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- PDB-8oxd: Structure of the human LYVE-1 (lymphatic vessel endothelial recep... -

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Basic information

Entry
Database: PDB / ID: 8oxd
TitleStructure of the human LYVE-1 (lymphatic vessel endothelial receptor-1) hyaluronan binding domain bound with decasaccharide hyaluronan.
ComponentsLymphatic vessel endothelial hyaluronic acid receptor 1
KeywordsCELL ADHESION / Hyaluronan binding / cell migration / lymphatic system
Function / homology
Function and homology information


positive regulation of cellular extravasation / Hyaluronan degradation / hyaluronic acid binding / hyaluronan catabolic process / cargo receptor activity / anatomical structure morphogenesis / receptor-mediated endocytosis / cell-matrix adhesion / response to wounding / transmembrane signaling receptor activity ...positive regulation of cellular extravasation / Hyaluronan degradation / hyaluronic acid binding / hyaluronan catabolic process / cargo receptor activity / anatomical structure morphogenesis / receptor-mediated endocytosis / cell-matrix adhesion / response to wounding / transmembrane signaling receptor activity / signaling receptor activity / extracellular exosome / membrane / plasma membrane
Similarity search - Function
CD44 antigen-like / 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 speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.32 Å
AuthorsNi, T. / Banerji, N. / 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
DepositionMay 1, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 13, 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.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)17,9225
Polymers16,1031
Non-polymers1,8204
Water1,63991
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: assay for oligomerization, Sedimentation velocity analytical ultracentrigfugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2680 Å2
ΔGint23 kcal/mol
Surface area6880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.590, 53.260, 53.740
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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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 / Hyaluronic acid receptor


Mass: 16102.712 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LYVE1, CRSBP1, HAR, XLKD1, UNQ230/PRO263 / Cell line (production host): CHO K1 / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: Q9Y5Y7
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-beta-D-glucopyranuronic acid-(1-3)-2-acetamido-2- ...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


Type: oligosaccharide / Mass: 1155.965 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpAb1-3DGlcpNAcb1-4DGlcpAb1-3DGlcpNAcb1-4DGlcpAb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,6,5/[a2122A-1b_1-5][a2122h-1b_1-5_2*NCC/3=O]/1-2-1-2-1-2/a4-b1_b3-c1_c4-d1_d3-e1_e4-f1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpA]{[(4+1)][b-D-GlcpNAc]{[(3+1)][b-D-GlcpA]{[(4+1)][b-D-GlcpNAc]{[(3+1)][b-D-GlcpA]{[(4+1)][b-D-GlcpNAc]{}}}}}}LINUCSPDB-CARE
#3: 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.: 3 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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

CrystalDensity Matthews: 1.76 Å3/Da / Density % sol: 30.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 20 %w/v Polyethylene Glycol 3350, 0.1 M bis-Tris Propane pH 6.5, 0.2 M Sodium Malonate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9159 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 23, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9159 Å / Relative weight: 1
ReflectionResolution: 1.32→53.3 Å / Num. obs: 27202 / % possible obs: 99.4 % / Redundancy: 10.4 % / Biso Wilson estimate: 16.19 Å2 / CC1/2: 1 / Rrim(I) all: 0.084 / Net I/σ(I): 15.4
Reflection shellResolution: 1.32→1.69 Å / Num. unique obs: 13958 / CC1/2: 0.6

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Processing

Software
NameVersionClassification
PHENIX1.21rc1_4899refinement
xia2data reduction
xia2data scaling
PHENIXphasing
EM softwareName: PHENIX / Version: 1.21rc1_4899 / Category: model refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.32→37.83 Å / SU ML: 0.1569 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.3016
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2173 1385 5.09 %
Rwork0.1724 25814 -
obs0.1748 27199 99.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.92 Å2
Refinement stepCycle: LAST / Resolution: 1.32→37.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms910 0 120 91 1121
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01221051
X-RAY DIFFRACTIONf_angle_d1.29351427
X-RAY DIFFRACTIONf_chiral_restr0.0911189
X-RAY DIFFRACTIONf_plane_restr0.0058168
X-RAY DIFFRACTIONf_dihedral_angle_d13.5603340
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.32-1.370.32291380.32812536X-RAY DIFFRACTION98.89
1.37-1.420.31051490.27312459X-RAY DIFFRACTION96.95
1.42-1.490.28911480.2262521X-RAY DIFFRACTION99.44
1.49-1.570.28141040.18682581X-RAY DIFFRACTION99.48
1.57-1.660.21981280.1732572X-RAY DIFFRACTION99.52
1.66-1.790.23471370.15662577X-RAY DIFFRACTION99.78
1.79-1.970.20271580.15022560X-RAY DIFFRACTION99.67
1.97-2.260.19191370.15892594X-RAY DIFFRACTION99.85
2.26-2.840.18451230.17432666X-RAY DIFFRACTION99.96
2.84-37.830.2161630.16192748X-RAY DIFFRACTION99.93

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