+Open data
-Basic information
Entry | Database: PDB / ID: 8ts1 | ||||||
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Title | Cryo-EM structure of human MRS2 with Mg2+ | ||||||
Components | Magnesium transporter MRS2 homolog, mitochondrial, Soluble cytochrome b562 fusion protein | ||||||
Keywords | METAL TRANSPORT / mitochondria / pentamer / cation channel | ||||||
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 / mitochondrial inner membrane / electron transfer activity / 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 / mitochondrial inner membrane / electron transfer activity / iron ion binding / heme binding / mitochondrion Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Escherichia coli (E. coli) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.92 Å | ||||||
Authors | He, Z. / Mount, J.W. / Zhang, J. / Yuan, P. | ||||||
Funding support | United States, 1items
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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, J.W. / Zhang, J. / Tsai, M. / Yuan, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8ts1.cif.gz | 726.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ts1.ent.gz | 483 KB | Display | PDB format |
PDBx/mmJSON format | 8ts1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8ts1_validation.pdf.gz | 1005.3 KB | Display | wwPDB validaton report |
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Full document | 8ts1_full_validation.pdf.gz | 1010.1 KB | Display | |
Data in XML | 8ts1_validation.xml.gz | 45.9 KB | Display | |
Data in CIF | 8ts1_validation.cif.gz | 63.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ts/8ts1 ftp://data.pdbj.org/pub/pdb/validation_reports/ts/8ts1 | HTTPS FTP |
-Related structure data
Related structure data | 41587MC 8ts2C 8ts3C M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: ens_1 / Beg auth comp-ID: VAL / Beg label comp-ID: VAL / End auth comp-ID: GLN / End label comp-ID: GLN / Auth seq-ID: 82 - 399 / Label seq-ID: 22 - 339
NCS oper:
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-Components
#1: Protein | Mass: 55471.691 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Escherichia coli (E. coli) Gene: MRS2, cybC / Production host: Komagataella pastoris (fungus) / References: UniProt: Q9HD23, UniProt: P0ABE7 #2: Chemical | ChemComp-MG / Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: hMRS2-BRIL with Mg2+ / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT | |||||||||||||||||||||||||
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Molecular weight | Experimental value: NO | |||||||||||||||||||||||||
Source (natural) | Organism: Homo sapiens (human) | |||||||||||||||||||||||||
Source (recombinant) | Organism: Komagataella pastoris (fungus) | |||||||||||||||||||||||||
Buffer solution | pH: 8 Details: 20 mM Tris pH 8.0, 150 mM NaCl, 40 mM MgCl2 and 0.04 mM GDN | |||||||||||||||||||||||||
Buffer component |
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Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||||||||||||
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Microscopy | Model: TFS GLACIOS |
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Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 120000 X / Nominal defocus max: 2400 nm / Nominal defocus min: 1000 nm |
Image recording | Electron dose: 41 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of real images: 2631 |
-Processing
EM software | Name: cryoSPARC / Category: 3D reconstruction | |||||||||||||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 937963 | |||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C5 (5 fold cyclic) | |||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.92 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 719778 / Symmetry type: POINT | |||||||||||||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | |||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 78.1 Å2 | |||||||||||||||||||||||||||||||||||
Refine LS restraints |
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Refine LS restraints NCS |
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