+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-18002 | |||||||||
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Title | Cryo-EM structure of horse NHE9 with a extracellular loop | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Na+/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 | |||||||||
Biological species | Equus caballus (horse) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.6 Å | |||||||||
Authors | Kokane S / Meier P / Matsuoka R / Drew D | |||||||||
Funding support | European Union, 1 items
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Citation | Journal: 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 |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_18002.map.gz | 26.3 MB | EMDB map data format | |
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Header (meta data) | emd-18002-v30.xml emd-18002.xml | 17.5 KB 17.5 KB | Display Display | EMDB header |
Images | emd_18002.png | 57 KB | ||
Masks | emd_18002_msk_1.map | 52.7 MB | Mask map | |
Filedesc metadata | emd-18002.cif.gz | 5.7 KB | ||
Others | emd_18002_additional_1.map.gz emd_18002_additional_2.map.gz emd_18002_half_map_1.map.gz emd_18002_half_map_2.map.gz | 49.4 MB 42.2 MB 48.9 MB 48.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-18002 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-18002 | HTTPS FTP |
-Validation report
Summary document | emd_18002_validation.pdf.gz | 950.8 KB | Display | EMDB validaton report |
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Full document | emd_18002_full_validation.pdf.gz | 950.4 KB | Display | |
Data in XML | emd_18002_validation.xml.gz | 11.9 KB | Display | |
Data in CIF | emd_18002_validation.cif.gz | 13.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-18002 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-18002 | HTTPS FTP |
-Related structure data
Related structure data | 8pxbMC 8pvrC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_18002.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.0375 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_18002_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: #1
File | emd_18002_additional_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: composite map
File | emd_18002_additional_2.map | ||||||||||||
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Annotation | composite map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_18002_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_18002_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Dimeric Horse Nhe9
Entire | Name: Dimeric Horse Nhe9 |
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Components |
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-Supramolecule #1: Dimeric Horse Nhe9
Supramolecule | Name: Dimeric Horse Nhe9 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Equus caballus (horse) |
-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: Equus caballus (horse) |
Molecular weight | Theoretical: 64.876086 KDa |
Recombinant expression | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Sequence | String: 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 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 6.5 |
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Grid | Model: Quantifoil R2/1 / Material: COPPER / Mesh: 300 |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 IS (4k x 4k) / Average electron dose: 80.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination 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 |
-Image processing
Startup model | Type of model: PDB ENTRY PDB model - PDB ID: |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 103815 |
Initial angle assignment | Type: ANGULAR RECONSTITUTION |
Final angle assignment | Type: ANGULAR RECONSTITUTION |