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- PDB-9hq5: Crystal structure of Tetraspanin CD63mutant Large Extracellular L... -

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Basic information

Entry
Database: PDB / ID: 9hq5
TitleCrystal structure of Tetraspanin CD63mutant Large Extracellular Loop (LEL) in complex with sybody SB3
Components
  • CD63 antigen
  • Sybody SB3
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: 2.6 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 16, 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

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Assembly

Deposited unit
A: CD63 antigen
B: Sybody SB3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4185
Polymers28,1292
Non-polymers2883
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1460 Å2
ΔGint-31 kcal/mol
Surface area11030 Å2
Unit cell
Length a, b, c (Å)65.230, 65.230, 138.640
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#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 / Mutation: N29S, N49T, N71S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD63, MLA1, TSPAN30 / Cell line (production host): Schneider 2 (S2) cells / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: P08962
#2: Antibody Sybody SB3


Mass: 15699.375 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Cell line (production host): E.coli MC1061 / Production host: Bacteria (eubacteria)
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
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: 2.65 Å3/Da / Density % sol: 53.64 % / Description: Tetragonal
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 200 mM Ammonium sulfate, 20.00 % w/v Polyethylene glycol 3,350

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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: 2.6→47.5 Å / Num. obs: 9778 / % possible obs: 99.85 % / Redundancy: 10.4 % / Biso Wilson estimate: 26.43 Å2 / CC1/2: 0.998 / Net I/σ(I): 19.94
Reflection shellResolution: 2.6→2.693 Å / Mean I/σ(I) obs: 4.88 / Num. unique obs: 940 / CC1/2: 0.95 / % possible all: 99.37

