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Yorodumi- EMDB-18439: mt-SSU assembly intermediate in GTPBP8 knock-out cells, state 2 -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-18439 | |||||||||
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Title | mt-SSU assembly intermediate in GTPBP8 knock-out cells, state 2 | |||||||||
Map data | mt-SSU assembly intermediate in GTPBP8 knock-out cells, state 2 | |||||||||
Sample |
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Keywords | Mitochondria / Assembly / GTPBP8 / RIBOSOME | |||||||||
Function / homology | Function and homology information rRNA (cytosine-N4-)-methyltransferase activity / mitochondrial ribosome binding / mitochondrial ribosome assembly / Mitochondrial translation elongation / Mitochondrial translation termination / Mitochondrial translation initiation / positive regulation of mitochondrial translation / rRNA base methylation / negative regulation of mitotic nuclear division / mitochondrial small ribosomal subunit ...rRNA (cytosine-N4-)-methyltransferase activity / mitochondrial ribosome binding / mitochondrial ribosome assembly / Mitochondrial translation elongation / Mitochondrial translation termination / Mitochondrial translation initiation / positive regulation of mitochondrial translation / rRNA base methylation / negative regulation of mitotic nuclear division / mitochondrial small ribosomal subunit / mitochondrial ribosome / mitochondrial translation / positive regulation of proteolysis / ribosomal small subunit binding / Mitochondrial protein degradation / Transferases; Transferring one-carbon groups; Methyltransferases / apoptotic signaling pathway / cell junction / regulation of translation / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / nuclear membrane / cytosolic small ribosomal subunit / cell population proliferation / mitochondrial inner membrane / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / mitochondrial matrix / translation / protein domain specific binding / intracellular membrane-bounded organelle / mRNA binding / nucleolus / GTP binding / mitochondrion / RNA binding / nucleoplasm / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.96 Å | |||||||||
Authors | Valentin Gese G / Cipullo M / Rorbach J / Hallberg BM | |||||||||
Funding support | 1 items
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Citation | Journal: Nat Commun / Year: 2024 Title: GTPBP8 is essential for mitoribosome formation in human mitochondria Authors: Cipullo M / Valentin Gese G / Gopalakrishna S / Krueger A / Lobo V / Pirozhkova MA / Marks J / Palenkova P / Shiriaev D / Liu Y / Misic J / Cai Y / Nguyen M / Abdelbagi A / Li X / Minczuk M ...Authors: Cipullo M / Valentin Gese G / Gopalakrishna S / Krueger A / Lobo V / Pirozhkova MA / Marks J / Palenkova P / Shiriaev D / Liu Y / Misic J / Cai Y / Nguyen M / Abdelbagi A / Li X / Minczuk M / Hafner M / Benhalevy D / Sarshad AA / Attanasov I / Hallberg BM / Rorbach J | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_18439.map.gz | 483.6 MB | EMDB map data format | |
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Header (meta data) | emd-18439-v30.xml emd-18439.xml | 14 KB 14 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_18439_fsc.xml | 17 KB | Display | FSC data file |
Images | emd_18439.png | 61.1 KB | ||
Masks | emd_18439_msk_1.map | 512 MB | Mask map | |
Filedesc metadata | emd-18439.cif.gz | 4.1 KB | ||
Others | emd_18439_half_map_1.map.gz emd_18439_half_map_2.map.gz | 475.6 MB 475.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-18439 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-18439 | HTTPS FTP |
-Validation report
Summary document | emd_18439_validation.pdf.gz | 1.3 MB | Display | EMDB validaton report |
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Full document | emd_18439_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | emd_18439_validation.xml.gz | 26.3 KB | Display | |
Data in CIF | emd_18439_validation.cif.gz | 34.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-18439 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-18439 | HTTPS FTP |
-Related structure data
Related structure data | 8qrlMC 8qrkC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_18439.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | mt-SSU assembly intermediate in GTPBP8 knock-out cells, state 2 | ||||||||||||||||||||||||||||||||||||
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
-Mask #1
File | emd_18439_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: mt-SSU assembly intermediate in GTPBP8 knock-out cells, state...
File | emd_18439_half_map_1.map | ||||||||||||
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Annotation | mt-SSU assembly intermediate in GTPBP8 knock-out cells, state 2, half map A | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: mt-SSU assembly intermediate in GTPBP8 knock-out cells, state...
File | emd_18439_half_map_2.map | ||||||||||||
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Annotation | mt-SSU assembly intermediate in GTPBP8 knock-out cells, state 2, half map B | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : mt-SSU assembly intermediate in GTPBP8 knock-out cells, state 2
Entire | Name: mt-SSU assembly intermediate in GTPBP8 knock-out cells, state 2 |
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Components |
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-Supramolecule #1: mt-SSU assembly intermediate in GTPBP8 knock-out cells, state 2
Supramolecule | Name: mt-SSU assembly intermediate in GTPBP8 knock-out cells, state 2 type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 1.7 MDa |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 48.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.2 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |