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Yorodumi- PDB-4d0a: 3D EM map of the sodium proton antiporter MjNhaP1 from Methanocal... -
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-Basic information
Entry | Database: PDB / ID: 4d0a | ||||||
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Title | 3D EM map of the sodium proton antiporter MjNhaP1 from Methanocaldococcus jannaschii | ||||||
Components | NA(+)/H(+) ANTIPORTER 1 | ||||||
Keywords | TRANSPORT PROTEIN / MEMBRANE PROTEIN / ANTIPORTER / TRANSPORTER / EXCHANGER / CPA | ||||||
Function / homology | Sodium/solute symporter superfamily / Cation/H+ exchanger / Sodium/hydrogen exchanger family / antiporter activity / sodium ion transport / proton transmembrane transport / identical protein binding / plasma membrane / Na(+)/H(+) antiporter 1 Function and homology information | ||||||
Biological species | METHANOCALDOCOCCUS JANNASCHII DSM 2661 (archaea) | ||||||
Method | ELECTRON CRYSTALLOGRAPHY / electron crystallography / cryo EM / Resolution: 6 Å | ||||||
Authors | Paulino, C. / Woehlert, D. / Yildiz, O. / Kuhlbrandt, W. | ||||||
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
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
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PDBx/mmCIF format | 4d0a.cif.gz | 93.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4d0a.ent.gz | 69.9 KB | Display | PDB format |
PDBx/mmJSON format | 4d0a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d0/4d0a ftp://data.pdbj.org/pub/pdb/validation_reports/d0/4d0a | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 45998.891 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) METHANOCALDOCOCCUS JANNASCHII DSM 2661 (archaea) Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q60362 |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON CRYSTALLOGRAPHY |
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EM experiment | Aggregation state: 2D ARRAY / 3D reconstruction method: electron crystallography |
-Sample preparation
Component | Name: sodium proton antiporter MjNhaP1 from Methanocaldococcus jannaschii Type: COMPLEX |
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Buffer solution | pH: 4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: NITROGEN |
Crystal grow | pH: 4 / Details: pH 4.0 |
-Data collection
Microscopy | Model: JEOL KYOTO-3000SFF / Date: Dec 1, 2012 |
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Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN |
Electron lens | Mode: OTHER / Nominal magnification: 60000 X / Nominal defocus max: 1800 nm / Nominal defocus min: 120 nm |
Image recording | Electron dose: 25 e/Å2 / Film or detector model: KODAK SO-163 FILM |
Diffraction | Mean temperature: 4 K |
Detector | Date: Dec 1, 2012 |
Radiation | Scattering type: electron |
Radiation wavelength | Relative weight: 1 |
-Processing
Software | Name: 2DX / Classification: refinement | ||||||||||||
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3D reconstruction | Resolution: 6 Å / Resolution method: OTHER / Symmetry type: 2D CRYSTAL | ||||||||||||
Refinement | Starting model: 4CZB Highest resolution: 6 Å | ||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 6 Å
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