[English] 日本語
![](img/lk-miru.gif)
- PDB-4czb: Structure of the sodium proton antiporter MjNhaP1 from Methanocal... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 4czb | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of the sodium proton antiporter MjNhaP1 from Methanocaldococcus jannaschii at pH 8. | ||||||
![]() | (NA(+)/H(+) ANTIPORTER 1) x 2 | ||||||
![]() | MEMBRANE PROTEIN / ANTIPORTER / TRANSPORTER / EXCHANGER / CPA | ||||||
Function / homology | ![]() antiporter activity / sodium ion transport / proton transmembrane transport / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Woehlert, D. / Paulino, C. / Kapotova, E. / Kuhlbrandt, W. / Yildiz, O. | ||||||
![]() | ![]() Title: Structure and transport mechanism of the sodium/proton antiporter MjNhaP1. Authors: Cristina Paulino / David Wöhlert / Ekaterina Kapotova / Özkan Yildiz / Werner Kühlbrandt / ![]() Abstract: Sodium/proton antiporters are essential for sodium and pH homeostasis and play a major role in human health and disease. We determined the structures of the archaeal sodium/proton antiporter MjNhaP1 ...Sodium/proton antiporters are essential for sodium and pH homeostasis and play a major role in human health and disease. We determined the structures of the archaeal sodium/proton antiporter MjNhaP1 in two complementary states. The inward-open state was obtained by x-ray crystallography in the presence of sodium at pH 8, where the transporter is highly active. The outward-open state was obtained by electron crystallography without sodium at pH 4, where MjNhaP1 is inactive. Comparison of both structures reveals a 7° tilt of the 6 helix bundle. (22)Na(+) uptake measurements indicate non-cooperative transport with an activity maximum at pH 7.5. We conclude that binding of a Na(+) ion from the outside induces helix movements that close the extracellular cavity, open the cytoplasmic funnel, and result in a ∼5 Å vertical relocation of the ion binding site to release the substrate ion into the cytoplasm. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 312.3 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 256.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 473 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 497 KB | Display | |
Data in XML | ![]() | 55.4 KB | Display | |
Data in CIF | ![]() | 73.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2636C ![]() 4d0aC ![]() 4cz8S S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 45998.891 Da / Num. of mol.: 3 / Fragment: TRANSPORTER DOMAIN, RESIDUES 1-426 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Production host: ![]() ![]() #2: Protein | | Mass: 46012.918 Da / Num. of mol.: 1 / Fragment: TRANSPORTER DOMAIN, RESIDUES 1-426 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Production host: ![]() ![]() #3: Chemical | #4: Chemical | ChemComp-TAM / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.49 Å3/Da / Density % sol: 61 % / Description: NONE |
---|---|
Crystal grow | pH: 8.2 / Details: pH 8.2 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Date: Jul 13, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 3.5→32 Å / Num. obs: 58249 / % possible obs: 99.3 % / Observed criterion σ(I): 1.7 / Redundancy: 7 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 6 |
Reflection shell | Resolution: 3.5→3.72 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 1.7 / % possible all: 99.2 |
-
Processing
Software |
| ||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 4CZ8 Resolution: 3.5→32 Å / σ(F): 6
| ||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.5→32 Å
|