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- EMDB-30368: cryo_EM map of SLC26A9 -

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Basic information

Entry
Database: EMDB / ID: EMD-30368
Titlecryo_EM map of SLC26A9
Map datacryo_EM map of SLC26A9
Sample
  • Complex: SLC26A9
    • Protein or peptide: Solute carrier family 26 member 9
  • Ligand: CHLORIDE ION
  • Ligand: SODIUM ION
  • Ligand: water
KeywordsMEMBRANE PROTEIN
Function / homology
Function and homology information


Inorganic anion exchange by SLC26 transporters / sulfate transmembrane transporter activity / oxalate transmembrane transporter activity / sulfate transmembrane transport / solute:inorganic anion antiporter activity / bicarbonate transmembrane transporter activity / monoatomic anion transport / chloride transport / chloride transmembrane transporter activity / chloride channel activity ...Inorganic anion exchange by SLC26 transporters / sulfate transmembrane transporter activity / oxalate transmembrane transporter activity / sulfate transmembrane transport / solute:inorganic anion antiporter activity / bicarbonate transmembrane transporter activity / monoatomic anion transport / chloride transport / chloride transmembrane transporter activity / chloride channel activity / monoatomic ion transport / chloride transmembrane transport / ATPase binding / endosome membrane / apical plasma membrane / Golgi membrane / positive regulation of gene expression / endoplasmic reticulum membrane / cell surface / extracellular exosome / plasma membrane
Similarity search - Function
SLC26A/SulP transporter / SLC26A/SulP transporter domain / Sulfate permease family / STAS domain / STAS domain profile. / STAS domain / STAS domain superfamily
Similarity search - Domain/homology
Solute carrier family 26 member 9
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.6 Å
AuthorsChi XM / Chen Y
Funding support China, 2 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31800628 China
National Natural Science Foundation of China (NSFC)31971123 China
CitationJournal: 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
DepositionJul 3, 2020-
Header (metadata) releaseAug 26, 2020-
Map releaseAug 26, 2020-
UpdateMar 27, 2024-
Current statusMar 27, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.035
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.035
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7ch1
  • Surface level: 0.035
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30368.png

Downloads & links

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Map

FileDownload / File: emd_30368.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationcryo_EM map of SLC26A9
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.09 Å/pix.
x 320 pix.
= 349.12 Å		1.09 Å/pix.
x 320 pix.
= 349.12 Å		1.09 Å/pix.
x 320 pix.
= 349.12 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.091 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.035 / Movie #1: 0.035
Minimum - Maximum-0.076386064 - 0.18091722
Average (Standard dev.)0.00007194531 (±0.0034861367)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 349.12 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0911.0911.091
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z349.120349.120349.120
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ480480480
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-0.0760.1810.000

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Supplemental data

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Sample components

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Entire : SLC26A9

EntireName: SLC26A9
Components
  • Complex: SLC26A9
    • Protein or peptide: Solute carrier family 26 member 9
  • Ligand: CHLORIDE ION
  • Ligand: SODIUM ION
  • Ligand: water

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Supramolecule #1: SLC26A9

SupramoleculeName: SLC26A9 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Solute carrier family 26 member 9

MacromoleculeName: Solute carrier family 26 member 9 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 87.066945 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: 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

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Macromolecule #2: CHLORIDE ION

MacromoleculeName: CHLORIDE ION / type: ligand / ID: 2 / Number of copies: 4 / Formula: CL
Molecular weightTheoretical: 35.453 Da

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Macromolecule #3: SODIUM ION

MacromoleculeName: SODIUM ION / type: ligand / ID: 3 / Number of copies: 2
Molecular weightTheoretical: 22.99 Da

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Macromolecule #4: water

MacromoleculeName: water / type: ligand / ID: 4 / Number of copies: 76 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 48.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.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 assignmentType: OTHER
Final angle assignmentType: MAXIMUM LIKELIHOOD

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