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Yorodumi- PDB-4czb: Structure of the sodium proton antiporter MjNhaP1 from Methanocal... -
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-Basic information
Entry | Database: PDB / ID: 4czb | ||||||
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Title | Structure of the sodium proton antiporter MjNhaP1 from Methanocaldococcus jannaschii at pH 8. | ||||||
Components | (NA(+)/H(+) ANTIPORTER 1) x 2 | ||||||
Keywords | MEMBRANE PROTEIN / ANTIPORTER / TRANSPORTER / EXCHANGER / CPA | ||||||
Function / homology | Function and homology information antiporter activity / sodium ion transport / proton transmembrane transport / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | METHANOCALDOCOCCUS JANNASCHII (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å | ||||||
Authors | Woehlert, D. / Paulino, C. / Kapotova, E. / Kuhlbrandt, W. / Yildiz, O. | ||||||
Citation | Journal: Elife / Year: 2014 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
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PDBx/mmCIF format | 4czb.cif.gz | 312.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4czb.ent.gz | 256.1 KB | Display | PDB format |
PDBx/mmJSON format | 4czb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cz/4czb ftp://data.pdbj.org/pub/pdb/validation_reports/cz/4czb | HTTPS FTP |
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-Related structure data
Related structure data | 2636C 4d0aC 4cz8S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-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.) METHANOCALDOCOCCUS JANNASCHII (archaea) Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q60362 #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.) METHANOCALDOCOCCUS JANNASCHII (archaea) Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q60362 #3: Chemical | #4: Chemical | ChemComp-TAM / | |
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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: 3.49 Å3/Da / Density % sol: 61 % / Description: NONE |
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Crystal grow | pH: 8.2 / Details: pH 8.2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9763 |
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 |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4CZ8 Resolution: 3.5→32 Å / σ(F): 6
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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
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