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Open data
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Basic information
Entry | ![]() | |||||||||
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Title | Mitochondrial DNA dependent RNA polymerase homodimer. | |||||||||
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Function / homology | ![]() Mitochondrial transcription initiation / mitochondrial DNA-directed RNA polymerase complex / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Das H / Hallberg BM | |||||||||
Funding support | 1 items
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![]() | ![]() Title: Non-coding 7S RNA inhibits transcription via mitochondrial RNA polymerase dimerization. Authors: Xuefeng Zhu / Xie Xie / Hrishikesh Das / Benedict G Tan / Yonghong Shi / Ali Al-Behadili / Bradley Peter / Elisa Motori / Sebastian Valenzuela / Viktor Posse / Claes M Gustafsson / B Martin ...Authors: Xuefeng Zhu / Xie Xie / Hrishikesh Das / Benedict G Tan / Yonghong Shi / Ali Al-Behadili / Bradley Peter / Elisa Motori / Sebastian Valenzuela / Viktor Posse / Claes M Gustafsson / B Martin Hällberg / Maria Falkenberg / ![]() ![]() Abstract: The mitochondrial genome encodes 13 components of the oxidative phosphorylation system, and altered mitochondrial transcription drives various human pathologies. A polyadenylated, non-coding RNA ...The mitochondrial genome encodes 13 components of the oxidative phosphorylation system, and altered mitochondrial transcription drives various human pathologies. A polyadenylated, non-coding RNA molecule known as 7S RNA is transcribed from a region immediately downstream of the light strand promoter in mammalian cells, and its levels change rapidly in response to physiological conditions. Here, we report that 7S RNA has a regulatory function, as it controls levels of mitochondrial transcription both in vitro and in cultured human cells. Using cryo-EM, we show that POLRMT dimerization is induced by interactions with 7S RNA. The resulting POLRMT dimer interface sequesters domains necessary for promoter recognition and unwinding, thereby preventing transcription initiation. We propose that the non-coding 7S RNA molecule is a component of a negative feedback loop that regulates mitochondrial transcription in mammalian cells. | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 97 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 18.9 KB 18.9 KB | Display Display | ![]() |
Images | ![]() | 95.2 KB | ||
Others | ![]() ![]() | 51.5 MB 51.9 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7pzpMC ![]() 7pzrC ![]() 7zc4C M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Voxel size | X=Y=Z: 1.01 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: localized reconstruction
File | emd_13735_additional_1.map | ||||||||||||
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Annotation | localized reconstruction | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: localized reconstruction
File | emd_13735_additional_2.map | ||||||||||||
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Annotation | localized reconstruction | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : POLRMT
Entire | Name: POLRMT![]() |
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Components |
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-Supramolecule #1: POLRMT
Supramolecule | Name: POLRMT / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: DNA-directed RNA polymerase, mitochondrial |
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Molecular weight | Theoretical: 137 KDa |
-Supramolecule #2: Mitochondrial DNA-directed RNA polymerase dimer.
