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- EMDB-48929: Structure of VcINDY-alpha ketoglutarate complex in Ci-Ci conformation -

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Basic information

Entry
Database: EMDB / ID: EMD-48929
TitleStructure of VcINDY-alpha ketoglutarate complex in Ci-Ci conformation
Map datasharpened map of VcINDY in alpha ketoglutarate
Sample
  • Complex: Dimer of VcINDY in complex with alpha ketoglutarate
    • Protein or peptide: Transporter, NadC family
  • Ligand: SODIUM ION
  • Ligand: 2-OXOGLUTARIC ACID
  • Ligand: water
KeywordsNa(+)/dicarboxylate cotransporter(VcINDY) / Solute carries / Elevator type alternating access / membrane protein / TRANSPORT 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 O1 biovar El Tor str. N16961 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.35 Å
AuthorsLi Y / Daab A / Song JM / Marden JJ / Mulligan C / Wang DN
Funding support United States, United Kingdom, 6 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)R01DK135088 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI165782 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM121994 United States
The G. Harold and Leila Y. Mathers FoundationMF-2002-00671 United States
Biotechnology and Biological Sciences Research Council (BBSRC)BB/V007424/1 United Kingdom
CitationJournal: To Be Published
Title: Structure of VcINDY-alpha ketoglutarate complex in Ci-Ci conformation
Authors: Li Y / Daab A / Song JM / Marden JJ / Mulligan C / Wang DN
History
DepositionFeb 4, 2025-
Header (metadata) releaseJul 29, 2026-
Map releaseJul 29, 2026-
UpdateJul 29, 2026-
Current statusJul 29, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_48929.png

Downloads & links

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Map

FileDownload / File: emd_48929.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpened map of VcINDY in alpha ketoglutarate
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 256 pix.
= 211.2 Å		0.83 Å/pix.
x 256 pix.
= 211.2 Å		0.83 Å/pix.
x 256 pix.
= 211.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.825 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.32
Minimum - Maximum-1.6797392 - 2.6104867
Average (Standard dev.)0.0013813273 (±0.077105336)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 211.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_48929_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: unsharpened map of VcINDY in alpha ketoglutarate

Fileemd_48929_additional_1.map
Annotationunsharpened map of VcINDY in alpha ketoglutarate
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map B of VcINDY in alpha ketoglutarate

Fileemd_48929_half_map_1.map
Annotationhalf map B of VcINDY in alpha ketoglutarate
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map A of VcINDY in alpha ketoglutarate

Fileemd_48929_half_map_2.map
Annotationhalf map A of VcINDY in alpha ketoglutarate
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Dimer of VcINDY in complex with alpha ketoglutarate

EntireName: Dimer of VcINDY in complex with alpha ketoglutarate
Components
  • Complex: Dimer of VcINDY in complex with alpha ketoglutarate
    • Protein or peptide: Transporter, NadC family
  • Ligand: SODIUM ION
  • Ligand: 2-OXOGLUTARIC ACID
  • Ligand: water

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Supramolecule #1: Dimer of VcINDY in complex with alpha ketoglutarate

SupramoleculeName: Dimer of VcINDY in complex with alpha ketoglutarate / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Vibrio cholerae O1 biovar El Tor str. N16961 (bacteria)
Molecular weightTheoretical: 192 KDa

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Macromolecule #1: Transporter, NadC family

