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- PDB-8os2: Structure of the human LYVE-1 (lymphatic vessel endothelial recep... -

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Basic information

Entry
Database: PDB / ID: 8os2
TitleStructure of the human 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


positive regulation of cellular extravasation / Hyaluronan uptake and 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 uptake and 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 / SAD / Resolution: 1.64 Å
AuthorsNi, T. / Bannerji, S. / Jackson, D.J. / Gilbert, R.J.C.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom) United Kingdom
CitationJournal: To be published
Title: A novel sliding interaction with hyaluronan underlies the mode of action of LYVE-1, the receptor for leucocyte entry and trafficking in the lymphatics
Authors: Bano, F. / Bannerji, 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 1.0Jul 31, 2024Provider: repository / Type: Initial release

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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)16,7295
Polymers16,1031
Non-polymers6274
Water2,846158
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: assay for oligomerization, Sedimentation velocity analytical ultracentrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area870 Å2
ΔGint10 kcal/mol
Surface area7340 Å2
Unit cell
Length a, b, c (Å)70.810, 70.810, 75.770
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-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 / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: Q9Y5Y7
#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: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 158 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.95 Å3/Da / Density % sol: 58.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 2.5M NaCl, 0.1M Sodium/Potassium Phosphate pH 5.5

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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: Jan 23, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 1.64→41.77 Å / Num. obs: 303577 / % possible obs: 100 % / Redundancy: 12.5 % / Biso Wilson estimate: 30.02 Å2 / CC1/2: 1 / Rrim(I) all: 0.059 / Net I/σ(I): 21
Reflection shellResolution: 1.64→1.67 Å / Mean I/σ(I) obs: 1.2 / Num. unique obs: 1181 / CC1/2: 0.5 / Rrim(I) all: 1.951

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Processing

Software
NameVersionClassification
xia2data scaling
PHENIX1.18.2_3874phasing
PHENIX1.18.2_3874refinement
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.64→41.77 Å / SU ML: 0.2249 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.2423
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2228 1180 4.87 %
Rwork0.1826 23035 -
obs0.1845 24215 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.97 Å2
Refinement stepCycle: LAST / Resolution: 1.64→41.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms944 0 40 158 1142
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00631021
X-RAY DIFFRACTIONf_angle_d0.96861382
X-RAY DIFFRACTIONf_chiral_restr0.0621163
X-RAY DIFFRACTIONf_plane_restr0.0064170
X-RAY DIFFRACTIONf_dihedral_angle_d16.352153
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.64-1.710.34241470.33742796X-RAY DIFFRACTION100
1.71-1.810.30951510.27182827X-RAY DIFFRACTION100
1.81-1.920.25331350.22192842X-RAY DIFFRACTION99.9
1.92-2.070.2511380.21192853X-RAY DIFFRACTION100
2.07-2.270.22361280.19312874X-RAY DIFFRACTION99.9
2.27-2.60.20141640.18642862X-RAY DIFFRACTION100
2.6-3.280.21681790.19222880X-RAY DIFFRACTION100
3.28-41.770.21361380.15453101X-RAY DIFFRACTION99.97
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
19.154726617043.94099801867-3.941591699138.48487450594-2.526523095391.79557788941-0.173710837791.49569896436-0.502178883476-1.369670036520.123645285429-0.114592287570.971447980964-0.593128791776-0.1470530667350.5056942297370.0658572813428-0.007020633992450.462314710207-0.07296752067360.30720709768128.54166450.46738647799.2297386439
28.75729321661-1.40791256911-2.05071068232.037449590824.098245435348.75199611073-0.213836508806-0.0496818701816-0.516783215670.4823799050210.1672031601890.4437031697280.551553750393-0.0103580310826-0.06755935801280.255707625514-0.0393648961305-0.001184401822320.295307946651-0.005247093769040.22478253038921.666682375753.836649689626.1567375927
36.57034625972.42644597099-0.1015047986435.690345800352.237948935328.13231225025-0.03243567474820.478292139721-0.820385768739-0.316310591363-0.141111196017-0.4114850998970.6953465161670.4131280148770.1900482059540.2995056526380.104306261391-0.03753370108630.290121225840.002169843997810.25203752831733.102788778750.201111858416.8838761544
43.20078311039-0.710261079314.013877737883.34331206470.1979121162695.438961738620.1442717842940.4337135688790.313219805403-0.554138117351-0.181411272801-0.0111699358684-0.1714162831850.4819216089040.1272359527820.3474473700820.0111808352083-0.002270222744740.3193916434040.03597451091970.16881151089331.947397906859.409039137913.4577752512
57.32083574898-1.24293305374-0.7968475692963.43949331192-1.429698352756.28182593509-0.0121266174398-0.9893475046830.01234552720740.345060259327-0.0127753587655-0.0980494962821-0.3156855976240.437394013630.03461797030850.200791908422-0.0536688483518-0.02852718178360.32167632057-0.01264443226690.21208052919729.442688737958.263680114329.2623338351
62.22939942145-0.642632815106-3.185916182653.80438200436-1.676411613586.478998715740.329673127364-0.7268268741550.1530502319490.320158368849-0.151585057212-0.192683351195-0.6074879733780.644592723448-0.002999771933950.251265186209-0.0455592826579-0.01671277739460.4491993421870.02046042276230.22935107494136.708755390258.182794344226.598799982
76.554345162020.6761379008882.916783553423.820629157643.124045628043.442416587240.2487446086820.21055969016-0.8129485194230.8866875612260.502112109155-0.8618538242541.54107083468-0.0826948759726-0.6884496498080.7025261214780.0638435684842-0.0905531850330.5264168678670.1691861981080.55061748147136.736212168847.524435932937.1580531617
86.15843512042.73925099936-5.973542510231.26213497759-2.658646497865.81523007947-0.453469263784-0.5321257908630.523617561281-0.3574139616050.4355761911510.2028783423650.573729841345-0.1830363214920.01587101245530.347216575849-0.000821397119346-0.05753491329830.5922244169880.0046801792090.24721644519740.127612217558.190878745631.1149818605
99.32775848723-0.732931760467-2.524452205294.62723493492-0.7595792457865.584260339830.1933054509690.55755553071-0.118538299034-0.262312191905-0.1354913432250.1055146574470.1044543225590.183515150364-0.05795350486780.269102412589-0.0178551953583-0.04486982339230.2752607153760.01095093479930.11574282420932.121599132358.136956798521.2306709597
102.14696707785-0.01107879997261.528852786994.56685637637-0.4028461211917.22262447929-0.2052207557140.3439975882740.525655945320.03327046223280.1215323446960.658387604621-0.141171666355-0.688072097066-0.04367547473340.227051443525-0.03495820390680.02840879707090.3755100754860.04250771239220.3950216944039.2422868585558.65136477230.6266410534
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 24 through 32 )24 - 321 - 11
22chain 'A' and (resid 33 through 40 )33 - 4012 - 19
33chain 'A' and (resid 41 through 53 )41 - 5320 - 32
44chain 'A' and (resid 54 through 64 )54 - 6433 - 43
55chain 'A' and (resid 65 through 87 )65 - 8744 - 70
66chain 'A' and (resid 88 through 99 )88 - 9971 - 82
77chain 'A' and (resid 100 through 111 )100 - 11183 - 94
88chain 'A' and (resid 112 through 117 )112 - 11795 - 100
99chain 'A' and (resid 118 through 134 )118 - 134101 - 117
1010chain 'A' and (resid 135 through 146 )135 - 146118 - 129

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