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- PDB-8orx: Structure of the murine LYVE-1 (lymphatic vessel endothelial rece... -

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Basic information

Entry
Database: PDB / ID: 8orx
TitleStructure of the murine LYVE-1 (lymphatic vessel endothelial receptor-1) hyaluronan binding domain in an unliganded state
ComponentsLymphatic vessel endothelial hyaluronic acid receptor 1
KeywordsCELL ADHESION / Hyaluronan binding / cell migration / lymphatic system
Function / homology
Function and homology information


glycosaminoglycan catabolic process / positive regulation of cellular extravasation / Hyaluronan uptake and degradation / hyaluronic acid binding / hyaluronan catabolic process / cargo receptor activity / receptor-mediated endocytosis / cell periphery / transmembrane signaling receptor activity / cell adhesion / plasma membrane
Similarity search - Function
CD44 antigen-like / Link domain signature. / Link domain / Extracellular link domain / Link domain profile. / Link (Hyaluronan-binding) / C-type lectin-like/link domain superfamily / C-type lectin fold
Similarity search - Domain/homology
Lymphatic vessel endothelial hyaluronic acid receptor 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.54 Å
AuthorsNi, T. / Banerji, S. / Jackson, D.J. / Gilbert, R.J.C.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom) United Kingdom
CitationJournal: Nature Communications / Year: 2025
Title: Structure of the murine LYVE-1 (lymphatic vessel endothelial receptor-1) hyaluronan binding domain in an unliganded state
Authors: Bano, F. / Banerji, S. / Ni, T. / Green, D.E. / DeAngelis, P.L. / Paci, E. / Lepsik, M. / Jackson, D.J. / Gilbert, R.J.C.
History
DepositionApr 17, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 16, 2024Provider: repository / Type: Initial release
Revision 1.1Mar 26, 2025Group: Database references / Structure summary / Category: audit_author / citation / citation_author
Item: _audit_author.name / _citation.journal_abbrev ..._audit_author.name / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.year / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lymphatic vessel endothelial hyaluronic acid receptor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,0523
Polymers34,6101
Non-polymers4422
Water2,414134
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: assay for oligomerization, Sedimentation velocity analytical ultracentrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area590 Å2
ΔGint8 kcal/mol
Surface area6820 Å2
Unit cell
Length a, b, c (Å)31.370, 58.320, 52.350
Angle α, β, γ (deg.)90.000, 94.620, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-506-

HOH

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Components

#1: Protein Lymphatic vessel endothelial hyaluronic acid receptor 1 / LYVE-1 / Cell surface retention sequence-binding protein 1 / CRSBP-1 / Extracellular link domain- ...LYVE-1 / Cell surface retention sequence-binding protein 1 / CRSBP-1 / Extracellular link domain-containing protein 1


Mass: 34609.551 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Lyve1, Crsbp1, Xlkd1 / Plasmid: pHR SIN / Details (production host): variant / Cell line (production host): CHO K1 / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: Q8BHC0
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 134 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 25% PEG3350 0.1M bis-Tris. Protein concentration 17.6 mg/ml.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 29, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 1.54→29.16 Å / Num. obs: 18090 / % possible obs: 100 % / Redundancy: 6.5 % / Biso Wilson estimate: 16.73 Å2 / CC1/2: 1 / Rrim(I) all: 0.067 / Net I/σ(I): 16
Reflection shellResolution: 1.54→1.64 Å / Num. unique obs: 2315 / CC1/2: 0.8

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Processing

Software
NameVersionClassification
PHENIX1.21rc1_4899refinement
autoPROC1.0.5data reduction
autoPROC1.0.5data scaling
PHENIX1.18.2_3874phasing
Coot0.9.4.1model building
RefinementMethod to determine structure: SAD / Resolution: 1.54→29.16 Å / SU ML: 0.1449 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 19.1028
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1947 775 5.55 %
Rwork0.1692 13182 -
obs0.1706 13957 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.01 Å2
Refinement stepCycle: LAST / Resolution: 1.54→29.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms883 0 28 134 1045
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006929
X-RAY DIFFRACTIONf_angle_d0.85741255
X-RAY DIFFRACTIONf_chiral_restr0.0518142
X-RAY DIFFRACTIONf_plane_restr0.0061160
X-RAY DIFFRACTIONf_dihedral_angle_d12.5272330
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.54-1.640.24721520.20632163X-RAY DIFFRACTION99.78
1.64-1.760.22691380.1932166X-RAY DIFFRACTION99.96
1.76-1.940.19061270.17042199X-RAY DIFFRACTION100
1.94-2.220.1981130.16682216X-RAY DIFFRACTION99.96
2.22-2.80.20881130.18322213X-RAY DIFFRACTION99.96
2.8-29.160.17591320.15422225X-RAY DIFFRACTION99.75

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