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Yorodumi- PDB-7qic: Structure of magnesium-bound EleNRMT in complex with two nanobodi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7qic | ||||||
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Title | Structure of magnesium-bound EleNRMT in complex with two nanobodies at 4.1A | ||||||
Components |
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Keywords | MEMBRANE PROTEIN / SLC11 / Magnesium / LeuT fold | ||||||
Function / homology | NRAMP family / Natural resistance-associated macrophage protein-like / cadmium ion transmembrane transporter activity / manganese ion transmembrane transporter activity / cellular response to iron ion / membrane / Divalent metal cation transporter Function and homology information | ||||||
Biological species | Eggerthella lenta (bacteria) synthetic construct (others) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.1 Å | ||||||
Authors | Ramanadane, K. / Straub, M.S. / Dutzler, R. / Manatschal, C. | ||||||
Funding support | Switzerland, 1items
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Citation | Journal: Elife / Year: 2022 Title: Structural and functional properties of a magnesium transporter of the SLC11/NRAMP family. Authors: Karthik Ramanadane / Monique S Straub / Raimund Dutzler / Cristina Manatschal / Abstract: Members of the ubiquitous SLC11/NRAMP family catalyze the uptake of divalent transition metal ions into cells. They have evolved to efficiently select these trace elements from a large pool of Ca and ...Members of the ubiquitous SLC11/NRAMP family catalyze the uptake of divalent transition metal ions into cells. They have evolved to efficiently select these trace elements from a large pool of Ca and Mg, which are both orders of magnitude more abundant, and to concentrate them in the cytoplasm aided by the cotransport of H serving as energy source. In the present study, we have characterized a member of a distant clade of the family found in prokaryotes, termed NRMTs, that were proposed to function as transporters of Mg. The protein transports Mg and Mn but not Ca by a mechanism that is not coupled to H. Structures determined by cryo-EM and X-ray crystallography revealed a generally similar protein architecture compared to classical NRAMPs, with a restructured ion binding site whose increased volume provides suitable interactions with ions that likely have retained much of their hydration shell. | ||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7qic.cif.gz | 120.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7qic.ent.gz | 91.9 KB | Display | PDB format |
PDBx/mmJSON format | 7qic.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7qic_validation.pdf.gz | 756.2 KB | Display | wwPDB validaton report |
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Full document | 7qic_full_validation.pdf.gz | 764.4 KB | Display | |
Data in XML | 7qic_validation.xml.gz | 29.6 KB | Display | |
Data in CIF | 7qic_validation.cif.gz | 41.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qi/7qic ftp://data.pdbj.org/pub/pdb/validation_reports/qi/7qic | HTTPS FTP |
-Related structure data
Related structure data | 13987MC 7qiaC 7qjiC 7qjjC C: citing same article (ref.) M: map data used to model this data |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 46848.828 Da / Num. of mol.: 1 Mutation: E88Q, A151S, E193Q, R207H, S244T, I256V, S275A, V366I, V385I, V418L, V429A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Eggerthella lenta (bacteria) / Gene: C1853_09580, C1871_08405 / Production host: Escherichia coli MC1061 (bacteria) / References: UniProt: A0A369N1S1 |
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#2: Antibody | Mass: 13126.760 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli MC1061 (bacteria) |
#3: Antibody | Mass: 13767.339 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli MC1061 (bacteria) |
#4: Chemical | ChemComp-MG / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
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Molecular weight |
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Source (natural) |
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Source (recombinant) |
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Buffer solution | pH: 7 | |||||||||||||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 3.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||||||||||||||||||||||
Specimen support | Grid material: GOLD / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R1.2/1.3 | |||||||||||||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE-PROPANE / Humidity: 100 % / Chamber temperature: 277.15 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 130000 X / Nominal defocus max: 2400 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 1.01 sec. / Electron dose: 69.554 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 3 / Num. of real images: 12427 |
-Processing
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 2582066 | ||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 100176 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 46.51 Å2 | ||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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