Supramolecule | Name: Mitochondrial DNA-directed RNA polymerase dimer. / type: complex / Chimera: Yes / ID: 2 / Parent: 1 / Macromolecule list: all / Details: DNA-directed RNA polymerase dimer, mitochondrial |
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Source (natural) | Organism: ![]() ![]() |
Recombinant expression | Organism: ![]() ![]() ![]() |
-Macromolecule #1: DNA-directed RNA polymerase, mitochondrial
Macromolecule | Name: DNA-directed RNA polymerase, mitochondrial / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: ![]() |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 137.292125 KDa |
Recombinant expression | Organism: ![]() ![]() ![]() |
Sequence | String: MHHHHHHTSG VDLGTENLYF QSSSASPQEQ DQDRRKDWGH VELLEVLQAR VRQLQAESVS EVVVNRVDVA RLPECGSGDG SLQPPRKVQ MGAKDATPVP CGRWAKILEK DKRTQQMRMQ RLKAKLQMPF QSGEFKALTR RLQVEPRLLS KQMAGCLEDC T RQAPESPW ...String: MHHHHHHTSG VDLGTENLYF QSSSASPQEQ DQDRRKDWGH VELLEVLQAR VRQLQAESVS EVVVNRVDVA RLPECGSGDG SLQPPRKVQ MGAKDATPVP CGRWAKILEK DKRTQQMRMQ RLKAKLQMPF QSGEFKALTR RLQVEPRLLS KQMAGCLEDC T RQAPESPW EEQLARLLQE APGKLSLDVE QAPSGQHSQA QLSGQQQRLL AFFKCCLLTD QLPLAHHLLV VHHGQRQKRK LL TLDMYNA VMLGWARQGA FKELVYVLFM VKDAGLTPDL LSYAAALQCM GRQDQDAGTI ERCLEQMSQE GLKLQALFTA VLL SEEDRA TVLKAVHKVK PTFSLPPQLP PPVNTSKLLR DVYAKDGRVS YPKLHLPLKT LQCLFEKQLH MELASRVCVV SVEK PTLPS KEVKHARKTL KTLRDQWEKA LCRALRETKN RLEREVYEGR FSLYPFLCLL DEREVVRMLL QVLQALPAQG ESFTT LARE LSARTFSRHV VQRQRVSGQV QALQNHYRKY LCLLASDAEV PEPCLPRQYW EELGAPEALR EQPWPLPVQM ELGKLL AEM LVQATQMPCS LDKPHRSSRL VPVLYHVYSF RNVQQIGILK PHPAYVQLLE KAAEPTLTFE AVDVPMLCPP LPWTSPH SG AFLLSPTKLM RTVEGATQHQ ELLETCPPTA LHGALDALTQ LGNCAWRVNG RVLDLVLQLF QAKGCPQLGV PAPPSEAP Q PPEAHLPHSA APARKAELRR ELAHCQKVAR EMHSLRAEAL YRLSLAQHLR DRVFWLPHNM DFRGRTYPCP PHFNHLGSD VARALLEFAQ GRPLGPHGLD WLKIHLVNLT GLKKREPLRK RLAFAEEVMD DILDSADQPL TGRKWWMGAE EPWQTLACCM EVANAVRAS DPAAYVSHLP VHQDGSCNGL QHYAALGRDS VGAASVNLEP SDVPQDVYSG VAAQVEVFRR QDAQRGMRVA Q VLEGFITR KVVKQTVMTV VYGVTRYGGR LQIEKRLREL SDFPQEFVWE ASHYLVRQVF KSLQEMFSGT RAIQHWLTES AR LISHMGS VVEWVTPLGV PVIQPYRLDS KVKQIGGGIQ SITYTHNGDI SRKPNTRKQK NGFPPNFIHS LDSSHMMLTA LHC YRKGLT FVSVHDCYWT HAADVSVMNQ VCREQFVRLH SEPILQDLSR FLVKRFCSEP QKILEASQLK ETLQAVPKPG AFDL EQVKR STYFFS |
-Experimental details
-Structure determination
Method | ![]() |
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Aggregation state | particle |
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Sample preparation
Concentration | 2.1 mg/mL |
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Buffer | pH: 8 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | TFS KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 20.0 µm / Calibrated defocus min: 0.3 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD![]() |
Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 10 eV |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 5 / Number real images: 42131 / Average exposure time: 1.5 sec. / Average electron dose: 48.6 e/Å2 |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
CTF correction | Software - Name: cryoSPARC (ver. 3.2.0) |
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Startup model | Type of model: PDB ENTRY PDB model - PDB ID: |
Initial angle assignment | Type: PROJECTION MATCHING / Software - Name: cryoSPARC (ver. 3.2.0) |
Final 3D classification | Software: (Name: cryoSPARC (ver. 3.2.0), RELION (ver. 3.1)) |
Final angle assignment | Type: PROJECTION MATCHING / Software - Name: cryoSPARC (ver. 3.2.0) |
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.2.0) / Number images used: 13500 |