9B1R | pdb_00009b1r

Functional implication of the homotrimeric multidomain vacuolar sorting receptor 1 from Arabidopsis thaliana

• PDB DOI: https://doi.org/10.2210/pdb9B1R/pdb

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


• Deposited: 2024-03-13 Released: 2024-05-15 
• Deposition Author(s): Park, H., Youn, B., Park, D.J., Puthanveettil, S.V., Kang, C.
• Funding Organization(s): United States Department of Agriculture (USDA), National Science Foundation (NSF, United States)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.50 Å
• R-Value Free: 
  0.216 (Depositor), 0.217 (DCC) 
• R-Value Work: 
  0.180 (Depositor), 0.183 (DCC) 
• R-Value Observed: 
  0.184 (Depositor) 

Starting Model: experimental

Literature

Functional implication of the homotrimeric multidomain vacuolar sorting receptor 1 (VSR1) from Arabidopsis thaliana.

Park, H., Youn, B., Park, D.J., Puthanveettil, S.V., Kang, C.

(2024) Sci Rep 14: 9622-9622

• PubMed: 38671060 
• DOI: https://doi.org/10.1038/s41598-024-57975-2
• Primary Citation Related Structures: 
  9B1R


• PubMed Abstract: 
  

  The vacuolar sorting receptors (VSRs) are specific to plants and are responsible for sorting and transporting particular proteins from the trans-Golgi network to the vacuole. This process is critically important for various cellular functions, including storing nutrients during seed development. Despite many years of intense studies on VSRs, a complete relation between function and structure has not yet been revealed. Here, we present the crystal structure of the entire luminal region of glycosylated VSR1 from Arabidopsis thaliana (AtVSR1) for the first time. The structure provides insights into the tertiary and quaternary structures of VSR1, which are composed of an N-terminal protease-associated (PA) domain, a unique central region, and one epidermal growth factor (EGF)-like domain followed by two disordered EGF-like domains. The structure of VSR1 exhibits unique characteristics, the significance of which is yet to be fully understood.

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Organizational Affiliation: 
• X-Ray Core, UF Scripps Biomedical Research, University of Florida, Jupiter, FL, 33458, USA.
Department of Biological Sciences, Pusan National University, Busan, 46241, Republic of Korea.
Burnett School of Biomedical Sciences, University of Central Florida, Orlando, FL, 32827, USA.
Department of Neuroscience, UF Scripps Biomedical Research, University of Florida, Jupiter, FL, 33458, USA.
Department of Chemistry, Washington State University, Pullman, WA, 99164, USA. [e-mail].

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)

Macromolecule Content 

• Total Structure Weight: 62.48 kDa 
• Atom Count: 3,341 
• Modeled Residue Count: 427 
• Deposited Residue Count: 562 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Vacuolar-sorting receptor 1	A	562	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: 1

Oligosaccharides

Help  

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.50 Å
• R-Value Free:  0.216 (Depositor), 0.217 (DCC) 
• R-Value Work:  0.180 (Depositor), 0.183 (DCC) 
• R-Value Observed: 0.184 (Depositor) 

Space Group: P 2₁ 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 145.543	α = 90
b = 145.543	β = 90
c = 145.543	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-05-15 
Deposition Author(s): Park, H., Youn, B., Park, D.J., Puthanveettil, S.V., Kang, C.

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Funding Organization	Location	Grant Number
United States Department of Agriculture (USDA)	United States	2023-67013-39629
United States Department of Agriculture (USDA)	United States	2003-35318-13672
National Science Foundation (NSF, United States)	United States	MCB-2043248

Revision History  

• Version 1.0: 2024-05-15
  Type: Initial release
  
• Version 1.1: 2024-10-23
  Changes: Structure summary