7NF6

Ovine b0,+AT-rBAT heterodimer


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.05 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Ca 2+ -mediated higher-order assembly of heterodimers in amino acid transport system b 0,+ biogenesis and cystinuria.

Lee, Y.Wiriyasermkul, P.Kongpracha, P.Moriyama, S.Mills, D.J.Kuhlbrandt, W.Nagamori, S.

(2022) Nat Commun 13: 2708-2708

  • DOI: https://doi.org/10.1038/s41467-022-30293-9
  • Primary Citation of Related Structures:  
    7NF6, 7NF7, 7NF8

  • PubMed Abstract: 

    Cystinuria is a genetic disorder characterized by overexcretion of dibasic amino acids and cystine, causing recurrent kidney stones and kidney failure. Mutations of the regulatory glycoprotein rBAT and the amino acid transporter b 0,+ AT, which constitute system b 0,+ , are linked to type I and non-type I cystinuria respectively and they exhibit distinct phenotypes due to protein trafficking defects or catalytic inactivation. Here, using electron cryo-microscopy and biochemistry, we discover that Ca 2+ mediates higher-order assembly of system b 0,+ . Ca 2+ stabilizes the interface between two rBAT molecules, leading to super-dimerization of b 0,+ AT-rBAT, which in turn facilitates N-glycan maturation and protein trafficking. A cystinuria mutant T216M and mutations of the Ca 2+ site of rBAT cause the loss of higher-order assemblies, resulting in protein trapping at the ER and the loss of function. These results provide the molecular basis of system b 0,+ biogenesis and type I cystinuria and serve as a guide to develop new therapeutic strategies against it. More broadly, our findings reveal an unprecedented link between transporter oligomeric assembly and protein-trafficking diseases.


  • Organizational Affiliation

    Department of Structural Biology, Max Planck Institute of Biophysics, 60438, Frankfurt, Germany. yongchan.lee@biophys.mpg.de.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
B(0,+)-type amino acid transporter 1A [auth B]515Ovis ariesMutation(s): 0 
Gene Names: SLC7A9
Membrane Entity: Yes 
UniProt
Find proteins for A0A6P3EL78 (Ovis aries)
Explore A0A6P3EL78 
Go to UniProtKB:  A0A6P3EL78
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A6P3EL78
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
neutral and basic amino acid transport protein rBATB [auth A]686Ovis ariesMutation(s): 1 
Gene Names: SLC3A1
Membrane Entity: Yes 
UniProt
Find proteins for W5P8K2 (Ovis aries)
Explore W5P8K2 
Go to UniProtKB:  W5P8K2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupW5P8K2
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

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Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
C, D
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
LBN
Query on LBN

Download Ideal Coordinates CCD File 
G [auth A]1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine
C42 H82 N O8 P
WTJKGGKOPKCXLL-VYOBOKEXSA-N
CLR
Query on CLR

Download Ideal Coordinates CCD File 
E [auth B],
F [auth B]
CHOLESTEROL
C27 H46 O
HVYWMOMLDIMFJA-DPAQBDIFSA-N
NAG
Query on NAG

Download Ideal Coordinates CCD File 
I [auth A],
J [auth A],
K [auth A],
L [auth A]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
CA (Subject of Investigation/LOI)
Query on CA

Download Ideal Coordinates CCD File 
H [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.05 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Max Planck SocietyGermany--
Human Frontier Science Program (HFSP)--

Revision History  (Full details and data files)

  • Version 1.0: 2022-01-19
    Type: Initial release
  • Version 1.1: 2022-06-01
    Changes: Database references