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- EMDB-12003: CryoEM structure of the human sodium proton exchanger NHA2 in nanodisc -

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Basic information

Entry
Database: EMDB / ID: EMD-12003
TitleCryoEM structure of the human sodium proton exchanger NHA2 in nanodisc
Map data
Sample
  • Complex: Human sodium proton exchanger NHA2 in nanodisc
    • Protein or peptide: Sodium/hydrogen exchanger 9B2
Keywordssecondary active transporter / membrane transport / ion antiport / pH regulation / MEMBRANE PROTEIN
Function / homology
Function and homology information


lithium:proton antiporter activity / lithium ion transport / positive regulation of osteoclast development / sperm principal piece / sodium ion homeostasis / sodium:proton antiporter activity / regulation of insulin secretion involved in cellular response to glucose stimulus / clathrin-dependent endocytosis / flagellated sperm motility / : ...lithium:proton antiporter activity / lithium ion transport / positive regulation of osteoclast development / sperm principal piece / sodium ion homeostasis / sodium:proton antiporter activity / regulation of insulin secretion involved in cellular response to glucose stimulus / clathrin-dependent endocytosis / flagellated sperm motility / : / sodium ion transport / recycling endosome / mitochondrial membrane / Stimuli-sensing channels / recycling endosome membrane / synaptic vesicle membrane / monoatomic ion transmembrane transport / basolateral plasma membrane / mitochondrial inner membrane / apical plasma membrane / mitochondrion / identical protein binding / plasma membrane
Similarity search - Function
: / Sodium/solute symporter superfamily / Cation/H+ exchanger / Sodium/hydrogen exchanger, transmembrane
Similarity search - Domain/homology
Sodium/hydrogen exchanger 9B2
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.2 Å
AuthorsWoehlert D / Kuhlbrandt W
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 in nanodisc
Authors: Woehlert D / Kuhlbrandt W / Yildiz O
History
DepositionDec 2, 2020-
Header (metadata) releaseJan 12, 2022-
Map releaseJan 12, 2022-
UpdateJul 10, 2024-
Current statusJul 10, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.3
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.3
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7b4m
  • Surface level: 0.3
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7b4m
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_12003.png

Downloads & links

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Map

FileDownload / File: emd_12003.map.gz / Format: CCP4 / Size: 107.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 304 pix.
= 253.232 Å		0.83 Å/pix.
x 304 pix.
= 253.232 Å		0.83 Å/pix.
x 304 pix.
= 253.232 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.833 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.27 / Movie #1: 0.3
Minimum - Maximum-0.40364844 - 0.8103925
Average (Standard dev.)0.0037477647 (±0.057154432)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions304304304
Spacing304304304
CellA=B=C: 253.232 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.8330.8330.833
M x/y/z304304304
origin x/y/z0.0000.0000.000
length x/y/z253.232253.232253.232
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS304304304
D min/max/mean-0.4040.8100.004

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Supplemental data

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Mask #1

Fileemd_12003_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_12003_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_12003_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 in nanodisc

EntireName: Human sodium proton exchanger NHA2 in nanodisc
Components
  • Complex: Human sodium proton exchanger NHA2 in nanodisc
    • Protein or peptide: Sodium/hydrogen exchanger 9B2

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Supramolecule #1: Human sodium proton exchanger NHA2 in nanodisc

SupramoleculeName: Human sodium proton exchanger NHA2 in nanodisc / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 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

UniProtKB: Sodium/hydrogen exchanger 9B2

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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
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Number real images: 1251 / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 285970
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 7.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 47284
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-7b4m:
CryoEM structure of the human sodium proton exchanger NHA2 in nanodisc

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