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- EMDB-4998: Cryo-EM density of murine Solute Carrier 26 family member A9 (Slc... -

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Basic information

Entry
Database: EMDB / ID: EMD-4998
TitleCryo-EM density of murine Solute Carrier 26 family member A9 (Slc26a9) anion transporter in an intermediate state
Map data
Sample
  • Complex: Murine Solute Carrier 26 family member A9 (Slc26a9) in MSP1E3D1 nanodisc
    • Protein or peptide: Solute carrier family 26 member 9,Solute carrier family 26 member 9
KeywordsSLC26 family / anion transporter / membrane protein structure / transport mechanism / cryo-EM / single particle / MEMBRANE PROTEIN
Function / homology
Function and homology information


Multifunctional anion exchangers / regulation of pH / chloride:bicarbonate antiporter activity / solute:inorganic anion antiporter activity / bicarbonate transport / bicarbonate transmembrane transporter activity / monoatomic anion transport / chloride transport / chloride channel activity / ATPase binding ...Multifunctional anion exchangers / regulation of pH / chloride:bicarbonate antiporter activity / solute:inorganic anion antiporter activity / bicarbonate transport / bicarbonate transmembrane transporter activity / monoatomic anion transport / chloride transport / chloride channel activity / ATPase binding / endosome membrane / apical plasma membrane / Golgi membrane / positive regulation of gene expression / endoplasmic reticulum membrane / cell surface / identical protein binding
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 / Solute carrier family 26 member 9
Similarity search - Component
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.77 Å
AuthorsSawicka M / Walter JD
Funding support1 items
OrganizationGrant numberCountry
Swiss National Science Foundation31003A_163421
CitationJournal: Elife / Year: 2019
Title: Cryo-EM structures and functional characterization of murine Slc26a9 reveal mechanism of uncoupled chloride transport.
Authors: Justin D Walter / Marta Sawicka / Raimund Dutzler /
Abstract: The epithelial anion transporter SLC26A9 contributes to airway surface hydration and gastric acid production. Colocalizing with CFTR, SLC26A9 has been proposed as a target for the treatment of cystic ...The epithelial anion transporter SLC26A9 contributes to airway surface hydration and gastric acid production. Colocalizing with CFTR, SLC26A9 has been proposed as a target for the treatment of cystic fibrosis. To provide molecular details of its transport mechanism, we present cryo-EM structures and a functional characterization of murine Slc26a9. These structures define the general architecture of eukaryotic SLC26 family members and reveal an unusual mode of oligomerization which relies predominantly on the cytosolic STAS domain. Our data illustrates conformational transitions of Slc26a9, supporting a rapid alternate-access mechanism which mediates uncoupled chloride transport with negligible bicarbonate or sulfate permeability. The characterization of structure-guided mutants illuminates the properties of the ion transport path, including a selective anion binding site located in the center of a mobile module within the transmembrane domain. This study thus provides a structural foundation for the understanding of the entire SLC26 family and potentially facilitates their therapeutic exploitation.
History
DepositionMay 23, 2019-
Header (metadata) releaseJul 24, 2019-
Map releaseJul 24, 2019-
UpdateMay 22, 2024-
Current statusMay 22, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.103
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.103
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6rtf
  • Surface level: 0.103
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4998.png

Downloads & links

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Map

FileDownload / File: emd_4998.map.gz / Format: CCP4 / Size: 47.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 232 pix.
= 249.4 Å		1.08 Å/pix.
x 232 pix.
= 249.4 Å		1.08 Å/pix.
x 232 pix.
= 249.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.075 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.103 / Movie #1: 0.103
Minimum - Maximum-0.23323655 - 0.4097729
Average (Standard dev.)0.0032016425 (±0.016340526)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions232232232
Spacing232232232
CellA=B=C: 249.40001 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0751.0751.075
M x/y/z232232232
origin x/y/z0.0000.0000.000
length x/y/z249.400249.400249.400
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS232232232
D min/max/mean-0.2330.4100.003

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Supplemental data

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Mask #1

Fileemd_4998_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_4998_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_4998_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : Murine Solute Carrier 26 family member A9 (Slc26a9) in MSP1E3D1 n...

EntireName: Murine Solute Carrier 26 family member A9 (Slc26a9) in MSP1E3D1 nanodisc
Components
  • Complex: Murine Solute Carrier 26 family member A9 (Slc26a9) in MSP1E3D1 nanodisc
    • Protein or peptide: Solute carrier family 26 member 9,Solute carrier family 26 member 9

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Supramolecule #1: Murine Solute Carrier 26 family member A9 (Slc26a9) in MSP1E3D1 n...

SupramoleculeName: Murine Solute Carrier 26 family member A9 (Slc26a9) in MSP1E3D1 nanodisc
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Mus musculus (house mouse)

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Macromolecule #1: Solute carrier family 26 member 9,Solute carrier family 26 member 9

MacromoleculeName: Solute carrier family 26 member 9,Solute carrier family 26 member 9
type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 70.597641 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MNQPRPRYVV DRAAYSLSLF DDEFEKKDRA YPVGEKLRNT FRCSSAKFKA FVFGLLPVLS WLPKYKIKDY IIPDLLGGLS GGCIQVPQG MAFALLANLP AVNGLYSSFF PLLTYFFLGG IHQMVPGTFA VISILVGNIC LQLAPESKFQ IFNNVTNETY V DTAAMEAE ...String:
MNQPRPRYVV DRAAYSLSLF DDEFEKKDRA YPVGEKLRNT FRCSSAKFKA FVFGLLPVLS WLPKYKIKDY IIPDLLGGLS GGCIQVPQG MAFALLANLP AVNGLYSSFF PLLTYFFLGG IHQMVPGTFA VISILVGNIC LQLAPESKFQ IFNNVTNETY V DTAAMEAE RLHVSATLAC LTAVIQMALG FMQFGFVAIY LSESFIRGFM TAAGLQILIS VLKYIFGLTI PSYTGPGSIV FT FIDICKN LPHTNIASLI FALVSGVFLV LVKELNARYM HKIHFPIPTE MIVVVVATAI SGSCKMPKKY HMQIVGEIRQ GFP TPVAPM VSQWKDMVGT AFSLAIVGYV INLAMGRTLA SKHGYDVDSN QEMIALGCSN FFGSFFKIHV ICCALSVTLA VDGA GGKSQ VASLCVSLVV MITMLVLGSY LYPLPKAVLG ALIAVNLKNS LKQLTDPYYL WRKSKLDCCV WVVSFLSSFF LSLPY GVAV GVAFSILVVI FQTQFRNGST LAQVMDTDIY VNPKTYNRAQ EIAGVKIVTY CSPLYFANSE IFRQKVIAKT GMDGST FHT LILDMSGVSF VDLMGIKALA KLSSTYEKIG VQIFLVNIHA QVYNDISHGG VFEDGCVQRS HVFPSIHDAV LFAQANA RE A

UniProtKB: Solute carrier family 26, member 9, Solute carrier family 26, member 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

Concentration1 mg/mL
BufferpH: 7.4
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI POLARA 300
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number real images: 3134 / Average exposure time: 0.25 sec. / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 37313 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal magnification: 37313
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 711032
Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 7.77 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 17442
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
FSC plot (resolution estimation)

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