).
The atomic structure of human EC (PDB ID: 4BOC ( 24 )) is fitted into the 3D reconstruction (correlation coefficient 0.84).
The atomic structure of human EC (PDB ID: 4BOC ( 24 )) is fitted into the 3D reconstruction (correlation coefficient 0.92).
Publication Year: 2014
Structure of human mitochondrial RNA polymerase elongation complex.
(2013) Nat Struct Mol Biol 20
PubMed: 24096365 | PubMedCentral: null | DOI: 10.1038/nsmb.2683
Coordinates of the mitochondrial RNA polymerase elongation complex structure have been deposited with the protein data bank under accession code 4BOC.
Publication Year: 2013
PubMed ID is not available.
Published in 2015
The IC model was generated using mtRNAP ‘open’ conformation found in the elongation complex (PDB ID 4BOC).
Publication Year: 2015
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