+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-5037 | |||||||||
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Title | 3D EM map of E.coli NhaA | |||||||||
Map data | NhaA | |||||||||
Sample |
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Keywords | Sodium proton antiporter | |||||||||
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 (E. coli) | |||||||||
Method | electron crystallography / cryo EM | |||||||||
Authors | Williams K / Kuehlbrandt W | |||||||||
Citation | Journal: Nature / Year: 2000 Title: Three-dimensional structure of the ion-coupled transport protein NhaA. Authors: K A Williams / Abstract: Ion-coupled membrane-transport proteins, or secondary transporters, comprise a diverse and abundant group of membrane proteins that are found in all organisms. These proteins facilitate solute ...Ion-coupled membrane-transport proteins, or secondary transporters, comprise a diverse and abundant group of membrane proteins that are found in all organisms. These proteins facilitate solute accumulation and toxin removal against concentration gradients using energy supplied by ion gradients across membranes. NhaA is a Na+/H+ antiporter of relative molecular mass 42,000, which is found in the inner membrane of Escherichia coli, and which has been cloned and characterized. NhaA uses the H+ electrochemical gradient to expel Na+ from the cytoplasm, and functions primarily in the adaptation to high salinity at alkaline pH. Most secondary transporters, including NhaA, are predicted to have 12 transmembrane helices. Here we report the structure of NhaA, at 7 A resolution in the membrane plane and at 14 A vertical resolution, determined from two-dimensional crystals using electron cryo-microscopy. The three-dimensional map of NhaA reveals 12 tilted, bilayer-spanning helices. A roughly linear arrangement of six helices is adjacent to a compact bundle of six helices, with the density for one helix in the bundle not continuous through the membrane. The molecular organization of NhaA represents a new membrane-protein structural motif and offers the first insights into the architecture of an ion-coupled transport protein. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_5037.map.gz | 187.8 KB | EMDB map data format | |
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Header (meta data) | emd-5037-v30.xml emd-5037.xml | 8.1 KB 8.1 KB | Display Display | EMDB header |
Images | emd_5037_1.png | 173.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-5037 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-5037 | HTTPS FTP |
-Validation report
Summary document | emd_5037_validation.pdf.gz | 314.6 KB | Display | EMDB validaton report |
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Full document | emd_5037_full_validation.pdf.gz | 314.2 KB | Display | |
Data in XML | emd_5037_validation.xml.gz | 4.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5037 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5037 | HTTPS FTP |
-Related structure data
Related structure data | 3fi1M M: atomic model generated by this map |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_5037.map.gz / Format: CCP4 / Size: 335 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | NhaA | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X: 1.97917 Å / Y: 2.06136 Å / Z: 2.08333 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 18 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : 3D EM map of NhaA 2D crystals
Entire | Name: 3D EM map of NhaA 2D crystals |
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Components |
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-Supramolecule #1000: 3D EM map of NhaA 2D crystals
Supramolecule | Name: 3D EM map of NhaA 2D crystals / type: sample / ID: 1000 / Details: 2D crystals / Oligomeric state: Dimer / Number unique components: 2 |
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-Supramolecule #1: NhaA
Supramolecule | Name: NhaA / type: organelle_or_cellular_component / ID: 1 / Name.synonym: NhaA / Oligomeric state: dimer / Recombinant expression: Yes |
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Source (natural) | Organism: Escherichia coli (E. coli) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | electron crystallography |
Aggregation state | 2D array |
-Sample preparation
Concentration | 0.5 mg/mL |
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Vitrification | Cryogen name: NITROGEN / Instrument: OTHER |
-Electron microscopy
Microscope | JEOL 3000SFF |
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Temperature | Min: 4 K |
Image recording | Category: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7 µm |
Tilt angle min | 0 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: DIFFRACTION |
Sample stage | Specimen holder: Holder / Specimen holder model: OTHER / Tilt angle max: 45 / Tilt series - Axis1 - Min angle: 0 ° / Tilt series - Axis1 - Max angle: 45 ° |
-Image processing
Details | ab is plane as defined by unit cell parameters (s.g P 21 21 2) |
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Final reconstruction | Software - Name: CCP4 |
Crystal parameters | Unit cell - A: 47.50 Å / Unit cell - B: 181.40 Å / Unit cell - C: 200.00 Å / Unit cell - γ: 90.00 ° / Unit cell - α: 90.00 ° / Unit cell - β: 90.00 ° / Plane group: P 2 21 21 |