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- EMDB-17841: Cryo-EM structure of Sodium proton exchanger NhaA with bound card... -

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Basic information

Entry
Database: EMDB / ID: EMD-17841
TitleCryo-EM structure of Sodium proton exchanger NhaA with bound cardiolipin
Map data
Sample
  • Complex: NhaA dimer
    • Protein or peptide: Na(+)/H(+) antiporter NhaA
  • Ligand: CARDIOLIPIN
KeywordsSodium proton exchanger / Cardiolipin / NhaA / TRANSPORT PROTEIN
Function / homologyNa+/H+ antiporter NhaA / Na+/H+ antiporter domain superfamily / Na+/H+ antiporter 1 / sodium:proton antiporter activity / regulation of pH / plasma membrane / Na(+)/H(+) antiporter NhaA
Function and homology information
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.37 Å
AuthorsGulati A / Meier P / Kokane S / Drew D
Funding supportEuropean Union, 1 items
OrganizationGrant numberCountry
European Research Council (ERC)CoG-820187European Union
CitationJournal: To Be Published
Title: Cryo-EM structure of Sodium proton exchanger NhaA with bound cardiolipin
Authors: Kokane S / Meier P / Gulati A / Matsuoka R / Pipatpolkai T / Delemotte L / Drew D
History
DepositionJul 13, 2023-
Header (metadata) releaseFeb 21, 2024-
Map releaseFeb 21, 2024-
UpdateFeb 21, 2024-
Current statusFeb 21, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_17841.png

Downloads & links

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Map

FileDownload / File: emd_17841.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.9137 Å
Density
Contour LevelBy AUTHOR: 8.0
Minimum - Maximum-41.509846000000003 - 79.94014
Average (Standard dev.)0.000000000000374 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 292.384 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_17841_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_17841_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_17841_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : NhaA dimer

EntireName: NhaA dimer
Components
  • Complex: NhaA dimer
    • Protein or peptide: Na(+)/H(+) antiporter NhaA
  • Ligand: CARDIOLIPIN

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Supramolecule #1: NhaA dimer

SupramoleculeName: NhaA dimer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Escherichia coli (E. coli)

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Macromolecule #1: Na(+)/H(+) antiporter NhaA

MacromoleculeName: Na(+)/H(+) antiporter NhaA / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 42.304422 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MKHLHRFFSS DASGGIILII AAILAMIMAN SGATSGWYHD FLETPVQLRV GSLEINKNML LWINDALMAV FFLLVGLEVK RELMQGSLA SLRQAAFPVI AAIGGMIVPT LLYLAFNYAD PITREGWAIP AATDIAFALG VLALLGSRVP LALKIFLMAL A IIDDLGAI ...String:
MKHLHRFFSS DASGGIILII AAILAMIMAN SGATSGWYHD FLETPVQLRV GSLEINKNML LWINDALMAV FFLLVGLEVK RELMQGSLA SLRQAAFPVI AAIGGMIVPT LLYLAFNYAD PITREGWAIP AATDIAFALG VLALLGSRVP LALKIFLMAL A IIDDLGAI IIIALFYTND LSMASLGVAA VAIAVLAVLN LCGARRTGVY ILVGVVLWTA VLKSGVHATL AGVIVGFFIP LK EKHGRSP AKRLEHVLHP WVAYLILPLF AFANAGVSLG GVTLDGLTSI LPLGIIAGML IGKPLGISLF CWLALRLKLA HLP EGTTYQ QIMVVGILCG IGFTMSIFIA SLAFGSVDPE LINWAKLGIL VGSISSAVIG YSWLRVRLRP SVGSENLYFQ

UniProtKB: Na(+)/H(+) antiporter NhaA

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Macromolecule #2: CARDIOLIPIN

MacromoleculeName: CARDIOLIPIN / type: ligand / ID: 2 / Number of copies: 3 / Formula: CDL
Molecular weightTheoretical: 1.464043 KDa
Chemical component information

ChemComp-CDL:
CARDIOLIPIN / phospholipid*YM

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 68.11 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.6 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.37 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 78917
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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