8OX3 | pdb_00008ox3

Structure of the murine LYVE-1 (lymphatic vessel endothelial receptor-1) hyaluronan binding domain bound with octasaccharide hyaluronan.

• PDB DOI: https://doi.org/10.2210/pdb8OX3/pdb

• Classification: CELL ADHESION
• Organism(s): Mus musculus
• Expression System: Cricetulus griseus
• Mutation(s): No 


• Deposited: 2023-04-30 Released: 2025-02-12 
• Deposition Author(s): Ni, T., Banerji, N., 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: 1.05 Å
• R-Value Free: 
  0.163 (Depositor), 0.162 (DCC) 
• R-Value Work: 
  0.151 (Depositor), 0.149 (DCC) 
• R-Value Observed: 
  0.151 (Depositor) 

Starting Model: experimental

Literature

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

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

(2025) Nature Communications 

Biological Assembly 1  

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

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

Biological Assembly Evidence: assay for oligomerization

Macromolecule Content 

• Total Structure Weight: 36.65 kDa 
• Atom Count: 1,221 
• Modeled Residue Count: 113 
• Deposited Residue Count: 318 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lymphatic vessel endothelial hyaluronic acid receptor 1	A	318	Mus musculus	Mutation(s): 0  Gene Names: Lyve1, Crsbp1, Xlkd1
UniProt
Find proteins for Q8BHC0 (Mus musculus) Explore Q8BHC0  Go to UniProtKB:  Q8BHC0
Glycosylation
Glycosylation Sites: 2		Go to GlyGen: Q8BHC0-1

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-beta-D-glucopyranuronic acid-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-beta-D-glucopyranuronic acid-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-beta-D-glucopyranuronic acid	B [auth C]	6		N/A
Glycosylation Resources
GlyTouCan:  G97733LD GlyCosmos:  G97733LD GlyGen:  G97733LD

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG (Subject of Investigation/LOI)	C [auth A], D [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
PEG	F [auth A], G [auth A], H [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL	E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL	I [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.05 Å
• R-Value Free:  0.163 (Depositor), 0.162 (DCC) 
• R-Value Work:  0.151 (Depositor), 0.149 (DCC) 
• R-Value Observed: 0.151 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.107	α = 90
b = 56.963	β = 106.272
c = 30.908	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
xia2	data reduction
xia2	data scaling
PHENIX	phasing

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21rc1_4899

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-02-12 
Deposition Author(s): Ni, T., Banerji, N., 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: 2025-02-12
  Type: Initial release
  
• Version 1.1: 2025-03-26
  Changes: Database references, Structure summary