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- EMDB-13796: 2021-10-18 -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-13796
Title2021-10-18
Map data
Sample
  • Complex: Mitochondrial DNA dependent RNA polymerase (POLRMT)
    • Protein or peptide: Mitochondrial DNA dependent RNA polymerase (POLRMT)
KeywordsMitochondria / DNA dependent RNA polymerase / 7S RNA / TRANSCRIPTION
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsDas H / Hallberg BM
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: 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
DepositionOct 29, 2021-
Header (metadata) releaseNov 16, 2022-
Map releaseNov 16, 2022-
UpdateMay 31, 2023-
Current statusMay 31, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_13796.png

Downloads & links

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Map

FileDownload / File: emd_13796.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.01 Å
Density
Contour LevelBy AUTHOR: 0.09
Minimum - Maximum-0.17303519 - 0.66762704
Average (Standard dev.)0.0006586545 (±0.017501336)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 303.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Mitochondrial DNA dependent RNA polymerase (POLRMT)

EntireName: Mitochondrial DNA dependent RNA polymerase (POLRMT)
Components
  • Complex: Mitochondrial DNA dependent RNA polymerase (POLRMT)
    • Protein or peptide: Mitochondrial DNA dependent RNA polymerase (POLRMT)

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Supramolecule #1: Mitochondrial DNA dependent RNA polymerase (POLRMT)

SupramoleculeName: Mitochondrial DNA dependent RNA polymerase (POLRMT) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: DNA-directed RNA polymerase, mitochondrial
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 274 KDa

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Macromolecule #1: Mitochondrial DNA dependent RNA polymerase (POLRMT)

MacromoleculeName: Mitochondrial DNA dependent RNA polymerase (POLRMT) / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
SequenceString: 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

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration2.1 mg/mL
BufferpH: 8
Component:
ConcentrationFormula
50.0 mMTris
150.0 mMNaClSodium chloride
5.0 mMMgCl2
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 20.0 µm / Calibrated defocus min: 0.3 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.3 µm / Nominal magnification: 165000
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 10 eV
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm 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

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

3spa

Initial angle assignmentType: PROJECTION MATCHING / Software - Name: cryoSPARC (ver. 3.2.0)
Final 3D classificationSoftware - Name: cryoSPARC (ver. 3.2.0)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: cryoSPARC (ver. 3.2.0)
Final reconstructionApplied 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: 95388

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Atomic model buiding 1

Initial modelPDB ID:

3spa

RefinementSpace: REAL / Protocol: OTHER

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