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- EMDB-5037: 3D EM map of E.coli NhaA -

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Basic information

Entry
Database: EMDB / ID: EMD-5037
Title3D EM map of E.coli NhaA
Map dataNhaA
Sample
  • Sample: 3D EM map of NhaA 2D crystals
  • Organelle or cellular component: NhaA
KeywordsSodium 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
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 (E. coli)
Methodelectron crystallography / cryo EM
AuthorsWilliams K / Kuehlbrandt W
CitationJournal: 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
DepositionDec 10, 2008-
Header (metadata) releaseDec 23, 2008-
Map releaseMay 5, 2009-
UpdateNov 9, 2016-
Current statusNov 9, 2016Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 8
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 8
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-3fi1
  • Surface level: 8
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-3fi1
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_5037_1.png

Downloads & links

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Map

FileDownload / File: emd_5037.map.gz / Format: CCP4 / Size: 335 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNhaA
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesY (Sec.)X (Row.)Z (Col.)
2.06 Å/pix.
x 56 pix.
= 181.4 Å		1.98 Å/pix.
x 41 pix.
= 47.5 Å		2.08 Å/pix.
x 38 pix.
= 200. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX: 1.97917 Å / Y: 2.06136 Å / Z: 2.08333 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy EMDB: 8.0 / Movie #1: 8
Minimum - Maximum-29.815614700000001 - 61.20326996
Average (Standard dev.)-0.14365764 (±8.409098630000001)
SymmetrySpace group: 18
Details

EMDB XML:

Map geometry
Axis orderZXY
Origin-20-19-28
Dimensions413856
Spacing882496
CellA: 47.50008 Å / B: 181.39967 Å / C: 199.99966 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.97916666666672.06136363636362.0833333333333
M x/y/z248896
origin x/y/z0.0000.0000.000
length x/y/z47.500181.400200.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-20-28-19
NX/NY/NZ415638
MAP C/R/S312
start NC/NR/NS-19-20-28
NC/NR/NS384156
D min/max/mean-29.81661.203-0.144

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Supplemental data

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Sample components

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Entire : 3D EM map of NhaA 2D crystals

EntireName: 3D EM map of NhaA 2D crystals
Components
  • Sample: 3D EM map of NhaA 2D crystals
  • Organelle or cellular component: NhaA

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Supramolecule #1000: 3D EM map of NhaA 2D crystals

SupramoleculeName: 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

SupramoleculeName: NhaA / type: organelle_or_cellular_component / ID: 1 / Name.synonym: NhaA / Oligomeric state: dimer / Recombinant expression: Yes
Source (natural)Organism: Escherichia coli (E. coli)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Experimental details

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Structure determination

Methodcryo EM
Processingelectron crystallography
Aggregation state2D array

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Sample preparation

Concentration0.5 mg/mL
VitrificationCryogen name: NITROGEN / Instrument: OTHER

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Electron microscopy

MicroscopeJEOL 3000SFF
TemperatureMin: 4 K
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7 µm
Tilt angle min0
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: DIFFRACTION
Sample stageSpecimen holder: Holder / Specimen holder model: OTHER / Tilt angle max: 45 / Tilt series - Axis1 - Min angle: 0 ° / Tilt series - Axis1 - Max angle: 45 °

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Image processing

Detailsab is plane as defined by unit cell parameters (s.g P 21 21 2)
Final reconstructionSoftware - Name: CCP4
Crystal parametersUnit 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

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