8R4Y | pdb_00008r4y

Homotrimer for the lumenal domain of Vacuolar Sorting Receptor 1 (VSR1)

• PDB DOI: https://doi.org/10.2210/pdb8R4Y/pdb

• Classification: PROTEIN TRANSPORT
• Organism(s): Arabidopsis thaliana
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2023-11-14 Released: 2025-08-13 
• Deposition Author(s): Borges, R.J., Eldahshoury, M.K., Nettleship, J., Bird, L., An, J., Levada, A.J.L., Shah, N., Thomson, M., Fontes, M.R.M., Owens, R., Denecke, J., Postis, V., Uson, I., Goldman, A., De Marcos Lousa, C.
• Funding Organization(s): Leverhulme Trust

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.51 Å
• R-Value Free: 
  0.272 (Depositor), 0.273 (DCC) 
• R-Value Work: 
  0.256 (Depositor), 0.256 (DCC) 
• R-Value Observed: 
  0.257 (Depositor) 

Literature

The crystal structure of Vacuolar Sorting Receptor 1 (VSR1) lumenal domain reveals a stable domain-swapped trimer and a potential new cargo binding site

Borges, R.J., Eldahshoury, M.K., Nettleship, J., Bird, L., An, J., Levada, A.J.L., Shah, N., Thomson, M., Fontes, M.R.M., Owens, R., Denecke, J., Postis, V., Uson, I., Goldman, A., De Marcos Lousa, C.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 61.57 kDa 
• Atom Count: 3,472 
• Modeled Residue Count: 436 
• Deposited Residue Count: 544 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Vacuolar-sorting receptor 1	A	544	Arabidopsis thaliana	Mutation(s): 0  Gene Names: VSR1, BP80B, ELP, ELP1, At3g52850, F8J2.20
UniProt
Find proteins for P93026 (Arabidopsis thaliana) Explore P93026  Go to UniProtKB:  P93026
Glycosylation
Glycosylation Sites: 3

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B	4		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G81315DD GlyCosmos:  G81315DD GlyGen:  G81315DD

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG (Subject of Investigation/LOI)	D [auth A], E [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
MAN (Subject of Investigation/LOI)	C [auth A]	alpha-D-mannopyranose C6 H12 O6 WQZGKKKJIJFFOK-PQMKYFCFSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.51 Å
• R-Value Free:  0.272 (Depositor), 0.273 (DCC) 
• R-Value Work:  0.256 (Depositor), 0.256 (DCC) 
• R-Value Observed: 0.257 (Depositor) 

Space Group: P 2₁ 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 141.477	α = 90
b = 141.477	β = 90
c = 141.477	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
Arcimboldo	phasing
Coot	model building
PHASER	phasing
xia2	data reduction
Aimless	data scaling

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-08-13 
Deposition Author(s): Borges, R.J., Eldahshoury, M.K., Nettleship, J., Bird, L., An, J., Levada, A.J.L., Shah, N., Thomson, M., Fontes, M.R.M., Owens, R., Denecke, J., Postis, V., Uson, I., Goldman, A., De Marcos Lousa, C.

---

Funding Organization	Location	Grant Number
Leverhulme Trust	United Kingdom	F/10 105/E

Revision History  

• Version 1.0: 2025-08-13
  Type: Initial release