+Open data
-Basic information
Entry | Database: PDB / ID: 3fi1 | ||||||
---|---|---|---|---|---|---|---|
Title | NhaA dimer model | ||||||
Components | Na(+)/H(+) antiporter nhaA | ||||||
Keywords | MEMBRANE PROTEIN / membrane protein sodium proton antiporter / Antiport / Cell inner membrane / Cell membrane / Ion transport / Membrane / Sodium transport / Transmembrane / Transport | ||||||
Function / homology | Function and homology information response to alkaline pH / sodium:proton antiporter activity / cardiolipin binding / response to salt stress / regulation of intracellular pH / plasma membrane Similarity search - Function | ||||||
Biological species | Escherichia coli K-12 (bacteria) | ||||||
Method | ELECTRON CRYSTALLOGRAPHY / electron crystallography / cryo EM / Resolution: 7 Å | ||||||
Authors | Appel, M. / Hizlan, D. / Vinothkumar, K.R. / Ziegler, C. / Kuehlbrandt, W. | ||||||
Citation | Journal: J Mol Biol / Year: 2009 Title: Conformations of NhaA, the Na/H exchanger from Escherichia coli, in the pH-activated and ion-translocating states. Authors: Matthias Appel / Dilem Hizlan / Kutti R Vinothkumar / Christine Ziegler / Werner Kühlbrandt / Abstract: NhaA, the main sodium-proton exchanger in the inner membrane of Escherichia coli, regulates the cytosolic concentrations of H and Na. It is inactive at acidic pH, becomes active between pH 6 and pH ...NhaA, the main sodium-proton exchanger in the inner membrane of Escherichia coli, regulates the cytosolic concentrations of H and Na. It is inactive at acidic pH, becomes active between pH 6 and pH 7, and reaches maximum activity at pH 8. By cryo-electron microscopy of two-dimensional crystals grown at pH 4 and incubated at higher pH, we identified two sequential conformational changes in the protein in response to pH or substrate ions. The first change is induced by a rise in pH from 6 to 7 and marks the transition from the inactive state to the pH-activated state. pH activation, which precedes the ion-induced conformational change, is accompanied by an overall expansion of the NhaA monomer and a local ordering of the N-terminus. The second conformational change is induced by the substrate ions Na and Li at pH above 7 and involves a 7-A displacement of helix IVp. This movement would cause a charge imbalance at the ion-binding site that may trigger the release of the substrate ion and open a periplasmic exit channel. | ||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 3fi1.cif.gz | 72.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3fi1.ent.gz | 52.2 KB | Display | PDB format |
PDBx/mmJSON format | 3fi1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3fi1_validation.pdf.gz | 367.6 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3fi1_full_validation.pdf.gz | 402.3 KB | Display | |
Data in XML | 3fi1_validation.xml.gz | 14.5 KB | Display | |
Data in CIF | 3fi1_validation.cif.gz | 21.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fi/3fi1 ftp://data.pdbj.org/pub/pdb/validation_reports/fi/3fi1 | HTTPS FTP |
-Related structure data
Related structure data | 5037M M: map data used to model this data |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 39846.578 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: K12 / References: UniProt: P13738 |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON CRYSTALLOGRAPHY |
---|---|
EM experiment | Aggregation state: 2D ARRAY / 3D reconstruction method: electron crystallography |
-Sample preparation
Component | Name: NhaA dimer / Type: COMPLEX |
---|---|
Specimen | Conc.: 0.5 mg/ml / Embedding applied: YES / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
EM embedding | Material: tannin or trehalose |
Vitrification | Cryogen name: NITROGEN Details: Frozen hydrated specimens were prepared by the back-injection of the crystals into a tannin or trehalose solution. |
-Data collection
Microscopy | Model: JEOL 3000SFF |
---|---|
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: DIFFRACTION |
Specimen holder | Temperature: 4 K |
Image recording | Electron dose: 20 e/Å2 / Film or detector model: KODAK SO-163 FILM |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: electron |
Radiation wavelength | Relative weight: 1 |
-Processing
3D reconstruction | Method: CRYSTALLOGRAPHY / Symmetry type: 2D CRYSTAL | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 7→14 Å | ||||||||||||
Refinement step | Cycle: LAST / Resolution: 7→14 Å
|