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- EMDB-21904: Structure of VcINDY-Na+ in amphipol -

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Basic information

Entry
Database: EMDB / ID: EMD-21904
TitleStructure of VcINDY-Na+ in amphipol
Map dataVcINDY-Na+ in amphipol
Sample
  • Organelle or cellular component: Dimeric structure of VcINDY in complex with sodium
    • Protein or peptide: VcINDY
KeywordsTransporter / MEMBRANE PROTEIN
Function / homology
Function and homology information


succinate transmembrane transporter activity / transmembrane transporter activity / transmembrane transport / identical protein binding / plasma membrane
Similarity search - Function
Citrate transporter-like domain / Citrate transporter / Sodium/sulphate symporter, conserved site / Sodium:sulfate symporter family signature. / Solute carrier family 13
Similarity search - Domain/homology
Transporter, NadC family
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.16 Å
AuthorsSauer DB / Marden JJ
Funding support United States, 3 items
OrganizationGrant numberCountry
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) 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: 7.01
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 7.01
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6wu3
  • Surface level: 7.01
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_21904.png

Downloads & links

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Map

FileDownload / File: emd_21904.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationVcINDY-Na+ in amphipol
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.57 Å/pix.
x 384 pix.
= 219.264 Å		0.57 Å/pix.
x 384 pix.
= 219.264 Å		0.57 Å/pix.
x 384 pix.
= 219.264 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.571 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 7.01 / Movie #1: 7.01
Minimum - Maximum-19.659732999999999 - 32.277755999999997
Average (Standard dev.)0.000000000002788 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 219.26399 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.5710.5710.571
M x/y/z384384384
origin x/y/z0.0000.0000.000
length x/y/z219.264219.264219.264
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-19.66032.2780.000

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Supplemental data

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Half map: VcINDY-Na+ in amphipol

Fileemd_21904_half_map_1.map
AnnotationVcINDY-Na+ in amphipol
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: VcINDY-Na+ in amphipol

Fileemd_21904_half_map_2.map
AnnotationVcINDY-Na+ in amphipol
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Dimeric structure of VcINDY in complex with sodium

EntireName: Dimeric structure of VcINDY in complex with sodium
Components
  • Organelle or cellular component: Dimeric structure of VcINDY in complex with sodium
    • Protein or peptide: VcINDY

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Supramolecule #1: Dimeric structure of VcINDY in complex with sodium

SupramoleculeName: Dimeric structure of VcINDY in complex with sodium / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Vibrio cholerae (bacteria)

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Macromolecule #1: VcINDY

MacromoleculeName: VcINDY / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Vibrio cholerae (bacteria)
Molecular weightTheoretical: 48.157359 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: REWFLHRNSL IVLADVALFL ALYHFLPFEH NVVLGISMLA FIAVLWLTEA LHVTVTAILV PVMAVFFGIF ETQAALNNFA NSIIFLFLG GFALAAAMHH QGLDKVIADK VLAMAQGKMS VAVFMLFGVT ALLSMWISNT ATAAMMLPLV LGVLSKVDAD K QRSTYVFV ...String:
REWFLHRNSL IVLADVALFL ALYHFLPFEH NVVLGISMLA FIAVLWLTEA LHVTVTAILV PVMAVFFGIF ETQAALNNFA NSIIFLFLG GFALAAAMHH QGLDKVIADK VLAMAQGKMS VAVFMLFGVT ALLSMWISNT ATAAMMLPLV LGVLSKVDAD K QRSTYVFV LLGVAYSASI GGIATLVGSP PNAIAAAEVG LSFTDWMKFG LPTAMMMLPM AIAILYFLLK PTLNGMFELD RA PVNWDKG KVVTLGIFGL TVFLWIFSSP INAALGGFKS FDTLVALGAI LMLSFARVVH WKEIQKTADW GVLLLFGGGL CLS NVLKQT GTSVFLANAL SDMVSHMGIF VVILVVATFV VFLTEFASNT ASAALLIPVF ATVAEAFGMS PVLLSVLIAV AASC AFMLP VATPPNAIVF ASGHIKQSEM MRVGLYLNIA CIGLLTAIAM LFWQ

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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 TALOS ARCTICA
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Number real images: 1670 / Average exposure time: 12.0 sec. / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 36000
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.16 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2.12) / Number images used: 192836
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 2.12)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 2.12)

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