MacromoleculeName: Transporter, NadC family / type: protein_or_peptide / ID: 1 / Details: Indy_Vibrio, wild type / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Vibrio cholerae O1 biovar El Tor str. N16961 (bacteria)
Molecular weightTheoretical: 49.59893 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MNRNDSVPLP TNTREWFLHR NSLIVLADVA LFLALYHFLP FEHNVVLGIS MLAFIAVLWL TEALHVTVTA ILVPVMAVFF GIFETQAAL NNFANSIIFL FLGGFALAAA MHHQGLDKVI ADKVLAMAQG KMSVAVFMLF GVTALLSMWI SNTATAAMML P LVLGVLSK ...String:
MNRNDSVPLP TNTREWFLHR NSLIVLADVA LFLALYHFLP FEHNVVLGIS MLAFIAVLWL TEALHVTVTA ILVPVMAVFF GIFETQAAL NNFANSIIFL FLGGFALAAA MHHQGLDKVI ADKVLAMAQG KMSVAVFMLF GVTALLSMWI SNTATAAMML P LVLGVLSK VDADKQRSTY VFVLLGVAYS ASIGGIATLV GSPPNAIAAA EVGLSFTDWM KFGLPTAMMM LPMAIAILYF LL KPTLNGM FELDRAPVNW DKGKVVTLGI FGLTVFLWIF SSPINAALGG FKSFDTLVAL GAILMLSFAR VVHWKEIQKT ADW GVLLLF GGGLCLSNVL KQTGTSVFLA NALSDMVSHM GIFVVILVVA TFVVFLTEFA SNTASAALLI PVFATVAEAF GMSP VLLSV LIAVAASCAF MLPVATPPNA IVFASGHIKQ SEMMRVGLYL NIACIGLLTA IAMLFWQ

UniProtKB: Transporter, NadC family

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Macromolecule #2: SODIUM ION

MacromoleculeName: SODIUM ION / type: ligand / ID: 2 / Number of copies: 4
Molecular weightTheoretical: 22.99 Da

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Macromolecule #3: 2-OXOGLUTARIC ACID

MacromoleculeName: 2-OXOGLUTARIC ACID / type: ligand / ID: 3 / Number of copies: 2 / Formula: AKG
Molecular weightTheoretical: 146.098 Da
Chemical component information

ChemComp-AKG:
2-OXOGLUTARIC ACID

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Macromolecule #4: water

MacromoleculeName: water / type: ligand / ID: 4 / Number of copies: 2 / 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

Concentration4 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
25.0 mMTrisTris(hydroxymethyl)aminomethane
100.0 mMNaClsodium chloride
0.2 %LMNGLauryl maltose neopentyl glycol
20.0 mMa-KGalpha ketoglutarate
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Support film - Film thickness: 50 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 2 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.026000000000000002 kPa / Details: Hold 10s before glow discharge
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
TemperatureMin: 80.0 K / Max: 80.0 K
Alignment procedureComa free - Residual tilt: 0.05 mrad
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 1 / Number real images: 3948 / Average exposure time: 1.8 sec. / Average electron dose: 53.11 e/Å2
Details: 3948 untilted images were collected in super resolution mode at 40 frames per micrograph
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Calibrated defocus max: 3.0 µm / Calibrated defocus min: 0.8 µm / Calibrated magnification: 105000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.6 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 105000
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

DetailsThe micrographs with an overall resolution worse than 5 angstroms were excluded
Particle selectionNumber selected: 3717199 / Details: Particles were selected from 3948 untilted images
CTF correctionSoftware - Name: cryoSPARC (ver. v 4.4.1) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: Ab -initio reconstruction in cryoSPARC
Final reconstructionNumber classes used: 1 / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.35 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. V 4.4.1) / Details: C2 / Number images used: 290548
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. v 4.4.1) / Details: branch-and-bound maximum likelihood
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. v 4.4.1) / Details: branch-and-bound maximum likelihood
Final 3D classificationNumber classes: 3 / Software - Name: cryoSPARC (ver. v 4.4.1)
Details: Number of particles for 3 classes are 11245, 290548, 44980. The reported resolutions are 8.51, 4.22, 6.95 angstoms, respectively.
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

7t9f


Chain - Chain ID: AB / Chain - Residue range: 1-462 / Chain - Source name: PDB / Chain - Initial model type: experimental model / Details: the whole model was used
DetailsInitial local fitting was done using Chimera and then coot was used for ajustment.
RefinementSpace: REAL / Protocol: OTHER / Overall B value: 52.28 / Target criteria: cross-correlation coefficient
Output model

PDB-9n5n:
Structure of VcINDY-alpha ketoglutarate complex in Ci-Ci conformation

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