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
MxCuBEdata collection
XDS202440712data reduction
XSCALEdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→47.5 Å / SU ML: 0.2985 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 26.0431
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2917 488 4.99 %
Rwork0.245 9288 -
obs0.2473 9776 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.77 Å2
Refinement stepCycle: LAST / Resolution: 2.6→47.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1591 0 15 0 1606
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00191638
X-RAY DIFFRACTIONf_angle_d0.40372225
X-RAY DIFFRACTIONf_chiral_restr0.04234
X-RAY DIFFRACTIONf_plane_restr0.0031291
X-RAY DIFFRACTIONf_dihedral_angle_d18.9601556
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.980.34481590.28923020X-RAY DIFFRACTION99.81
2.98-3.750.30841590.25143039X-RAY DIFFRACTION99.97
3.75-47.50.25781700.22093229X-RAY DIFFRACTION99.82
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)
10.00549414546340.00801933395283-0.01401660080020.0119323102082-0.02040207205380.034063907371-0.0230477506819-0.0082126590692-0.02697879791540.0136347176118-0.00548024623758-0.05252093001580.05166800566960.01626595617980.02319758637490.2611555546490.04797211856650.1361531722120.2017204049840.1349152593150.321658697798-7.5121401341327.8724562391-19.1577494233
20.619065942894-0.08897974456650.004155546767750.6452770583730.2158085287170.25303430094-0.157727685602-0.01381970266540.0909087910896-0.03531455519120.0694624960419-0.09992084141090.01056323524190.133101634579-0.09664523179240.0950326102162-0.01838229741510.03833272265680.0831924568697-0.01395383052590.34147309353-12.18656509433.7970054571-10.3833411583
30.1211837964570.0391923618590.06765812083310.01563663745110.0151306884440.0572282366625-0.0351514569047-0.0547386395920.06167503078390.0137592686744-0.01826227465660.05637869753340.00942939242614-0.03692074142050.06451931930350.2920457255220.2656869937030.04688418697220.195893699663-0.1659463479840.157027293951-21.874726883735.1814118693-0.466889350094
40.0933762373872-0.00421307113057-0.01700871321140.028298142348-0.02082834925430.0281451908084-0.0352769762995-0.0010830371602-0.0479747975875-0.0197998369512-0.03432735707030.03169346557840.0138261572184-0.00434289611159-0.3545532607380.1875218946890.0299868754624-0.03946142304610.0017399551156-0.06860262411160.128965368808-18.709336144324.1073923861-5.31762624988
50.255686653196-0.07764802971170.14146836480.193323147607-0.05693374362780.08089283650470.0142000565468-0.0253914605712-0.1000398812860.01060006817780.0345788693451-0.04031486884680.03819377050690.09150163317070.01812205069330.2946179646420.207187900720.06244030551250.3414015770090.00447633511640.323210317159-18.448587934924.87260292824.08266288918
60.326866351915-0.0209741350630.003833914751870.185138223315-0.1291486725780.08549173604370.0168356883665-0.148823596948-0.3023596931450.1007359963360.04552272656680.1443208307070.107713449542-0.04588079270140.2299178964160.23369965581-0.1671160545820.0656532540377-0.01872601335110.06702560234780.156328875818-23.742049161924.7168722059-6.4147854349
70.0631558176499-0.0168657202293-0.02899288573580.0327173226947-0.03078468196330.147967932773-0.03270370146650.0219406558614-0.032463199509-0.017604729273-0.0178892384194-0.0220275694187-0.01747756610040.0733304468174-0.2186822518280.126942858882-0.03054258774160.09317625567780.12337591646-0.02140181460630.06462481085-3.1161709187317.4527998776-22.0072758719
80.1843530995270.13951385516-0.03870181592260.1103063455110.01265359981680.1783652226340.007549450091090.02499405475980.2373018233230.157607320076-0.0451978520860.127169125273-0.1791947201840.009196103686690.3738779548430.2227030961880.0194004329150.04183357093110.0563897524660.08518532312370.2017995436970.023154471837211.0339752518-13.8152509499
90.151742417143-0.06297732572630.04017292037710.0323435283043-0.01709667331510.01247999434620.0594200392925-0.0369003417241-0.04504131018920.06317451277040.01652140340310.0815866480028-0.06387597065280.005574422813370.4452060081340.1859465712680.23944808551-0.05978794082-0.007803218606310.173928498135-0.030557056899-5.446907462744.73672773355-10.309726169
100.0596602918920.0138685936889-0.01024255531310.04522876319740.08000006329040.1648069637190.0560938190384-0.0179983994604-0.01598163856450.02307857533950.0279097203361-0.0279213269476-0.02598551266840.05751624997490.2920241910130.3432112358320.0642144661775-0.04980608714960.223236244857-0.2051560415970.0526353188778-1.4563915206416.6443390563-9.92326366917
110.005679565208338.06705194987E-7-0.02803589866180.00393210963295-0.004620555584040.146894749426-0.0341684073181-0.0355140731763-0.03223749904110.03483153141920.0346943254999-0.03183982458760.05604418674160.118642746514-0.0876976601820.2091450132620.1711028046920.03396652908240.0371662544025-0.04763857603930.0707872341908-1.748041349975.92095921673-17.6124740026
120.0510189223276-0.004536410369090.009038374545620.102900995370.0434114649340.02083183199150.0384803969935-0.0624530016361-0.09188247257970.0980859597807-0.0313377416921-0.134674559680.126841461330.123333631784-0.05544642316160.2271371760460.144998790459-0.004186560810770.2102980147470.1638801727810.2131095865289.015424366826.07392963514-18.0847289064
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 103 through 109 )AA103 - 1091 - 7
22chain 'A' and (resid 110 through 124 )AA110 - 1248 - 22
33chain 'A' and (resid 125 through 142 )AA125 - 14223 - 40
44chain 'A' and (resid 143 through 156 )AA143 - 15641 - 54
55chain 'A' and (resid 157 through 169 )AA157 - 16955 - 67
66chain 'A' and (resid 170 through 201 )AA170 - 20168 - 99
77chain 'B' and (resid 5 through 11 )BB5 - 111 - 7
88chain 'B' and (resid 12 through 43 )BB12 - 438 - 39
99chain 'B' and (resid 44 through 77 )BB44 - 7740 - 73
1010chain 'B' and (resid 78 through 87 )BB78 - 8774 - 83
1111chain 'B' and (resid 88 through 109 )BB88 - 10984 - 105
1212chain 'B' and (resid 110 through 119 )BB110 - 119106 - 115

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