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- PDB-9hur: Crystal structure of Tetraspanin CD63mutant Large Extracellular L... -

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Basic information

Entry
Database: PDB / ID: 9hur
TitleCrystal structure of Tetraspanin CD63mutant Large Extracellular Loop (LEL) in complex with sybody LA4
Components
  • CD63 antigen
  • sybody LA4
KeywordsCELL ADHESION / virus entry and infection modulator / regulation of cell adhesion and migration / regulation of immune response
Function / homology
Function and homology information


pigment granule maturation / regulation of vascular endothelial growth factor signaling pathway / endosome to melanosome transport / platelet dense granule membrane / positive regulation of integrin-mediated signaling pathway / negative regulation of epithelial cell migration / multivesicular body, internal vesicle / multivesicular body membrane / regulation of potassium ion transmembrane transport / azurophil granule membrane ...pigment granule maturation / regulation of vascular endothelial growth factor signaling pathway / endosome to melanosome transport / platelet dense granule membrane / positive regulation of integrin-mediated signaling pathway / negative regulation of epithelial cell migration / multivesicular body, internal vesicle / multivesicular body membrane / regulation of potassium ion transmembrane transport / azurophil granule membrane / positive regulation of receptor internalization / epithelial cell differentiation / positive regulation of cell adhesion / cell-matrix adhesion / endosome lumen / late endosome membrane / melanosome / cell migration / Platelet degranulation / protein transport / endosome membrane / lysosomal membrane / intracellular membrane-bounded organelle / Neutrophil degranulation / protein-containing complex binding / cell surface / protein-containing complex / extracellular space / extracellular exosome / nucleoplasm / plasma membrane
Similarity search - Function
CD63, extracellular domain / Tetraspanin, conserved site / Transmembrane 4 family signature. / Tetraspanin, animals / Tetraspanin, EC2 domain superfamily / Tetraspanin/Peripherin / Tetraspanin family
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsNagarathinam, K. / Krey, T.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Evolutionary relationship of Tetraspanins
Authors: Nagarathinam, K. / Karakulova, D. / Thiyagaraj, D. / Krey, T.
History
DepositionDec 23, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 19, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CD63 antigen
B: sybody LA4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1624
Polymers29,0432
Non-polymers1192
Water1,40578
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2240 Å2
ΔGint-38 kcal/mol
Surface area10490 Å2
Unit cell
Length a, b, c (Å)45.630, 45.630, 228.440
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 CD63 antigen / Granulophysin / Lysosomal-associated membrane protein 3 / LAMP-3 / Lysosome integral membrane ...Granulophysin / Lysosomal-associated membrane protein 3 / LAMP-3 / Lysosome integral membrane protein 1 / Limp1 / Melanoma-associated antigen ME491 / OMA81H / Ocular melanoma-associated antigen / Tetraspanin-30 / Tspan-30


Mass: 12430.112 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD63, MLA1, TSPAN30 / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: P08962
#2: Antibody sybody LA4


Mass: 16613.275 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 78 / 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

CrystalDensity Matthews: 2.06 Å3/Da / Density % sol: 40.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2M Sodium formate;0.2M Ammonium acetate; 0.2M Sodium citrate tribasic dihydrate; 0.2M Potassium sodium tartrate tetrahydrate: 0.2M Sodium oxamate; 25% v/v MPD; 25% PEG 1000; 25% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.984002 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 6, 2024
RadiationMonochromator: Si(111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.984002 Å / Relative weight: 1
ReflectionResolution: 1.65→44.75 Å / Num. obs: 30367 / % possible obs: 96.42 % / Redundancy: 15.3 % / Biso Wilson estimate: 35.65 Å2 / CC1/2: 0.998 / Net I/σ(I): 17.5
Reflection shellResolution: 1.65→1.709 Å / Mean I/σ(I) obs: 1.42 / Num. unique obs: 1916 / CC1/2: 0.802

