+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-30368 | |||||||||
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Title | cryo_EM map of SLC26A9 | |||||||||
Map data | cryo_EM map of SLC26A9 | |||||||||
Sample |
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Keywords | MEMBRANE PROTEIN | |||||||||
Function / homology | Function and homology information : / Multifunctional anion exchangers / sulfate transmembrane transporter activity / secondary active sulfate transmembrane transporter activity / oxalate transmembrane transporter activity / bicarbonate transport / bicarbonate transmembrane transporter activity / monoatomic anion transport / chloride transport / chloride transmembrane transporter activity ...: / Multifunctional anion exchangers / sulfate transmembrane transporter activity / secondary active sulfate transmembrane transporter activity / oxalate transmembrane transporter activity / bicarbonate transport / bicarbonate transmembrane transporter activity / monoatomic anion transport / chloride transport / chloride transmembrane transporter activity / chloride channel activity / plasma membrane => GO:0005886 / monoatomic ion transport / ATPase binding / apical plasma membrane / positive regulation of gene expression / cell surface / extracellular exosome / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.6 Å | |||||||||
Authors | Chi XM / Chen Y | |||||||||
Funding support | China, 2 items
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Citation | Journal: Cell Discov / Year: 2020 Title: Structural insights into the gating mechanism of human SLC26A9 mediated by its C-terminal sequence. Authors: Ximin Chi / Xueqin Jin / Yun Chen / Xiaoli Lu / Xinyu Tu / Xiaorong Li / Yuanyuan Zhang / Jianlin Lei / Jing Huang / Zhuo Huang / Qiang Zhou / Xiaojing Pan / Abstract: The human SLC26 transporter family exhibits various transport characteristics, and family member SLC26A9 performs multiple roles, including acting as Cl/HCO exchangers, Cl channels, and Na ...The human SLC26 transporter family exhibits various transport characteristics, and family member SLC26A9 performs multiple roles, including acting as Cl/HCO exchangers, Cl channels, and Na transporters. Some mutations of SLC26A9 are correlated with abnormalities in respiration and digestion systems. As a potential target colocalizing with CFTR in cystic fibrosis patients, SLC26A9 is of great value in drug development. Here, we present a cryo-EM structure of the human SLC26A9 dimer at 2.6 Å resolution. A segment at the C-terminal end is bound to the entry of the intracellular vestibule of the putative transport pathway, which has been proven by electrophysiological experiments to be a gating modulator. Multiple chloride and sodium ions are resolved in the high-resolution structure, identifying novel ion-binding pockets for the first time. Together, our structure takes important steps in elucidating the structural features and regulatory mechanism of SLC26A9, with potential significance in the treatment of cystic fibrosis. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_30368.map.gz | 115 MB | EMDB map data format | |
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Header (meta data) | emd-30368-v30.xml emd-30368.xml | 11.2 KB 11.2 KB | Display Display | EMDB header |
Images | emd_30368.png | 39 KB | ||
Filedesc metadata | emd-30368.cif.gz | 5.4 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-30368 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-30368 | HTTPS FTP |
-Validation report
Summary document | emd_30368_validation.pdf.gz | 532.4 KB | Display | EMDB validaton report |
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Full document | emd_30368_full_validation.pdf.gz | 532 KB | Display | |
Data in XML | emd_30368_validation.xml.gz | 6.5 KB | Display | |
Data in CIF | emd_30368_validation.cif.gz | 7.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-30368 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-30368 | HTTPS FTP |
-Related structure data
Related structure data | 7ch1MC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_30368.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | cryo_EM map of SLC26A9 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.091 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : SLC26A9
Entire | Name: SLC26A9 |
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Components |
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-Supramolecule #1: SLC26A9
Supramolecule | Name: SLC26A9 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: Solute carrier family 26 member 9
Macromolecule | Name: Solute carrier family 26 member 9 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 87.066945 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MSQPRPRYVV DRAAYSLTLF DDEFEKKDRT YPVGEKLRNA FRCSSAKIKA VVFGLLPVLS WLPKYKIKDY IIPDLLGGLS GGSIQVPQG MAFALLANLP AVNGLYSSFF PLLTYFFLGG VHQMVPGTFA VISILVGNIC LQLAPESKFQ VFNNATNESY V DTAAMEAE ...String: MSQPRPRYVV DRAAYSLTLF DDEFEKKDRT YPVGEKLRNA FRCSSAKIKA VVFGLLPVLS WLPKYKIKDY IIPDLLGGLS GGSIQVPQG MAFALLANLP AVNGLYSSFF PLLTYFFLGG VHQMVPGTFA VISILVGNIC LQLAPESKFQ VFNNATNESY V DTAAMEAE RLHVSATLAC LTAIIQMGLG FMQFGFVAIY LSESFIRGFM TAAGLQILIS VLKYIFGLTI PSYTGPGSIV FT FIDICKN LPHTNIASLI FALISGAFLV LVKELNARYM HKIRFPIPTE MIVVVVATAI SGGCKMPKKY HMQIVGEIQR GFP TPVSPV VSQWKDMIGT AFSLAIVSYV INLAMGRTLA NKHGYDVDSN QEMIALGCSN FFGSFFKIHV ICCALSVTLA VDGA GGKSQ VASLCVSLVV MITMLVLGIY LYPLPKSVLG ALIAVNLKNS LKQLTDPYYL WRKSKLDCCI WVVSFLSSFF LSLPY GVAV GVAFSVLVVV FQTQFRNGYA LAQVMDTDIY VNPKTYNRAQ DIQGIKIITY CSPLYFANSE IFRQKVIAKT GMDPQK VLL AKQKYLKKQE KRRMRPTQQR RSLFMKTKTV SLQELQQDFE NAPPTDPNNN QTPANGTSVS YITFSPDSSS PAQSEPP AS AEAPGEPSDM LASVPPFVTF HTLILDMSGV SFVDLMGIKA LAKLSSTYGK IGVKVFLVNI HAQVYNDISH GGVFEDGS L ECKHVFPSIH DAVLFAQANA RDVTPGHNFQ GAPGDAELSL YDSEEDIRSY WDLEQEMFGS MFHAETLTAL UniProtKB: Solute carrier family 26 member 9 |
-Macromolecule #2: CHLORIDE ION
Macromolecule | Name: CHLORIDE ION / type: ligand / ID: 2 / Number of copies: 4 / Formula: CL |
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Molecular weight | Theoretical: 35.453 Da |
-Macromolecule #3: SODIUM ION
Macromolecule | Name: SODIUM ION / type: ligand / ID: 3 / Number of copies: 2 |
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Molecular weight | Theoretical: 22.99 Da |
-Macromolecule #4: water
Macromolecule | Name: water / type: ligand / ID: 4 / Number of copies: 76 / Formula: HOH |
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Molecular weight | Theoretical: 18.015 Da |
Chemical component information | ChemComp-HOH: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 48.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: OTHER |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0.6) / Number images used: 624027 |
Initial angle assignment | Type: OTHER |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |