8OXD | pdb_00008oxd

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

• PDB DOI: https://doi.org/10.2210/pdb8OXD/pdb

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


• Deposited: 2023-05-01 Released: 2024-11-13 
• 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: 1.32 Å
• R-Value Free: 
  0.217 (Depositor), 0.216 (DCC) 
• R-Value Work: 
  0.172 (Depositor), 0.172 (DCC) 
• R-Value Observed: 
  0.175 (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: 17.92 kDa 
• Atom Count: 1,125 
• Modeled Residue Count: 119 
• 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: 3		Go to GlyGen: Q9Y5Y7-1

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.32 Å
• R-Value Free:  0.217 (Depositor), 0.216 (DCC) 
• R-Value Work:  0.172 (Depositor), 0.172 (DCC) 
• R-Value Observed: 0.175 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.59	α = 90
b = 53.26	β = 90
c = 53.74	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: 2024-11-13 
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: 2024-11-13
  Type: Initial release
  
• Version 1.1: 2025-03-26
  Changes: Database references, Structure summary