+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-13796 | |||||||||
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Title | 2021-10-18 | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Mitochondria / DNA dependent RNA polymerase / 7S RNA / TRANSCRIPTION | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.5 Å | |||||||||
Authors | Das H / Hallberg BM | |||||||||
Funding support | 1 items
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Citation | Journal: Cell / Year: 2022 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 | emd_13796.map.gz | 51.5 MB | EMDB map data format | |
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Header (meta data) | emd-13796-v30.xml emd-13796.xml | 13.4 KB 13.4 KB | Display Display | EMDB header |
Images | emd_13796.png | 59 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-13796 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-13796 | HTTPS FTP |
-Validation report
Summary document | emd_13796_validation.pdf.gz | 443.6 KB | Display | EMDB validaton report |
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Full document | emd_13796_full_validation.pdf.gz | 443.2 KB | Display | |
Data in XML | emd_13796_validation.xml.gz | 6.3 KB | Display | |
Data in CIF | emd_13796_validation.cif.gz | 7.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-13796 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-13796 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_13796.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
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
-Sample components
-Entire : Mitochondrial DNA dependent RNA polymerase (POLRMT)
Entire | Name: Mitochondrial DNA dependent RNA polymerase (POLRMT) |
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Components |
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-Supramolecule #1: Mitochondrial DNA dependent RNA polymerase (POLRMT)
Supramolecule | Name: Mitochondrial DNA dependent RNA polymerase (POLRMT) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: DNA-directed RNA polymerase, mitochondrial |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 274 KDa |
-Macromolecule #1: Mitochondrial DNA dependent RNA polymerase (POLRMT)
Macromolecule | Name: Mitochondrial DNA dependent RNA polymerase (POLRMT) / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Sequence | String: MHHHHHHTSG VDLGTENLYF QSSSASPQEQ DQDRRKDWGH VELLEVLQAR VRQLQAESVS EVVVNRVDVA RLPECGSGDG SLQPPRKVQM GAKDATPVPC GRWAKILEKD KRTQQMRMQR LKAKLQMPFQ SGEFKALTRR LQVEPRLLSK QMAGCLEDCT RQAPESPWEE ...String: MHHHHHHTSG VDLGTENLYF QSSSASPQEQ DQDRRKDWGH VELLEVLQAR VRQLQAESVS EVVVNRVDVA RLPECGSGDG SLQPPRKVQM GAKDATPVPC GRWAKILEKD KRTQQMRMQR LKAKLQMPFQ SGEFKALTRR LQVEPRLLSK QMAGCLEDCT RQAPESPWEE QLARLLQEAP GKLSLDVEQA PSGQHSQAQL SGQQQRLLAF FKCCLLTDQL PLAHHLLVVH HGQRQKRKLL TLDMYNAVML GWARQGAFKE LVYVLFMVKD AGLTPDLLSY AAALQCMGRQ DQDAGTIERC LEQMSQEGLK LQALFTAVLL SEEDRATVLK AVHKVKPTFS LPPQLPPPVN TSKLLRDVYA KDGRVSYPKL HLPLKTLQCL FEKQLHMELA SRVCVVSVEK PTLPSKEVKH ARKTLKTLRD QWEKALCRAL RETKNRLERE VYEGRFSLYP FLCLLDEREV VRMLLQVLQA LPAQGESFTT LARELSARTF SRHVVQRQRV SGQVQALQNH YRKYLCLLAS DAEVPEPCLP RQYWEELGAP EALREQPWPL PVQMELGKLL AEMLVQATQM PCSLDKPHRS SRLVPVLYHV YSFRNVQQIG ILKPHPAYVQ LLEKAAEPTL TFEAVDVPML CPPLPWTSPH SGAFLLSPTK LMRTVEGATQ HQELLETCPP TALHGALDAL TQLGNCAWRV NGRVLDLVLQ LFQAKGCPQL GVPAPPSEAP QPPEAHLPHS AAPARKAELR RELAHCQKVA REMHSLRAEA LYRLSLAQHL RDRVFWLPHN MDFRGRTYPC PPHFNHLGSD VARALLEFAQ GRPLGPHGLD WLKIHLVNLT GLKKREPLRK RLAFAEEVMD DILDSADQPL TGRKWWMGAE EPWQTLACCM EVANAVRASD PAAYVSHLPV HQDGSCNGLQ HYAALGRDSV GAASVNLEPS DVPQDVYSGV AAQVEVFRRQ DAQRGMRVAQ VLEGFITRKV VKQTVMTVVY GVTRYGGRLQ IEKRLRELSD FPQEFVWEAS HYLVRQVFKS LQEMFSGTRA IQHWLTESAR LISHMGSVVE WVTPLGVPVI QPYRLDSKVK QIGGGIQSIT YTHNGDISRK PNTRKQKNGF PPNFIHSLDS SHMMLTALHC YRKGLTFVSV HDCYWTHAAD VSVMNQVCRE QFVRLHSEPI LQDLSRFLVK RFCSEPQKIL EASQLKETLQ AVPKPGAFDL EQVKRSTYFF S |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 2.1 mg/mL | ||||||||
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Buffer | pH: 8 Component:
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | TFS KRIOS |
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Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 10 eV |
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 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 20.0 µm / Calibrated defocus min: 0.3 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.3 µm / Nominal magnification: 165000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Initial model | PDB ID: |
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Refinement | Space: REAL / Protocol: OTHER |