[English] 日本語
![](img/lk-miru.gif)
- PDB-7qjj: X-Ray Structure of a Mn2+ soak of EleNRMT in complex with two Nan... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 7qjj | ||||||
---|---|---|---|---|---|---|---|
Title | X-Ray Structure of a Mn2+ soak of EleNRMT in complex with two Nanobodies at 4.6A | ||||||
![]() |
| ||||||
![]() | MEMBRANE PROTEIN / SLC11 / NRAMP-related Mg2+ transporter / Nanobody complex | ||||||
Function / homology | ![]() manganese ion transmembrane transporter activity / cadmium ion transmembrane transporter activity / intracellular manganese ion homeostasis / cellular response to iron ion / iron ion transport / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ramanadane, K. / Straub, M.S. / Dutzler, R. / Manatschal, C. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() 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 |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 601.4 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 422.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 452.5 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 471.4 KB | Display | |
Data in XML | ![]() | 45.2 KB | Display | |
Data in CIF | ![]() | 61.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7qiaSC ![]() 7qicC ![]() 7qjiC C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
2 | ![]()
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Unit cell |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
NCS oper:
|
-
Components
#1: Protein | Mass: 46848.828 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Antibody | Mass: 12952.605 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #3: Antibody | Mass: 13351.896 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #4: Chemical | Has ligand of interest | N | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.59 Å3/Da / Density % sol: 52.49 % |
---|---|
Crystal grow | Temperature: 277.17 K / Method: vapor diffusion, sitting drop Details: 50 mM MgAc, 50 mM HEPES pH 7.2-7.6 and 25-30% PEG400 and crystals soaked in 25mM MnAc |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Mar 27, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.892738 Å / Relative weight: 1 |
Reflection | Resolution: 4.6→12 Å / Num. obs: 32816 / % possible obs: 99.7 % / Redundancy: 14 % / Biso Wilson estimate: 189.78 Å2 / CC1/2: 1 / Rrim(I) all: 0.144 / Net I/σ(I): 11.42 |
Reflection shell | Resolution: 4.6→4.7 Å / Mean I/σ(I) obs: 1.85 / Num. unique obs: 2039 / CC1/2: 0.91 / Rrim(I) all: 1.474 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDBID 7QIA Resolution: 4.6→12 Å / SU ML: 0.7298 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 40.4518 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| |||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 270.79 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 4.6→12 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints NCS |
| |||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: -23.375792412 Å / Origin y: -20.0962169733 Å / Origin z: -30.5290581484 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group | Selection details: all |