7NF8 | pdb_00007nf8

Ovine (b0,+AT-rBAT)2 hetero-tetramer, asymmetric unit, rigid-body fitted

• PDB DOI: https://doi.org/10.2210/pdb7NF8/pdb
• EM Map EMD-12298: EMDB EMDataResource

• Classification: TRANSLOCASE
• Organism(s): Ovis aries
• Expression System: Homo sapiens
• Mutation(s): No 
• Membrane Protein: Yes  OPMPDBTMMemProtMD


• Deposited: 2021-02-05 Released: 2022-01-19 
• Deposition Author(s): Lee, Y., Kuehlbrandt, W.
• Funding Organization(s): Max Planck Society, Human Frontier Science Program (HFSP)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.83 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

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

• PubMed: 35577790 
• DOI: https://doi.org/10.1038/s41467-022-30293-9
• Primary Citation 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.

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Organizational Affiliation: 
• Department of Structural Biology, Max Planck Institute of Biophysics, 60438, Frankfurt, Germany. [e-mail].
Graduate School of Medical Life Science, Yokohama City University, Kanagawa, 230-0045, Japan. [e-mail].
Department of Laboratory Medicine, The Jikei University School of Medicine, Tokyo, 105-8461, Japan.
Department of Collaborative Research for Bio-Molecular Dynamics, Nara Medical University, Nara, 634-8521, Japan.
Department of Structural Biology, Max Planck Institute of Biophysics, 60438, Frankfurt, Germany.
Department of Laboratory Medicine, The Jikei University School of Medicine, Tokyo, 105-8461, Japan. [e-mail].
Department of Collaborative Research for Bio-Molecular Dynamics, Nara Medical University, Nara, 634-8521, Japan. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: cross-linking

Macromolecule Content 

• Total Structure Weight: 138.38 kDa 
• Atom Count: 8,817 
• Modeled Residue Count: 1,078 
• Deposited Residue Count: 1,201 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
B(0,+)-type amino acid transporter 1	A [auth B]	515	Ovis aries	Mutation(s): 0  Gene Names: SLC7A9

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
neutral and basic amino acid transport protein rBAT	B [auth A]	686	Ovis aries	Mutation(s): 0  Gene Names: SLC3A1 Membrane Entity: Yes
UniProt
Find proteins for A0A6P7DVK7 (Ovis aries) Explore A0A6P7DVK7  Go to UniProtKB:  A0A6P7DVK7
Glycosylation
Glycosylation Sites: 6

Oligosaccharides

Help  

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C, D	2		N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
LBN	G [auth A]	1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine C42 H82 N O8 P WTJKGGKOPKCXLL-VYOBOKEXSA-N
CLR	E [auth B], F [auth B]	CHOLESTEROL C27 H46 O HVYWMOMLDIMFJA-DPAQBDIFSA-N
NAG	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)	H [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.83 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-01-19 
Deposition Author(s): Lee, Y., Kuehlbrandt, W.

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Funding Organization	Location	Grant Number
Max Planck Society	Germany	--
Human Frontier Science Program (HFSP)		--

Revision History  

• Version 1.0: 2022-01-19
  Type: Initial release
  
• Version 1.1: 2022-06-01
  Changes: Database references, Derived calculations
• Version 1.2: 2022-06-08
  Changes: Database references
• Version 1.3: 2024-10-16
  Changes: Data collection, Database references, Structure summary
• Version 1.4: 2025-07-09
  Changes: Data collection