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- PDB-3fi1: NhaA dimer model -

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Basic information

Entry
Database: PDB / ID: 3fi1
TitleNhaA dimer model
ComponentsNa(+)/H(+) antiporter nhaA
KeywordsMEMBRANE 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
Na+/H+ antiporter NhaA / Na+/H+ antiporter domain superfamily / Na+/H+ antiporter 1
Similarity search - Domain/homology
Na(+)/H(+) antiporter NhaA
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodELECTRON CRYSTALLOGRAPHY / electron crystallography / cryo EM / Resolution: 7 Å
AuthorsAppel, M. / Hizlan, D. / Vinothkumar, K.R. / Ziegler, C. / Kuehlbrandt, W.
CitationJournal: 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
DepositionDec 10, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 13, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 15, 2012Group: Derived calculations / Other
Revision 1.3May 22, 2019Group: Author supporting evidence / Data collection / Refinement description
Category: em_image_scans / em_single_particle_entity / refine
Item: _refine.pdbx_refine_id
Revision 1.4Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_sheet
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_sheet.number_strands

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Assembly

Deposited unit
A: Na(+)/H(+) antiporter nhaA


Theoretical massNumber of molelcules
Total (without water)39,8471
Polymers39,8471
Non-polymers00
Water0
1
A: Na(+)/H(+) antiporter nhaA

A: Na(+)/H(+) antiporter nhaA


Theoretical massNumber of molelcules
Total (without water)79,6932
Polymers79,6932
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Unit cell
Length a, b, c (Å)48.000, 181.000, 200.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Na(+)/H(+) antiporter nhaA / Sodium/proton antiporter nhaA


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

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Experimental details

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Experiment

ExperimentMethod: ELECTRON CRYSTALLOGRAPHY
EM experimentAggregation state: 2D ARRAY / 3D reconstruction method: electron crystallography

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Sample preparation

ComponentName: NhaA dimer / Type: COMPLEX
SpecimenConc.: 0.5 mg/ml / Embedding applied: YES / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
EM embeddingMaterial: tannin or trehalose
VitrificationCryogen name: NITROGEN
Details: Frozen hydrated specimens were prepared by the back-injection of the crystals into a tannin or trehalose solution.

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Data collection

MicroscopyModel: JEOL 3000SFF
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: DIFFRACTION
Specimen holderTemperature: 4 K
Image recordingElectron dose: 20 e/Å2 / Film or detector model: KODAK SO-163 FILM
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: electron
Radiation wavelengthRelative weight: 1

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Processing

3D reconstructionMethod: CRYSTALLOGRAPHY / Symmetry type: 2D CRYSTAL
RefinementResolution: 7→14 Å
Refinement stepCycle: LAST / Resolution: 7→14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2809 0 0 0 2809

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