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- PDB-9hv7: Crystal structure of Tetraspanin TSPAN10mutant Large Extracellula... -

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Basic information

Entry
Database: PDB / ID: 9hv7
TitleCrystal structure of Tetraspanin TSPAN10mutant Large Extracellular Loop (LEL)
ComponentsTetraspanin-10
KeywordsSIGNALING PROTEIN / Membrane organization / Signal Transductions
Function / homologyTetraspanin, conserved site / Transmembrane 4 family signature. / Tetraspanin, EC2 domain superfamily / Tetraspanin/Peripherin / Tetraspanin family / establishment of protein localization to organelle / enzyme binding / plasma membrane / Tetraspanin-10
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 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 24, 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: Tetraspanin-10
B: Tetraspanin-10


Theoretical massNumber of molelcules
Total (without water)27,9752
Polymers27,9752
Non-polymers00
Water1,910106
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1130 Å2
ΔGint1 kcal/mol
Surface area13050 Å2
Unit cell
Length a, b, c (Å)62.300, 62.300, 117.480
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
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 176 through 186 or resid 188...
d_2ens_1(chain "B" and (resid 176 through 186 or resid 188...

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11GLYGLYLEULEUAA176 - 1864 - 14
d_12VALVALASPASPAA188 - 24616 - 74
d_13GLNGLNLEULEUAA257 - 26385 - 91
d_14LEULEUARGARGAA265 - 28493 - 112
d_15TRPTRPLEULEUAA286 - 294114 - 122
d_16PHEPHEGLNGLNAA296 - 297124 - 125
d_21GLYGLYLEULEUBB176 - 1864 - 14
d_22VALVALASPASPBB188 - 24616 - 74
d_23GLNGLNLEULEUBB257 - 26385 - 91
d_24LEULEUARGARGBB265 - 28493 - 112
d_25TRPTRPLEULEUBB286 - 294114 - 122
d_26PHEPHEGLNGLNBB296 - 297124 - 125

NCS oper: (Code: givenMatrix: (-0.128220821005, 0.991458773817, 0.0238520624392), (0.991662452239, 0.127861471305, 0.0160319984484), (0.0128453057263, 0.0257088307329, -0.999586941763)Vector: 31. ...NCS oper: (Code: given
Matrix: (-0.128220821005, 0.991458773817, 0.0238520624392), (0.991662452239, 0.127861471305, 0.0160319984484), (0.0128453057263, 0.0257088307329, -0.999586941763)
Vector: 31.3299057783, -27.9509909054, 0.0752010663314)

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Components

#1: Protein Tetraspanin-10 / Tspan-10 / Oculospanin


Mass: 13987.688 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TSPAN10, OCSP / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: Q9H1Z9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 106 / Source method: isolated from a natural source / Formula: H2O
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: 2.09 Å3/Da / Density % sol: 41.24 % / Description: Tetragonal
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.3M Diethylene glycol; 0.3M Triethylene glycol; 0.3M Tetraethylene glycol;0.3M Pentaethylene glycol; 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: 1.55→44.05 Å / Num. obs: 34211 / % possible obs: 99.91 % / Redundancy: 10.29 % / Biso Wilson estimate: 29.61 Å2 / CC1/2: 0.999 / Net I/σ(I): 16.22
Reflection shellResolution: 1.552→1.608 Å / Mean I/σ(I) obs: 1.18 / Num. unique obs: 3322 / CC1/2: 0.671

