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- PDB-8wk6: Human AGT1-rBAT complex in the apo-state -

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Basic information

Entry
Database: PDB / ID: 8wk6
TitleHuman AGT1-rBAT complex in the apo-state
Components
  • Amino acid transporter heavy chain SLC3A1
  • Solute carrier family 7 member 13
KeywordsMEMBRANE PROTEIN / complex / transport amino acid / leu-T fold
Function / homology
Function and homology information


Defective SLC3A1 causes cystinuria (CSNU) / Defective SLC7A9 causes cystinuria (CSNU) / basic amino acid transport / basic amino acid transmembrane transporter activity / L-cystine transmembrane transporter activity / L-cystine transport / amino acid transmembrane transport / L-amino acid transmembrane transporter activity / aspartate transmembrane transport / L-glutamate transmembrane transport ...Defective SLC3A1 causes cystinuria (CSNU) / Defective SLC7A9 causes cystinuria (CSNU) / basic amino acid transport / basic amino acid transmembrane transporter activity / L-cystine transmembrane transporter activity / L-cystine transport / amino acid transmembrane transport / L-amino acid transmembrane transporter activity / aspartate transmembrane transport / L-glutamate transmembrane transport / amino acid transmembrane transporter activity / Amino acid transport across the plasma membrane / vacuolar membrane / antiporter activity / amino acid transport / 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
: / 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
Amino acid transporter heavy chain SLC3A1 / Solute carrier family 7 member 13
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.64 Å
AuthorsYan, R.H. / Shi, T.H. / Dong, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Human AGT1-rBAT complex in the apo-state
Authors: Yan, R.H. / Shi, T.H. / Dong, J.
History
DepositionSep 27, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Apr 2, 2025Provider: repository / Type: Initial release
Revision 1.0Apr 2, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 2, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 2, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 2, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 2, 2025Data 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
C: Amino acid transporter heavy chain SLC3A1
B: Solute carrier family 7 member 13
D: Amino acid transporter heavy chain SLC3A1
A: Solute carrier family 7 member 13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)282,35716
Polymers278,0334
Non-polymers4,32412
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Amino acid transporter heavy chain SLC3A1 / D2h / Neutral and basic amino acid transport protein / NBAT / Solute carrier family 3 member 1 / ...D2h / Neutral and basic amino acid transport protein / NBAT / Solute carrier family 3 member 1 / b(0 / +)-type amino acid transporter-related heavy chain / rBAT


Mass: 83856.781 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SLC3A1, NBAT / Production host: Homo sapiens (human) / References: UniProt: Q07837
#2: Protein Solute carrier family 7 member 13 / Sodium-independent aspartate/glutamate transporter 1 / X-amino acid transporter 2


Mass: 55159.797 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SLC7A13, AGT1, XAT2 / Production host: Homo sapiens (human) / References: UniProt: Q8TCU3
#3: Polysaccharide
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
Has ligand of interestN
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: Human AGT1-rBAT complex in the apo-state / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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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: OTHER
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 5000 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.64 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 462604 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00217916
ELECTRON MICROSCOPYf_angle_d0.51124380
ELECTRON MICROSCOPYf_dihedral_angle_d12.0982442
ELECTRON MICROSCOPYf_chiral_restr0.0422818
ELECTRON MICROSCOPYf_plane_restr0.0043012

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