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- EMDB-21903: Structure of the LaINDY-malate complex -

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Basic information

Entry
Database: EMDB / ID: EMD-21903
TitleStructure of the LaINDY-malate complex
Map dataLaINDY-malate complex
Sample
  • Organelle or cellular component: LaINDY-malate complex
    • Protein or peptide: DASS family sodium-coupled anion symporter
  • Ligand: HEXANE
  • Ligand: DECANE
  • Ligand: N-OCTANEOctane
KeywordsTransporter / Structural Genomics / PSI-Biology / New York Consortium on Membrane Protein Structure / NYCOMPS / MEMBRANE PROTEIN
Function / homologyCitrate carrier CitT-related / Sodium:sulfate symporter transmembrane region / Solute carrier family 13 / transmembrane transporter activity / membrane => GO:0016020 / membrane / DASS family sodium-coupled anion symporter / 2-oxoglutarate-malate translocator
Function and homology information
Biological speciesLactobacillus acidophilus (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.36 Å
AuthorsSauer DB / Marden JJ
Funding support United States, 4 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U54GM095315 United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)R01NS108151 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM121994 United States
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)R01DK099023 United States
CitationJournal: Elife / Year: 2020
Title: Structural basis for the reaction cycle of DASS dicarboxylate transporters.
Authors: David B Sauer / Noah Trebesch / Jennifer J Marden / Nicolette Cocco / Jinmei Song / Akiko Koide / Shohei Koide / Emad Tajkhorshid / Da-Neng Wang /
Abstract: Citrate, α-ketoglutarate and succinate are TCA cycle intermediates that also play essential roles in metabolic signaling and cellular regulation. These di- and tricarboxylates are imported into the ...Citrate, α-ketoglutarate and succinate are TCA cycle intermediates that also play essential roles in metabolic signaling and cellular regulation. These di- and tricarboxylates are imported into the cell by the divalent anion sodium symporter (DASS) family of plasma membrane transporters, which contains both cotransporters and exchangers. While DASS proteins transport substrates via an elevator mechanism, to date structures are only available for a single DASS cotransporter protein in a substrate-bound, inward-facing state. We report multiple cryo-EM and X-ray structures in four different states, including three hitherto unseen states, along with molecular dynamics simulations, of both a cotransporter and an exchanger. Comparison of these outward- and inward-facing structures reveal how the transport domain translates and rotates within the framework of the scaffold domain through the transport cycle. Additionally, we propose that DASS transporters ensure substrate coupling by a charge-compensation mechanism, and by structural changes upon substrate release.
History
DepositionMay 4, 2020-
Header (metadata) releaseSep 16, 2020-
Map releaseSep 16, 2020-
UpdateMar 6, 2024-
Current statusMar 6, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 5.33
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 5.33
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6wu2
  • Surface level: 5.33
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_21903.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationLaINDY-malate complex
Voxel sizeX=Y=Z: 0.5295 Å
Density
Contour LevelBy AUTHOR: 5.33 / Movie #1: 5.33
Minimum - Maximum-17.419167999999999 - 24.840199999999999
Average (Standard dev.)-0.000000000003342 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 203.328 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.52950.52950.5295
M x/y/z384384384
origin x/y/z0.0000.0000.000
length x/y/z203.328203.328203.328
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ310310310
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS384384384
D min/max/mean-17.41924.840-0.000

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Supplemental data

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Half map: LaINDY-malate complex

Fileemd_21903_half_map_1.map
AnnotationLaINDY-malate complex
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: LaINDY-malate complex

Fileemd_21903_half_map_2.map
AnnotationLaINDY-malate complex
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Sample components

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Entire : LaINDY-malate complex

EntireName: LaINDY-malate complex
Components
  • Organelle or cellular component: LaINDY-malate complex
    • Protein or peptide: DASS family sodium-coupled anion symporter
  • Ligand: HEXANE
  • Ligand: DECANE
  • Ligand: N-OCTANEOctane

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Supramolecule #1: LaINDY-malate complex

SupramoleculeName: LaINDY-malate complex / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Lactobacillus acidophilus (bacteria)

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Macromolecule #1: DASS family sodium-coupled anion symporter

MacromoleculeName: DASS family sodium-coupled anion symporter / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Lactobacillus acidophilus (bacteria)
Molecular weightTheoretical: 56.563758 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MHHHHHHHHH HSSGVDLGTE NLYFQSNAMK TLEKVNYKGF IWPLAVGIVL WLITPWRPGG LSVQAWEMFA IFVATIVGCI TKPLPIGGT TLLGMVVTVL VGLAPVKDVV NSKGVVIQTG ILSSFGNSAA WLIAMAFIMA HGISKTGLGN RVAYVMIEKF G KRSIGIGY ...String:
MHHHHHHHHH HSSGVDLGTE NLYFQSNAMK TLEKVNYKGF IWPLAVGIVL WLITPWRPGG LSVQAWEMFA IFVATIVGCI TKPLPIGGT TLLGMVVTVL VGLAPVKDVV NSKGVVIQTG ILSSFGNSAA WLIAMAFIMA HGISKTGLGN RVAYVMIEKF G KRSIGIGY AITGLELMMG ALIPSNSART GGVTWPVVES ISKSYDSKPN DPSRKKIGAY LDFMAFHANI LSTALFITGA AP NLVAQQM AAQKGYQMSW VSWFWAALVP VLVATVIIPL VIYKMYPPEV KETPNAKNWA DDKLKEMGPI SKPEKIMATV FCL AILLWV LSGFFKIPQL DSAFVAFLAV TLLLITGVLS MEDALHETGA WNILIWLSIL IFMAGKLISY GFIAWFAKFI QSEV HGINW GLVLVVLILL MFYTHYFFAS GTAHMTALYL PFLTVATAMG APLGLSAMLL AFTGVINAST THYANGPASI LATTG YVKQ SEWWKMNFIL GLIYMVIFGI VGTIWMKIIG IW

UniProtKB: DASS family sodium-coupled anion symporter

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Macromolecule #2: HEXANE

MacromoleculeName: HEXANE / type: ligand / ID: 2 / Number of copies: 6 / Formula: HEX
Molecular weightTheoretical: 86.175 Da
Chemical component information

ChemComp-HEX:
HEXANE / Hexane

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Macromolecule #3: DECANE

MacromoleculeName: DECANE / type: ligand / ID: 3 / Number of copies: 2 / Formula: D10
Molecular weightTheoretical: 142.282 Da
Chemical component information

ChemComp-D10:
DECANE / Decane

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Macromolecule #4: N-OCTANE

MacromoleculeName: N-OCTANE / type: ligand / ID: 4 / Number of copies: 2 / Formula: OCT
Molecular weightTheoretical: 114.229 Da
Chemical component information

ChemComp-OCT:
N-OCTANE / Octane

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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: 7.4
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 81000
Specialist opticsEnergy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 3255 / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 2.12)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 2.12)
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.36 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2.12) / Number images used: 277286

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