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- PDB-6yup: Heterotetrameric structure of the rBAT-b(0,+)AT1 complex -

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Basic information

Entry
Database: PDB / ID: 6yup
TitleHeterotetrameric structure of the rBAT-b(0,+)AT1 complex
Components
  • Neutral and basic amino acid transport protein rBAT
  • b(0,+)-type amino acid transporter 1
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 / broad specificity neutral L-amino acid:basic L-amino acid antiporter activity / L-cystine transmembrane transporter activity / L-cystine transport / L-glutamate transmembrane transport / aspartate transmembrane transport / amino acid transmembrane transport ...basic amino acid transmembrane transporter activity / Defective SLC3A1 causes cystinuria (CSNU) / Defective SLC7A9 causes cystinuria (CSNU) / basic amino acid transport / broad specificity neutral L-amino acid:basic L-amino acid antiporter activity / L-cystine transmembrane transporter activity / L-cystine transport / L-glutamate transmembrane transport / aspartate transmembrane transport / amino acid transmembrane transport / neutral amino acid transport / amino acid transmembrane transporter activity / Amino acid transport across the plasma membrane / neutral L-amino acid transmembrane transporter activity / Basigin interactions / antiporter activity / vacuolar membrane / amino acid transport / brush border membrane / peptide antigen binding / gene expression / protein-containing complex assembly / carbohydrate metabolic process / protein heterodimerization activity / apical plasma membrane / protein-containing complex binding / extracellular exosome / membrane / plasma membrane
Similarity search - Function
: / Amino acid/polyamine transporter I / Amino acid permease / 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
b(0,+)-type amino acid transporter 1 / Amino acid transporter heavy chain SLC3A1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 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
Revision 1.1Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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Structure visualization

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  • EMDB-10933
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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
D: b(0,+)-type amino acid transporter 1
E: b(0,+)-type amino acid transporter 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)266,75714
Polymers264,9074
Non-polymers1,85010
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_5551

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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: Protein b(0,+)-type amino acid transporter 1 / b(0 / +)AT1 / Glycoprotein-associated amino acid transporter b0 / +AT1 / Solute carrier family 7 member 9


Mass: 53515.992 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SLC7A9, BAT1 / Cell line (production host): FlpInTRex / Production host: Homo sapiens (human) / Strain (production host): HEK293 / Variant (production host): FlpInTRex / References: UniProt: P82251
#3: 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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
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
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY

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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: Heterotetrameric complex of rBAT and b(0,+)AT1 / Type: COMPLEX / Details: 2 x rBAT 2 x b(0,+)AT1 / Entity ID: #1-#2 / Source: RECOMBINANT
Molecular weightValue: 264.666 kDa/nm / Experimental value: YES
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human) / Strain: HEK293 / Plasmid: pcDNA5.1/pACMV-teto
Buffer solutionpH: 7.5
Buffer component
IDConc.NameBuffer-ID
125 mMTris1
2150 mMNaCl1
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 FIELD
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1RELION3.1particle selection
2Topaz0.2.3particle selection
5Gctf1.06CTF correction
8Coot0.89model fitting
10RELION3.1initial Euler assignment
11RELION3.1final Euler assignment
13RELION3.13D reconstruction
14PHENIXdev-3689model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 92789 / Symmetry type: POINT

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