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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.32 Å
R-Value Free:
0.217 (Depositor), 0.218 (DCC)
R-Value Work:
0.172 (Depositor), 0.173 (DCC)
R-Value Observed:
0.175 (Depositor)

Starting Model: experimental
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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

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

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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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9Y5Y7
Glycosylation
Glycosylation Sites: 3	Glycosylation Focus chain A	Go to GlyGen: Q9Y5Y7-1
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D 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	Interactions Focus chain B [auth C] Interactions & Density Focus chain B [auth C]
Glycosylation Resources
GlyTouCan: G97733LD GlyCosmos: G97733LD GlyGen: G97733LD

Small Molecules

Ligands 1 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] SDF format, chain C [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [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 C [auth A] Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.32 Å
R-Value Free: 0.217 (Depositor), 0.218 (DCC)
R-Value Work: 0.172 (Depositor), 0.173 (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

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Entry History

& Funding Information

Deposition Data

Released Date: 2024-11-13

Deposition Author(s):

Gilbert, R.J.C.

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

Revision History (Full details and data files)

Version 1.0: 2024-11-13
Type: Initial release
Version 1.1: 2025-03-26
Changes: Database references, Structure summary

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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.