8OS2

Structure of the human LYVE-1 (lymphatic vessel endothelial receptor-1) hyaluronan binding domain in an unliganded state

• PDB DOI: https://doi.org/10.2210/pdb8OS2/pdb

• Classification: CELL ADHESION
• Organism(s): Homo sapiens
• Expression System: Cricetulus griseus
• Mutation(s): No 


• Deposited: 2023-04-17 Released: 2024-07-31 
• Deposition Author(s): Ni, T., Bannerji, S., Jackson, D.J., Gilbert, R.J.C.
• Funding Organization(s): Medical Research Council (MRC, United Kingdom)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.64 Å
• R-Value Free: 0.223 
• R-Value Work: 0.183 
• R-Value Observed: 0.184 

Literature

A novel sliding interaction with hyaluronan underlies the mode of action of LYVE-1, the receptor for leucocyte entry and trafficking in the lymphatics

Bano, F., Bannerji, S., Ni, T., Green, D.E., DeAngelis, P.L., Paci, E., Lepsik, M., Jackson, D.J., Gilbert, R.J.C.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: assay for oligomerization

Macromolecule Content

• Total Structure Weight: 16.73 kDa 
• Atom Count: 1,160 
• Modelled Residue Count: 123 
• Deposited Residue Count: 146 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lymphatic vessel endothelial hyaluronic acid receptor 1	A	146	Homo sapiens	Mutation(s): 0  Gene Names: LYVE1, CRSBP1, HAR, XLKD1, UNQ230/PRO263
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y5Y7 (Homo sapiens) Explore Q9Y5Y7  Go to UniProtKB:  Q9Y5Y7
PHAROS:  Q9Y5Y7 GTEx:  ENSG00000133800
Glycosylation
Glycosylation Sites: 2		Go to GlyGen: Q9Y5Y7-1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	B [auth A], C [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
GOL	D [auth A], E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.64 Å
• R-Value Free: 0.223 
• R-Value Work: 0.183 
• R-Value Observed: 0.184 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.81	α = 90
b = 70.81	β = 90
c = 75.77	γ = 90

Software Package:

Software Name	Purpose
xia2	data scaling
PHENIX	phasing
PHENIX	refinement
Coot	model building

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-07-31 
Deposition Author(s): Ni, T., Bannerji, S., Jackson, D.J., Gilbert, R.J.C.

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Funding Organization	Location	Grant Number
Medical Research Council (MRC, United Kingdom)	United Kingdom	--

Revision History  

• Version 1.0: 2024-07-31
  Type: Initial release