8ORX | pdb_00008orx

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

PDB DOI: https://doi.org/10.2210/pdb8ORX/pdb

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

Deposited: 2023-04-17 Released: 2024-10-16
Deposition Author(s): Ni, T., Banerji, S., Jackson, D.J., Gilbert, R.J.C.
Funding Organization(s): Medical Research Council (MRC, United Kingdom)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.54 Å
R-Value Free:
0.195 (Depositor), 0.195 (DCC)
R-Value Work:
0.169 (Depositor), 0.169 (DCC)
R-Value Observed:
0.171 (Depositor)

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Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

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: 35.05 kDa
Atom Count: 1,045
Modeled Residue Count: 115
Deposited Residue Count: 318
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	318	Mus musculus	Mutation(s): 0 Gene Names: Lyve1, Crsbp1, Xlkd1
UniProt
Find proteins for Q8BHC0 (Mus musculus) Explore Q8BHC0 Go to UniProtKB: Q8BHC0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8BHC0
Glycosylation
Glycosylation Sites: 2	Glycosylation Focus chain A	Go to GlyGen: Q8BHC0-1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain B [auth A] mmCIF format, chain C [auth A] mmCIF format, chain B [auth A]	B [auth A], C [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.54 Å
R-Value Free: 0.195 (Depositor), 0.195 (DCC)
R-Value Work: 0.169 (Depositor), 0.169 (DCC)
R-Value Observed: 0.171 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 31.37	α = 90
b = 58.32	β = 94.62
c = 52.35	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
autoPROC	data reduction
autoPROC	data scaling
PHENIX	phasing
Coot	model building

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2024-10-16

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: 2024-10-16
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.