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- PDB-8ox3: Structure of the murine LYVE-1 (lymphatic vessel endothelial rece... -

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Basic information

Entry
Database: PDB / ID: 8ox3
TitleStructure of the murine LYVE-1 (lymphatic vessel endothelial receptor-1) hyaluronan binding domain bound with octasaccharide 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 / glycosaminoglycan catabolic process / Hyaluronan 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
DI(HYDROXYETHYL)ETHER / Lymphatic vessel endothelial hyaluronic acid receptor 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.05 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
DepositionApr 30, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 12, 2025Provider: 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)36,6549
Polymers34,6101
Non-polymers2,0448
Water3,117173
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: assay for oligomerization, sedimentation velocity ultracentrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3840 Å2
ΔGint22 kcal/mol
Surface area6200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.107, 56.963, 30.908
Angle α, β, γ (deg.)90.000, 106.272, 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-656-

HOH

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Components

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Protein , 1 types, 1 molecules A

#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 / Cell line (production host): CHO K1 / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: Q8BHC0

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Sugars , 2 types, 3 molecules

#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.: 2 / 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

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Non-polymers , 4 types, 178 molecules

#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 173 / Source method: isolated from a natural source / Formula: H2O

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Details

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

Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 20% PEG5000, 0.1M bis-Tris pH6.5, 18 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: Mar 10, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 1.05→46.95 Å / Num. obs: 46097 / % possible obs: 83 % / Redundancy: 6.4 % / Biso Wilson estimate: 7.9 Å2 / CC1/2: 1 / Rrim(I) all: 0.101 / Net I/σ(I): 11.1
Reflection shellResolution: 1.05→1.07 Å / Num. unique obs: 193 / CC1/2: 0.4 / Rrim(I) all: 1.075

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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: 1.05→46.9 Å / SU ML: 0.069 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.4149
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1629 2211 4.8 %
Rwork0.1506 43840 -
obs0.1512 46051 69.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 14.03 Å2
Refinement stepCycle: LAST / Resolution: 1.05→46.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms868 0 134 173 1175
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01171065
X-RAY DIFFRACTIONf_angle_d1.18911436
X-RAY DIFFRACTIONf_chiral_restr0.0932173
X-RAY DIFFRACTIONf_plane_restr0.0058176
X-RAY DIFFRACTIONf_dihedral_angle_d12.5972357
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.05-1.070.406790.3161275X-RAY DIFFRACTION6.88
1.07-1.10.254250.2207541X-RAY DIFFRACTION13.68
1.1-1.130.2011470.1781817X-RAY DIFFRACTION21.08
1.13-1.160.2001760.16741180X-RAY DIFFRACTION30.1
1.16-1.190.1674800.15621632X-RAY DIFFRACTION41.2
1.19-1.230.1438990.15152160X-RAY DIFFRACTION54.41
1.23-1.270.21331280.15342961X-RAY DIFFRACTION74.33
1.27-1.320.16681960.15523684X-RAY DIFFRACTION93.09
1.32-1.380.1741940.15543690X-RAY DIFFRACTION93.73
1.38-1.460.15831710.14733747X-RAY DIFFRACTION94.23
1.46-1.550.1571820.14353792X-RAY DIFFRACTION95.05
1.55-1.670.16141970.14043768X-RAY DIFFRACTION95.4
1.67-1.830.15022050.14963827X-RAY DIFFRACTION96.23
1.83-2.10.15932290.14633804X-RAY DIFFRACTION96.9
2.1-2.650.15441710.15333946X-RAY DIFFRACTION97.84
2.65-46.90.16452020.15024016X-RAY DIFFRACTION98.9

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