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- PDB-6yuz: Homodimeric structure of the rBAT complex -

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Basic information

Entry
Database: PDB / ID: 6yuz
TitleHomodimeric structure of the rBAT complex
ComponentsNeutral and basic amino acid transport protein rBAT
KeywordsMEMBRANE PROTEIN / Membrane transporter Heteromeric amino acid transporter Human transporter
Function / homology
Function and homology information


basic amino acid transmembrane transporter activity / Defective SLC3A1 causes cystinuria (CSNU) / Defective SLC7A9 causes cystinuria (CSNU) / basic amino acid transport / L-cystine transmembrane transporter activity / L-cystine transport / L-glutamate transmembrane transport / amino acid transmembrane transporter activity / aspartate transmembrane transport / Amino acid transport across the plasma membrane ...basic amino acid transmembrane transporter activity / Defective SLC3A1 causes cystinuria (CSNU) / Defective SLC7A9 causes cystinuria (CSNU) / basic amino acid transport / L-cystine transmembrane transporter activity / L-cystine transport / L-glutamate transmembrane transport / amino acid transmembrane transporter activity / aspartate transmembrane transport / Amino acid transport across the plasma membrane / amino acid transport / vacuolar membrane / brush border membrane / gene expression / carbohydrate metabolic process / apical plasma membrane / protein heterodimerization activity / protein-containing complex binding / extracellular exosome / membrane / plasma membrane
Similarity search - Function
Oligo-1,6-glucosidase, domain 2 / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Glycosyl hydrolase, all-beta / Glycoside hydrolase superfamily
Similarity search - Domain/homology
Amino acid transporter heavy chain SLC3A1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsWu, D. / Safarian, S. / Michel, H.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Federal Ministry for Education and Research Germany
Max Planck Society Germany
CitationJournal: Proc Natl Acad Sci U S A / Year: 2020
Title: Structural basis for amino acid exchange by a human heteromeric amino acid transporter.
Authors: Di Wu / Tamara N Grund / Sonja Welsch / Deryck J Mills / Max Michel / Schara Safarian / Hartmut Michel /
Abstract: Heteromeric amino acid transporters (HATs) comprise a group of membrane proteins that belong to the solute carrier (SLC) superfamily. They are formed by two different protein components: a light ...Heteromeric amino acid transporters (HATs) comprise a group of membrane proteins that belong to the solute carrier (SLC) superfamily. They are formed by two different protein components: a light chain subunit from an SLC7 family member and a heavy chain subunit from the SLC3 family. The light chain constitutes the transport subunit whereas the heavy chain mediates trafficking to the plasma membrane and maturation of the functional complex. Mutation, malfunction, and dysregulation of HATs are associated with a wide range of pathologies or represent the direct cause of inherited and acquired disorders. Here we report the cryogenic electron microscopy structure of the neutral and basic amino acid transport complex (bAT1-rBAT) which reveals a heterotetrameric protein assembly composed of two heavy and light chain subunits, respectively. The previously uncharacterized interaction between two HAT units is mediated via dimerization of the heavy chain subunits and does not include participation of the light chain subunits. The bAT1 transporter adopts a LeuT fold and is captured in an inward-facing conformation. We identify an amino-acid-binding pocket that is formed by transmembrane helices 1, 6, and 10 and conserved among SLC7 transporters.
History
DepositionApr 27, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 20, 2021Provider: repository / Type: Initial release

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Assembly

Deposited unit
A: Neutral and basic amino acid transport protein rBAT
C: Neutral and basic amino acid transport protein rBAT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,72512
Polymers157,8752
Non-polymers1,85010
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area3730 Å2
ΔGint-10 kcal/mol
Surface area48910 Å2
MethodPISA

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Components

#1: Protein Neutral and basic amino acid transport protein rBAT / NBAT / D2h / Solute carrier family 3 member 1 / b(0 / +)-type amino acid transport protein


Mass: 78937.703 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SLC3A1, RBAT / Cell line (production host): FlpInTRex / Production host: Homo sapiens (human) / Strain (production host): HEK293 / Variant (production host): FlpInTRex / References: UniProt: Q07837
#2: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
Has ligand of interestN

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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: Homodimeric complex of rBAT / Type: COMPLEX / Details: 2 x rBAT / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 157.704 kDa/nm / Experimental value: YES
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human) / Strain: HEK293 / Plasmid: pACMV-teto
Buffer solutionpH: 7.5
Buffer component
IDConc.NameBuffer-ID
125 mMTris1
2150 mMNaClSodium chloride1
30.1 % (w/V)Digitonin1
SpecimenConc.: 2.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: C-flat-1.2/1.3 4C
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 283.15 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
2Topaz0.2.3particle selection
5Gctf1.06CTF correction
8Coot0.89model fitting
10PHENIXdev-3689model refinement
11RELION3.1initial Euler assignment
12RELION3.1final Euler assignment
13RELION3.1classification
14RELION3.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 92789 / Symmetry type: POINT

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