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Open data
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Basic information
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Title | Cryo-EM structure of horse Nhe9 bound to PI(3,5)P2 | |||||||||
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![]() | Na+/H+ exchanger / membrane protein / SLC9A9 / ion transporter / PI(3 / 5)P2 / TRANSPORT PROTEIN | |||||||||
Function / homology | ![]() 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 / recycling endosome membrane / phagocytic vesicle 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 / recycling endosome membrane / phagocytic vesicle membrane / late endosome membrane / early endosome membrane / protein homodimerization activity / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.06 Å | |||||||||
![]() | Kokane S / Meier P / Gulati A / Delemotte L / Drew D | |||||||||
Funding support | European Union, 1 items
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![]() | ![]() 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 |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 50.8 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 13.9 KB 13.9 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 9.9 KB | Display | ![]() |
Images | ![]() | 112.2 KB | ||
Masks | ![]() | 103 MB | ![]() | |
Filedesc metadata | ![]() | 5.7 KB | ||
Others | ![]() ![]() | 95.4 MB 95.4 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 834 KB | Display | ![]() |
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Full document | ![]() | 833.6 KB | Display | |
Data in XML | ![]() | 18.3 KB | Display | |
Data in CIF | ![]() | 23.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8pvrMC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Map
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.9746 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_17971_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_17971_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Dimeric Horse Nhe9 with PI(3,5)P2
Entire | Name: Dimeric Horse Nhe9 with PI(3,5)P2 |
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Components |
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-Supramolecule #1: Dimeric Horse Nhe9 with PI(3,5)P2
Supramolecule | Name: Dimeric Horse Nhe9 with PI(3,5)P2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 64 KDa |
-Macromolecule #1: Sodium/hydrogen exchanger 9
Macromolecule | Name: Sodium/hydrogen exchanger 9 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 64.856055 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MSEKDEYQFQ HQGAVELLVF NFLLILTILT IWLFKNHRFR FLHETGGAMV YGLIMGLILR YATAPTDIES GTVYDCGKLA FSPSTLLIN ITDQVYEYKY KREISQHNIN PHLGNAILEK MTFDPEIFFN VLCPPIIFHA GYSLKKRHFF QNLGSILTYA F LGTAISCI ...String: MSEKDEYQFQ HQGAVELLVF NFLLILTILT IWLFKNHRFR FLHETGGAMV YGLIMGLILR YATAPTDIES GTVYDCGKLA FSPSTLLIN ITDQVYEYKY KREISQHNIN PHLGNAILEK MTFDPEIFFN VLCPPIIFHA 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 ACAFALAIRD TESQPKQMMF STTLLLVFFT VWVFGGGTTP MLTWL QIRV GVDLDEDLKE RPSSHQEANN LEKSTTKTES AWLFRMWYGF DHKYLKPILT HSGPPLTTTL PEWCGPISRL LTSPQA YGE QLKEGENLYF Q UniProtKB: Sodium/hydrogen exchanger 9 |
-Macromolecule #2: (2R)-3-{[(S)-hydroxy{[(1S,2R,3R,4S,5S,6R)-2,4,6-trihydroxy-3,5-bi...
Macromolecule | Name: (2R)-3-{[(S)-hydroxy{[(1S,2R,3R,4S,5S,6R)-2,4,6-trihydroxy-3,5-bis(phosphonooxy)cyclohexyl]oxy}phosphoryl]oxy}propane-1,2-diyl dioctanoate type: ligand / ID: 2 / Number of copies: 2 / Formula: EUJ |
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Molecular weight | Theoretical: 746.566 Da |
Chemical component information | ![]() ChemComp-EUJ: |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 8 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 68.5 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.4 µm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |