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

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Basic information

Entry
Database: PDB / ID: 9n5n
TitleStructure of VcINDY-alpha ketoglutarate complex in Ci-Ci conformation
ComponentsTransporter, NadC family
KeywordsTRANSPORT PROTEIN / Na(+)/dicarboxylate cotransporter(VcINDY) / Solute carries / Elevator type alternating access / 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
2-OXOGLUTARIC ACID / Transporter, NadC family
Similarity search - Component
Biological speciesVibrio cholerae O1 biovar El Tor str. N16961 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.35 Å
AuthorsLi, Y. / Daab, A. / Song, J.M. / Marden, J.J. / Mulligan, C. / Wang, D.N.
Funding support United States, United Kingdom, 6items
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, J.M. / Marden, J.J. / Mulligan, C. / Wang, D.N.
History
DepositionFeb 4, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 29, 2026Provider: repository / Type: Initial release
Revision 1.0Jul 29, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 29, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Jul 29, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jul 29, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 29, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 29, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 29, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Jul 29, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transporter, NadC family
B: Transporter, NadC family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,5828
Polymers99,1982
Non-polymers3846
Water362
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Transporter, NadC family


Mass: 49598.930 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Indy_Vibrio, wild type
Source: (gene. exp.) Vibrio cholerae O1 biovar El Tor str. N16961 (bacteria)
Gene: VC_A0025 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9KNE0
#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID


Mass: 146.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H6O5
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Dimer of VcINDY in complex with alpha ketoglutarate / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 0.192 MDa / Experimental value: YES
Source (natural)Organism: Vibrio cholerae O1 biovar El Tor str. N16961 (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
125 mMTris(hydroxymethyl)aminomethaneTris1
2100 mMsodium chlorideNaCl1
30.2 %Lauryl maltose neopentyl glycolLMNG1
420 mMalpha ketoglutaratea-KG1
SpecimenConc.: 4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: Hold 10s before glow discharge / Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: UltrAuFoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 281.15 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 105000 X / Calibrated magnification: 105000 X / Nominal defocus max: 1600 nm / Nominal defocus min: 1200 nm / Calibrated defocus min: 800 nm / Calibrated defocus max: 3000 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 80 K / Temperature (min): 80 K / Residual tilt: 0.05 mradians
Image recordingAverage exposure time: 1.8 sec. / Electron dose: 53.11 e/Å2 / Film or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 3948
Details: 3948 untilted images were collected in super resolution mode at 40 frames per micrograph
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV
Image scansSampling size: 5 µm / Width: 5760 / Height: 4092

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Processing

EM software
IDNameVersionCategory
1Warp1.0.9particle selection
2Topaz0.2.5aparticle selection
3Leginon3.5image acquisition
5cryoSPARCv 4.4.1CTF correction
8UCSF Chimera1.15model fitting
9Coot0.9.6model fitting
11PHENIX1.20.1_4487model refinement
12cryoSPARCv 4.4.1initial Euler assignment
13cryoSPARCv 4.4.1final Euler assignment
14cryoSPARCv 4.4.1classification
15cryoSPARCV 4.4.13D reconstruction
Image processingDetails: The micrographs with an overall resolution worse than 5 angstroms were excluded
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 3717199 / Details: Particles were selected from 3948 untilted images
3D reconstructionResolution: 2.35 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 290548 / Algorithm: FOURIER SPACE / Details: C2 / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingB value: 52.28 / Protocol: OTHER / Space: REAL / Target criteria: cross-correlation coefficient
Details: Initial local fitting was done using Chimera and then coot was used for ajustment.
Atomic model buildingPDB-ID: 7T9F

7t9f


Pdb chain-ID: AB / Accession code: 7T9F / Chain residue range: 1-462 / Details: the whole model was used / Pdb chain residue range: 1-462 / Source name: PDB / Type: experimental model

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