+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-41588 | |||||||||
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Title | Cryo-EM structure of human MRS2 with EDTA | |||||||||
Map data | ||||||||||
Sample |
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Keywords | mitochondria / pentamer / cation channel / METAL TRANSPORT | |||||||||
Function / homology | Function and homology information mitochondrial magnesium ion transmembrane transport / Miscellaneous transport and binding events / magnesium ion transmembrane transporter activity / lactate metabolic process / electron transport chain / transmembrane transport / periplasmic space / electron transfer activity / mitochondrial inner membrane / iron ion binding ...mitochondrial magnesium ion transmembrane transport / Miscellaneous transport and binding events / magnesium ion transmembrane transporter activity / lactate metabolic process / electron transport chain / transmembrane transport / periplasmic space / electron transfer activity / mitochondrial inner membrane / iron ion binding / heme binding / mitochondrion Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.95 Å | |||||||||
Authors | He Z / Mount JW / Zhang J / Yuan P | |||||||||
Funding support | United States, 1 items
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Citation | Journal: To Be Published Title: Human mitochondrial MRS2 is a Ca2+-regulated nonselective cation channel Authors: He Z / Tu Y / Tsai C / Mount JW / Zhang J / Tsai M / Yuan P | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_41588.map.gz | 26.4 MB | EMDB map data format | |
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Header (meta data) | emd-41588-v30.xml emd-41588.xml | 15.4 KB 15.4 KB | Display Display | EMDB header |
Images | emd_41588.png | 78 KB | ||
Filedesc metadata | emd-41588.cif.gz | 5.6 KB | ||
Others | emd_41588_half_map_1.map.gz emd_41588_half_map_2.map.gz | 43.9 MB 43.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-41588 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-41588 | HTTPS FTP |
-Validation report
Summary document | emd_41588_validation.pdf.gz | 679 KB | Display | EMDB validaton report |
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Full document | emd_41588_full_validation.pdf.gz | 678.5 KB | Display | |
Data in XML | emd_41588_validation.xml.gz | 12 KB | Display | |
Data in CIF | emd_41588_validation.cif.gz | 13.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-41588 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-41588 | HTTPS FTP |
-Related structure data
Related structure data | 8ts2MC 8ts1C 8ts3C C: citing same article (ref.) M: atomic model generated by this map |
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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_41588.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.2 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_41588_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_41588_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : hMRS2-BRIL with EDTA
Entire | Name: hMRS2-BRIL with EDTA |
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Components |
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-Supramolecule #1: hMRS2-BRIL with EDTA
Supramolecule | Name: hMRS2-BRIL with EDTA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: Magnesium transporter MRS2 homolog, mitochondrial, Soluble cytoch...
Macromolecule | Name: Magnesium transporter MRS2 homolog, mitochondrial, Soluble cytochrome b562 fusion protein type: protein_or_peptide / ID: 1 / Details: hMRS2-dNdC-BRIL,hMRS2-dNdC-BRIL / Number of copies: 5 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 55.471691 KDa |
Recombinant expression | Organism: Komagataella pastoris (fungus) |
Sequence | String: MVAGEVHRFR TSDVSQATLA SVAPVFTVTK FDKQGNVTSF ERKKTELYQE LGLQARDLRF QHVMSITVRN NRIIMRMEYL KAVITPECL LILDYRNLNL EQWLFRELPS QLSGEGQLVT YPLPFEFRAI EALLQYWINT LQGKLSILQP LILETLDALV D PKHSSVDR ...String: MVAGEVHRFR TSDVSQATLA SVAPVFTVTK FDKQGNVTSF ERKKTELYQE LGLQARDLRF QHVMSITVRN NRIIMRMEYL KAVITPECL LILDYRNLNL EQWLFRELPS QLSGEGQLVT YPLPFEFRAI EALLQYWINT LQGKLSILQP LILETLDALV D PKHSSVDR SKLHILLQNG KSLSELETDI KIFKESILEI LDEEELLEEL CVSKWSDPQV FEKSSAGIDH AEEMELLLEN YY RLADDLS NAARELRVLI DDSQSIIFIN LDSHRNVMMR LNLQLTMGTF SLSLFGLMGV AFGMNLESSL EEDHRIFWLI TGI MFMGSG LIWRRLLSFL GRQLEAPLPP MMASLPKKTL LADRSMELKN SLRLDADLED NWETLNDNLK VIEKADNAAQ VKDA LTKMR AAALDAQKAT PPKLEDKSPD SPEMKDFRHG FDILVGQIDD ALKLANEGKV KEAQAAAEQL KTTRNAYIQK YLSNS LEVL FQ UniProtKB: Magnesium transporter MRS2 homolog, mitochondrial, Soluble cytochrome b562 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 Component:
Details: 20 mM Tris pH 8.0, 150 mM NaCl, 10 mM EDTA and 0.04 mM GDN | |||||||||||||||
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | TFS GLACIOS |
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Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Number real images: 3477 / Average electron dose: 49.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 120000 |
+Image processing
-Atomic model buiding 1
Refinement | Protocol: RIGID BODY FIT |
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Output model | PDB-8ts2: |