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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 data
SampleDimeric structure of VcINDY in complex with sodium:
VcINDY
Biological speciesVibrio cholerae (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.16 Å
AuthorsSauer DB / Marden JJ / Song JM / Wang DN
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 Diabetes and Digestive and Kidney Disease (NIH/NIDDK) United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM121994 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.
Validation ReportPDB-ID: 6wu3

SummaryFull reportAbout validation report
History
DepositionMay 4, 2020-
Header (metadata) releaseSep 16, 2020-
Map releaseSep 16, 2020-
UpdateSep 16, 2020-
Current statusSep 16, 2020Processing 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

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)
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
Contour LevelBy AUTHOR: 7.01 / Movie #1: 7.01
Minimum - Maximum-19.659733 - 32.277756
Average (Standard dev.)0.0000000000 (±1)
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

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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

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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 / Number of components: 2

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Component #1: cellular-component, Dimeric structure of VcINDY in complex with sodium

Cellular-componentName: Dimeric structure of VcINDY in complex with sodium / Recombinant expression: No
SourceSpecies: Vibrio cholerae (bacteria)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #2: protein, VcINDY

ProteinName: VcINDY / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 48.157359 kDa
SourceSpecies: Vibrio cholerae (bacteria)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionpH: 7.4
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 277 K / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
ImagingMicroscope: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 40 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 36000 X (nominal) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 1000.0 - 2500.0 nm
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 1670

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C2 (2 fold cyclic) / Number of projections: 192836
3D reconstructionSoftware: cryoSPARC / Resolution: 3.16 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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