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
MxCuBEdata collection
XDS20240712data reduction
XSCALEdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→44.75 Å / SU ML: 0.3174 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.831
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.238 1519 5 %
Rwork0.2112 28848 -
obs0.2125 30367 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 46.26 Å2
Refinement stepCycle: LAST / Resolution: 1.65→44.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1690 0 6 78 1774
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01331728
X-RAY DIFFRACTIONf_angle_d1.2432348
X-RAY DIFFRACTIONf_chiral_restr0.0779259
X-RAY DIFFRACTIONf_plane_restr0.0109304
X-RAY DIFFRACTIONf_dihedral_angle_d14.4824589
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.70.691350.56892565X-RAY DIFFRACTION99.93
1.7-1.760.42471340.39532546X-RAY DIFFRACTION99.93
1.76-1.830.31871350.2892564X-RAY DIFFRACTION99.96
1.84-1.920.27461350.22222560X-RAY DIFFRACTION99.93
1.92-2.020.24721350.22252572X-RAY DIFFRACTION100
2.02-2.150.26241370.24422588X-RAY DIFFRACTION100
2.15-2.310.25831370.22212610X-RAY DIFFRACTION100
2.31-2.540.27661380.22482618X-RAY DIFFRACTION100
2.54-2.910.2621390.2332643X-RAY DIFFRACTION100
2.91-3.670.22891410.20952687X-RAY DIFFRACTION100
3.67-44.750.20291530.18042895X-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)
14.178208239050.381259967472.448283508241.401383513830.02717433415912.917339739420.421590592753-0.150825308229-0.5865728019550.303574749539-0.1082081518890.1550407784280.758941928494-0.4144960632420.01479250836920.549889626336-0.1079587485-0.05792001054140.3826550875260.1038341890360.483440129640.00239260146466-11.936917138638.7543449208
22.316454331090.774363490227-1.560878020043.401009262311.110723678441.891634454790.343495220719-0.519759346456-0.266982204930.549957586789-0.108982166518-0.01484545613940.337657634612-0.2759404575870.0722273586010.541425307968-0.0115193154629-0.03429436444440.337863006850.07635730335620.4010721695832.80089990312-6.2726252342941.6570014905
31.669082662470.812385604132-0.4616074466642.338291500921.254311382491.25453419845-0.1474195298020.336234145789-0.04933255383530.04784683614910.310359819333-0.151122624217-0.07727703583480.2657983670280.002896260201440.30689691024-0.0180409629396-0.0590856042280.360295045333-0.02413904878150.3279569721824.31702091642-9.1388925324610.879311812
42.14627891095-1.42257535581-0.09795690330150.9399938168610.1302589733793.173185747390.0849602303777-0.3674886564870.254178983960.482465791641-0.156461819389-0.36354686528-0.6293017112320.198692975027-2.70025144773E-50.482066255768-0.0422960362034-0.08057763176060.312215631155-0.001735194959280.364958361023-1.39996937401-2.9653786312918.2897092137
53.766273210180.6846468514660.8947234950533.03119049372-0.9447273416144.079135011720.004582714660080.156061026669-0.09846441832360.03225015680770.1929478504510.2398881239570.000152268425441-0.0627200457679-0.0005830960886750.3152128307930.00283023726477-0.07980684290130.2949502683170.01988816377640.344788622626-4.48913357857-6.6907733441911.689272577
61.012358753730.5283563076350.6094848311090.5317177960850.9419839947161.96646052209-0.0444526720885-0.09391758821640.1565816875980.2936902730140.103751781503-0.198079020783-0.1312547590640.161719084864-0.0002788377747380.3639477806070.00418232608962-0.03235198426150.2587466707110.0108690391180.3238842885481.19800831711-5.8696550431120.7917302487
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 108 through 156 )AA108 - 1561 - 49
22chain 'A' and (resid 157 through 209 )AA157 - 20950 - 102
33chain 'B' and (resid 3 through 36 )BB3 - 361 - 34
44chain 'B' and (resid 37 through 56 )BB37 - 5635 - 54
55chain 'B' and (resid 57 through 103 )BB57 - 10355 - 101
66chain 'B' and (resid 104 through 129 )BB104 - 129102 - 127

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