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- EMDB-12002: CryoEM structure of the human sodium proton exchanger NHA2 -

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Basic information

Entry
Database: EMDB / ID: EMD-12002
TitleCryoEM structure of the human sodium proton exchanger NHA2
Map data
Sample
  • Complex: Human sodium proton exchanger NHA2
    • Protein or peptide: Sodium/hydrogen exchanger 9B2
  • Ligand: SODIUM IONSodium
  • Ligand: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
  • Ligand: TETRADECANE
  • Ligand: UNDECANE
  • Ligand: water
Function / homology
Function and homology information


lithium:proton antiporter activity / : / positive regulation of osteoclast development / sperm principal piece / sodium:proton antiporter activity / flagellated sperm motility / regulation of insulin secretion involved in cellular response to glucose stimulus / clathrin-dependent endocytosis / sodium ion transport / monoatomic ion transmembrane transport ...lithium:proton antiporter activity / : / positive regulation of osteoclast development / sperm principal piece / sodium:proton antiporter activity / flagellated sperm motility / regulation of insulin secretion involved in cellular response to glucose stimulus / clathrin-dependent endocytosis / sodium ion transport / monoatomic ion transmembrane transport / mitochondrial membrane / Stimuli-sensing channels / synaptic vesicle membrane / basolateral plasma membrane / mitochondrial inner membrane / endosome membrane / apical plasma membrane / identical protein binding / plasma membrane
Similarity search - Function
Sodium/hydrogen exchanger 9B2 / Sodium/solute symporter superfamily / Cation/H+ exchanger / Sodium/hydrogen exchanger family
Similarity search - Domain/homology
Sodium/hydrogen exchanger 9B2
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsWoehlert D / Kuhlbrandt W / Yildiz O
Funding support Germany, 1 items
OrganizationGrant numberCountry
German Research Foundation (DFG)SFB807 Germany
CitationJournal: To Be Published
Title: CryoEM structure of the human sodium proton exchanger NHA2
Authors: Woehlert D / Kuhlbrandt W / Yildiz O
History
DepositionDec 2, 2020-
Header (metadata) releaseJan 12, 2022-
Map releaseJan 12, 2022-
UpdateJan 12, 2022-
Current statusJan 12, 2022Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.8
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.8
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7b4l
  • Surface level: 0.8
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_12002.png

Downloads & links

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Map

FileDownload / File: emd_12002.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.073 Å
Density
Contour LevelBy AUTHOR: 0.8 / Movie #1: 0.8
Minimum - Maximum-2.1142 - 3.2136207
Average (Standard dev.)0.0006076849 (±0.100409366)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 300.44 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0731.0731.073
M x/y/z280280280
origin x/y/z0.0000.0000.000
length x/y/z300.440300.440300.440
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS280280280
D min/max/mean-2.1143.2140.001

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Supplemental data

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Mask #1

Fileemd_12002_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_12002_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_12002_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 : Human sodium proton exchanger NHA2

EntireName: Human sodium proton exchanger NHA2
Components
  • Complex: Human sodium proton exchanger NHA2
    • Protein or peptide: Sodium/hydrogen exchanger 9B2
  • Ligand: SODIUM IONSodium
  • Ligand: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
  • Ligand: TETRADECANE
  • Ligand: UNDECANE
  • Ligand: water

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Supramolecule #1: Human sodium proton exchanger NHA2

SupramoleculeName: Human sodium proton exchanger NHA2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightExperimental: 150 KDa

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Macromolecule #1: Sodium/hydrogen exchanger 9B2

MacromoleculeName: Sodium/hydrogen exchanger 9B2 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 57.611672 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MGDEDKRITY EDSEPSTGMN YTPSMHQEAQ EETVMKLKGI DANEPTEGSI LLKSSEKKLQ ETPTEANHVQ RLRQMLACPP HGLLDRVIT NVTIIVLLWA VVWSITGSEC LPGGNLFGII ILFYCAIIGG KLLGLIKLPT LPPLPSLLGM LLAGFLIRNI P VINDNVQI ...String:
MGDEDKRITY EDSEPSTGMN YTPSMHQEAQ EETVMKLKGI DANEPTEGSI LLKSSEKKLQ ETPTEANHVQ RLRQMLACPP HGLLDRVIT NVTIIVLLWA VVWSITGSEC LPGGNLFGII ILFYCAIIGG KLLGLIKLPT LPPLPSLLGM LLAGFLIRNI P VINDNVQI KHKWSSSLRS IALSIILVRA GLGLDSKALK KLKGVCVRLS MGPCIVEACT SALLAHYLLG LPWQWGFILG FV LGAVSPA VVVPSMLLLQ GGGYGVEKGV PTLLMAAGSF DDILAITGFN TCLGIAFSTG STVFNVLRGV LEVVIGVATG SVL GFFIQY FPSRDQDKLV CKRTFLVLGL SVLAVFSSVH FGFPGSGGLC TLVMAFLAGM GWTSEKAEVE KIIAVAWDIF QPLL FGLIG AEVSIASLRP ETVGLCVATV GIAVLIRILT TFLMVCFAGF NLKEKIFISF AWLPKATVQA AIGSVALDTA RSHGE KQLE DYGMDVLTVA FLSILITAPI GSLLIGLLGP RLLQKVEHQN KDEEVQGETS VQV

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Macromolecule #2: SODIUM ION

MacromoleculeName: SODIUM ION / type: ligand / ID: 2 / Number of copies: 2
Molecular weightTheoretical: 22.99 Da

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Macromolecule #3: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(tri...

MacromoleculeName: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
type: ligand / ID: 3 / Number of copies: 4 / Formula: POV
Molecular weightTheoretical: 760.076 Da
Chemical component information

ChemComp-POV:
(2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate / phospholipid*YM / POPC

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Macromolecule #4: TETRADECANE

MacromoleculeName: TETRADECANE / type: ligand / ID: 4 / Number of copies: 6 / Formula: C14
Molecular weightTheoretical: 198.388 Da
Chemical component information

ChemComp-C14:
TETRADECANE / Tetradecane

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Macromolecule #5: UNDECANE

MacromoleculeName: UNDECANE / type: ligand / ID: 5 / Number of copies: 10 / Formula: UND
Molecular weightTheoretical: 156.308 Da
Chemical component information

ChemComp-UND:
UNDECANE / Undecane

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Macromolecule #6: water

MacromoleculeName: water / type: ligand / ID: 6 / Number of copies: 26 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER / Water

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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

Concentration3 mg/mL
BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Number real images: 4326 / Average electron dose: 60.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 2243669
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 165793
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-7b4l:
CryoEM structure of the human sodium proton exchanger NHA2

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