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)

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Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

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.

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

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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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P93026
Glycosylation
Glycosylation Sites: 3	Glycosylation Focus chain A
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D 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	Interactions Focus chain B Interactions & Density Focus chain B
Glycosylation Resources
GlyTouCan: G81315DD GlyCosmos: G81315DD GlyGen: G81315DD

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG (Subject of Investigation/LOI) Query on NAG Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	D [auth A], E [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A]
MAN (Subject of Investigation/LOI) Query on MAN Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	alpha-D-mannopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-PQMKYFCFSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

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

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-08-13

Deposition Author(s):

Eldahshoury, M.K.

De Marcos Lousa, C.

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

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.