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Yorodumi- PDB-7qji: X-Ray Structure of apo-EleNRMT in complex with two Nanobodies at 4.1A -
+Open data
-Basic information
Entry | Database: PDB / ID: 7qji | ||||||
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Title | X-Ray Structure of apo-EleNRMT in complex with two Nanobodies at 4.1A | ||||||
Components |
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Keywords | MEMBRANE PROTEIN / SLC11 / NRAMP-related Mg2+ transporter / Nanobody complex | ||||||
Function / homology | NRAMP family / Natural resistance-associated macrophage protein-like / manganese ion transmembrane transporter activity / cadmium ion transmembrane transporter activity / intracellular manganese ion homeostasis / cellular response to iron ion / iron ion transport / plasma membrane / Divalent metal cation transporter Function and homology information | ||||||
Biological species | Vicugna pacos (alpaca) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / 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
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7qji.cif.gz | 597.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7qji.ent.gz | 423 KB | Display | PDB format |
PDBx/mmJSON format | 7qji.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qj/7qji ftp://data.pdbj.org/pub/pdb/validation_reports/qj/7qji | HTTPS FTP |
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-Related structure data
Related structure data | 7qiaSC 7qicC 7qjjC C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
NCS oper:
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-Components
#1: Protein | Mass: 46848.828 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vicugna pacos (alpaca) / Gene: C1853_09580, C1871_08405 / Production host: Escherichia coli MC1061 (bacteria) / References: UniProt: A0A369N1S1 #2: Antibody | Mass: 12952.605 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vicugna pacos (alpaca) / Gene: C1867_11315 / Production host: Escherichia coli MC1061 (bacteria) #3: Antibody | Mass: 13351.896 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vicugna pacos (alpaca) / Gene: C1867_11315 / Production host: Escherichia coli MC1061 (bacteria) |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.75 Å3/Da / Density % sol: 55.24 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, sitting drop Details: 50 mM MgAc, 50 mM HEPES pH 7.2-7.6 and 25-30% PEG400 |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.999869 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 29, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.999869 Å / Relative weight: 1 |
Reflection | Resolution: 4.1→12 Å / Num. obs: 25065 / % possible obs: 99.2 % / Redundancy: 28.2 % / Biso Wilson estimate: 174.298 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.112 / Net I/σ(I): 15.36 |
Reflection shell | Resolution: 4.1→4.2 Å / Redundancy: 27.1 % / Mean I/σ(I) obs: 1.81 / Num. unique obs: 1742 / CC1/2: 0.95 / Rrim(I) all: 1.536 / % possible all: 98.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDBID 7QIA Resolution: 4.1→11.99 Å / SU ML: 0.4077 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 43.327 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 287.33 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 4.1→11.99 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -23.4158834813 Å / Origin y: -19.9665088173 Å / Origin z: -30.6155185713 Å
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Refinement TLS group | Selection details: all |