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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: 1.55→44.05 Å / SU ML: 0.2058 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.1094
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2276 1710 5 %
Rwork0.1971 32499 -
obs0.1986 34209 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 37.56 Å2
Refinement stepCycle: LAST / Resolution: 1.55→44.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1772 0 0 106 1878
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00591810
X-RAY DIFFRACTIONf_angle_d0.83482460
X-RAY DIFFRACTIONf_chiral_restr0.0495263
X-RAY DIFFRACTIONf_plane_restr0.0088331
X-RAY DIFFRACTIONf_dihedral_angle_d16.4645652
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.769710065019 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.60.33391400.30252662X-RAY DIFFRACTION99.29
1.6-1.650.25561380.26312622X-RAY DIFFRACTION100
1.65-1.710.29251400.26422655X-RAY DIFFRACTION100
1.71-1.780.32831400.28272673X-RAY DIFFRACTION99.96
1.78-1.860.24111410.24042680X-RAY DIFFRACTION100
1.86-1.960.23711410.20312673X-RAY DIFFRACTION100
1.96-2.080.22541420.19652693X-RAY DIFFRACTION100
2.08-2.240.23281410.19752685X-RAY DIFFRACTION100
2.24-2.460.2031430.18082717X-RAY DIFFRACTION100
2.46-2.820.21981440.20212739X-RAY DIFFRACTION100
2.82-3.550.23011450.19372756X-RAY DIFFRACTION100
3.55-44.050.21811550.18252944X-RAY DIFFRACTION99.81
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)
13.849762256730.715039383514-3.498166350281.25938795847-1.071862214554.29993965276-0.272462713640.102134642044-0.89371299395-0.146556052165-0.3361597346650.2336396212030.607099914571-0.509720940237-0.1766042888850.192018405732-0.0410410907297-0.05870804759890.3784733188020.01389893210630.335487663843.59767844117-14.7285320593-11.4750779876
20.688869582888-0.6193646749630.1636296659190.7954730906740.195005992630.4993846943470.1067187341360.1188872281450.0427952631194-0.121485191278-0.251383974042-0.256686443045-0.1331351130180.232881314092-7.05683736844E-50.3026581624870.03470166031960.007089800560110.3381841944810.05049824212320.30337594802610.7386381793-6.83690014309-19.2947354677
33.043275626231.313669647831.433354398891.27996532883-0.3541088116112.001902425070.0860481626950.178329510598-0.345470584242-0.142829409760.0931883595141-0.402413274610.002884387449210.225708764897-0.0007138056348130.2931403001990.00635593103646-0.0260767256480.3419381075780.07437568890960.39831093115319.1665964295-14.5851458142-14.4069805666
42.38486967821-4.61318377215-0.231415013152.000815490822.837781611933.489619352871.085904842521.315614901950.777182573031-1.18118342763-0.178381192124-2.66587587795-0.3782134463270.6141948090770.3141603381690.3538354726440.02867550967790.1277328230970.5533265990990.01151779057670.7061941837325.3403358658-5.53892866288-13.1552175278
51.902334613611.33553124467-0.3854447449921.41331528868-0.05380612217342.49332792717-0.0726641577876-0.0795034126981-0.0515650016076-0.174698324817-0.0639699889629-0.2657897080180.7865504843190.743109521603-0.3151472515010.3090600592890.0312367138094-0.01300990900070.5227527447090.1170825367050.30187712997323.0205027228-11.4957952502-4.33418019876
60.0173279909143-0.0152647110256-0.100032514246-0.001090713684180.0545235872340.491247502798-0.11695511217-0.1910672962450.3973830795740.137106819993-0.0590652102037-0.136783462198-0.2598726458720.0810569593665-3.13966856165E-50.359499062155-0.00743246527817-0.0299495872860.3903076408870.03569654123770.361402089752-2.03915726741-2.30721298594-8.22194759499
70.302285603954-0.325868776756-0.2987784716850.4480252137960.1084516349510.710178853572-0.3737542506740.20667380851-0.6034455276160.2010216943080.0154642199830.6205262680461.19738106157-0.373281371069-0.01606164216760.405518184048-0.02381706735270.01038657792560.3014805224210.02600202058960.35675954537916.0121627799-26.644648638510.5656101407
80.911022775432-0.7419825386710.5160178472670.648531288537-0.4618842829830.326615582194-0.148516535307-0.3680864687830.05908615403970.4480004345040.09721132216390.16654685667-0.493848759448-0.15998077212-0.000182429756930.3132442239820.0297328350201-0.03464995744350.3128349416490.01416974899620.2751262155822.6825599228-18.588053482619.2163200876
91.851024312560.6787701158760.7287839036161.61935693697-1.509908897692.998588256080.114952397686-0.2209880285660.4641215703640.1094247355840.04033848458960.0499601171627-0.323570775602-0.071540861295-9.81797188831E-50.30538624034-0.0122324743017-0.03782165468880.255560565044-0.008104128850910.33785017788712.992750833-11.196315700914.5708517531
100.5443487985570.0248286126466-0.280084299630.274970092439-0.4548980769650.858903310045-0.0803083618583-0.1748734902740.8388528118550.4548072487590.1854424902240.0593598935383-0.5135237614680.116234567589-8.21792081732E-50.401812512532-0.00869004573675-0.05440304989940.333496713673-0.01441812748820.46401627360222.2090069691-5.7086387860513.7552461708
111.047514449561.26086882973-0.01329644527191.51665434859-0.07311598597472.384764164360.1760446860410.4397477684350.123116511658-0.0448305228342-0.0981579052254-0.214515354019-0.112805716238-0.43846151703-0.01962508244410.2955806881460.0432093591513-0.03119263042530.2960507692440.07887069171820.28108575964216.8449687582-6.27658775984.62733443827
122.249570520621.34528611322-1.356436413071.71363071279-0.05596354303071.435548770090.056353556753-0.268727361092-0.595686266153-0.316863592812-0.148630613121-0.3407753110290.2839774366940.1559428368460.002392722565540.402746029442-0.0193544928761-0.03761524813760.3437479100410.03700328431320.40175616239429.2640178549-30.22231988748.05399513917
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 176 through 191 )AA176 - 1911 - 16
22chain 'A' and (resid 192 through 210 )AA192 - 21017 - 35
33chain 'A' and (resid 211 through 243 )AA211 - 24336 - 68
44chain 'A' and (resid 244 through 261 )AA244 - 26169 - 77
55chain 'A' and (resid 262 through 278 )AA262 - 27878 - 94
66chain 'A' and (resid 279 through 297 )AA279 - 29795 - 113
77chain 'B' and (resid 175 through 191 )BB175 - 1911 - 17
88chain 'B' and (resid 192 through 210 )BB192 - 21018 - 36
99chain 'B' and (resid 211 through 238 )BB211 - 23837 - 64
1010chain 'B' and (resid 239 through 261 )BB239 - 26165 - 79
1111chain 'B' and (resid 262 through 278 )BB262 - 27880 - 96
1212chain 'B' and (resid 279 through 297 )BB279 - 29797 - 115

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