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- EMDB-18002: Cryo-EM structure of horse NHE9 with a extracellular loop -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-18002
TitleCryo-EM structure of horse NHE9 with a extracellular loop
Map data
Sample
  • Complex: Dimeric Horse Nhe9
    • Protein or peptide: Sodium/hydrogen exchanger 9
KeywordsNa+/H+ exchanger / membrane protein / SLC9A9 / ion transporter / TRANSPORT PROTEIN
Function / homology
Function and homology information


potassium:proton antiporter activity / sodium:proton antiporter activity / sodium ion import across plasma membrane / sodium ion transmembrane transport / potassium ion transmembrane transport / proton transmembrane transport / regulation of intracellular pH / recycling endosome / phagocytic vesicle membrane / recycling endosome membrane ...potassium:proton antiporter activity / sodium:proton antiporter activity / sodium ion import across plasma membrane / sodium ion transmembrane transport / potassium ion transmembrane transport / proton transmembrane transport / regulation of intracellular pH / recycling endosome / phagocytic vesicle membrane / recycling endosome membrane / late endosome membrane / early endosome membrane / protein homodimerization activity / plasma membrane
Similarity search - Function
Sodium/hydrogen exchanger 6/7/9 / Na+/H+ exchanger / Cation/H+ exchanger, CPA1 family / Cation/H+ exchanger / Sodium/hydrogen exchanger family
Similarity search - Domain/homology
Sodium/hydrogen exchanger 9
Similarity search - Component
Biological speciesEquus caballus (horse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsKokane S / Meier P / Matsuoka R / Drew D
Funding supportEuropean Union, 1 items
OrganizationGrant numberCountry
European Research Council (ERC)CoG-820187European Union
CitationJournal: To Be Published
Title: PIP2 mediated oligomerization of the endosomal sodium/proton exchanger NHE9
Authors: Kokane S / Meier P / Gulati A / Matsuoka R / Pipatpolkai T / Delemotte L / Drew D
History
DepositionJul 23, 2023-
Header (metadata) releaseAug 7, 2024-
Map releaseAug 7, 2024-
UpdateAug 7, 2024-
Current statusAug 7, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_18002.png

Downloads & links

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Map

FileDownload / File: emd_18002.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.04 Å/pix.
x 240 pix.
= 249. Å		1.04 Å/pix.
x 240 pix.
= 249. Å		1.04 Å/pix.
x 240 pix.
= 249. Å

Surface

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0375 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.29
Minimum - Maximum-0.5614686 - 1.0837405
Average (Standard dev.)0.0042615277 (±0.050626494)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 249.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_18002_msk_1.map
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Additional map: #1

Fileemd_18002_additional_1.map
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Additional map: composite map

Fileemd_18002_additional_2.map
Annotationcomposite map
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Half map: #2

Fileemd_18002_half_map_1.map
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Half map: #1

Fileemd_18002_half_map_2.map
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Sample components

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Entire : Dimeric Horse Nhe9

EntireName: Dimeric Horse Nhe9
Components
  • Complex: Dimeric Horse Nhe9
    • Protein or peptide: Sodium/hydrogen exchanger 9

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Supramolecule #1: Dimeric Horse Nhe9

SupramoleculeName: Dimeric Horse Nhe9 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Equus caballus (horse)

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Macromolecule #1: Sodium/hydrogen exchanger 9

MacromoleculeName: Sodium/hydrogen exchanger 9 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Equus caballus (horse)
Molecular weightTheoretical: 64.876086 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MSEKDEYQFQ HQGAVELLVF NFLLILTILT IWLFKNHRFR FLHETGGAMV YGLIMGLILR YATAPTDIES GTVYDCGKLA FSPSTLLIN ITDQVYEYKY KREISQHNIN PHLGNAILEK MTFDPEIFFN VLLPPIIFHA GYSLKKRHFF QNLGSILTYA F LGTAISCI ...String:
MSEKDEYQFQ HQGAVELLVF NFLLILTILT IWLFKNHRFR FLHETGGAMV YGLIMGLILR YATAPTDIES GTVYDCGKLA FSPSTLLIN ITDQVYEYKY KREISQHNIN PHLGNAILEK MTFDPEIFFN VLLPPIIFHA GYSLKKRHFF QNLGSILTYA F LGTAISCI VIGLIMYGFV KAMVYAGQLK NGDFHFTDCL FFGSLMSATD PVTVLAIFHE LHVDPDLYTL LFGESVLNDA VA IVLTYSI SIYSPKENPN AFDAAAFFQS VGNFLGIFAG SFAMGSAYAV VTALLTKFTK LCEFPMLETG LFFLLSWSAF LSA EAAGLT GIVAVLFCGV TQAHYTYNNL SLDSKMRTKQ LFEFMNFLAE NVIFCYMGLA LFTFQNHIFN ALFILGAFLA IFVA RACNI YPLSFLLNLG RKHKIPWNFQ HMMMFSGLRG AIAFALAIRD TESQPKQMMF STTLLLVFFT VWVFGGGTTP MLTWL QIRV GVDLDEDLKE RPSSHQEANN LEKSTTKTES AWLFRMWYGF DHKYLKPILT HSGPPLTTTL PEWCGPISRL LTSPQA YGE QLKEGENLYF Q

UniProtKB: Sodium/hydrogen exchanger 9

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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: 6.5
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 300
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 IS (4k x 4k) / Average electron dose: 80.0 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: PDB ENTRY
PDB model - PDB ID:

6z3z

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 103815
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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