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- PDB-9ht6: Crystal structure of Tetraspanin CD82 Large Extracellular Loop (LEL) -

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Basic information

Entry
Database: PDB / ID: 9ht6
TitleCrystal structure of Tetraspanin CD82 Large Extracellular Loop (LEL)
ComponentsCD82 antigen
KeywordsENDOCYTOSIS / Cell Signalling and Adhesion / Immune function / Viral infection / Tumor supression
Function / homology
Function and homology information


phagocytic vesicle / extracellular exosome / plasma membrane
Similarity search - Function
Tetraspanin, conserved site / Transmembrane 4 family signature. / Tetraspanin, animals / Tetraspanin, EC2 domain superfamily / Tetraspanin/Peripherin / Tetraspanin family
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / CD82 antigen
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsNagarathinam, K. / Krey, T.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Crystal structure of Tetraspanin CD82 Large Extracellular Loop (LEL)
Authors: Nagarathinam, K. / Krey, T.
History
DepositionDec 19, 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: CD82 antigen
B: CD82 antigen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9328
Polymers28,2952
Non-polymers6376
Water18010
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4660 Å2
ΔGint-9 kcal/mol
Surface area11170 Å2
Unit cell
Length a, b, c (Å)51.420, 62.670, 97.610
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and ((resid 109 and (name N or name...
d_2ens_1(chain "B" and (resid 109 through 111 or resid 113...

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_11ASNASNGLYGLYAA109 - 1114 - 6
d_12LEULEUSERSERAA113 - 1858 - 80
d_13SERSERPROPROAA187 - 19682 - 91
d_14THRTHRASNASNAA200 - 22795 - 122
d_21ASNASNGLYGLYBB109 - 1114 - 6
d_22LEULEUPROPROBB113 - 1968 - 91
d_23THRTHRASNASNBB200 - 22795 - 122

NCS oper: (Code: givenMatrix: (-0.637959819936, 0.00839965898626, 0.770023839811), (-0.0252726878494, -0.999630236852, -0.0100339832202), (0.769654831334, -0.0258618502685, 0.637936207864)Vector: 18. ...NCS oper: (Code: given
Matrix: (-0.637959819936, 0.00839965898626, 0.770023839811), (-0.0252726878494, -0.999630236852, -0.0100339832202), (0.769654831334, -0.0258618502685, 0.637936207864)
Vector: 18.7731717613, -40.813038225, -9.34462979208)

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Components

#1: Protein CD82 antigen / C33 antigen / IA4 / Inducible membrane protein R2 / Metastasis suppressor Kangai-1 / Suppressor of ...C33 antigen / IA4 / Inducible membrane protein R2 / Metastasis suppressor Kangai-1 / Suppressor of tumorigenicity 6 protein / Tetraspanin-27 / Tspan-27


Mass: 14147.632 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD82, KAI1, SAR2, ST6, TSPAN27 / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: P27701
#2: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H10O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 2.84 Å3/Da / Density % sol: 56.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 1.0 M Ammonium phosphate dibasic, 0.1 M Sodium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 1.999 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 19, 2018
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.999 Å / Relative weight: 1
ReflectionResolution: 2.4→48.81 Å / Num. obs: 12818 / % possible obs: 99.58 % / Redundancy: 10.52 % / Biso Wilson estimate: 38.84 Å2 / CC1/2: 1 / Net I/σ(I): 24.79
Reflection shellResolution: 2.4→2.486 Å / Mean I/σ(I) obs: 1.54 / Num. unique obs: 1218 / CC1/2: 0.936 / % possible all: 97.13

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
MxCuBEdata collection
XDS20240712data reduction
XSCALEdata scaling
SHELXDEphasing
Coot0.9.8.7model building
BUCCANEERmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→48.8 Å / SU ML: 0.3556 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 29.8743
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2756 642 5.01 %
Rwork0.2263 12172 -
obs0.2288 12814 99.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 46.14 Å2
Refinement stepCycle: LAST / Resolution: 2.4→48.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1854 0 42 10 1906
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00181931
X-RAY DIFFRACTIONf_angle_d0.42162597
X-RAY DIFFRACTIONf_chiral_restr0.0362264
X-RAY DIFFRACTIONf_plane_restr0.0031337
X-RAY DIFFRACTIONf_dihedral_angle_d17.0609703
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.672488433642 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.590.35741240.31872346X-RAY DIFFRACTION98.02
2.59-2.850.30621260.28912394X-RAY DIFFRACTION100
2.85-3.260.31741280.27062429X-RAY DIFFRACTION100
3.26-4.10.22151280.19492436X-RAY DIFFRACTION100
4.1-48.80.27561360.19252567X-RAY DIFFRACTION99.89
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)
11.93687298406-1.181374840132.327251467790.890207528145-1.184403723933.7792453843-0.321515962089-0.5739492042380.1356379814940.448747850317-0.160922453969-0.136981749418-0.444729118409-0.0406257580482-1.035253825610.173326448545-0.0240340812920.143018852840.3018618455670.08941149991570.1919415893015.29056738572-20.8906314872-0.68816515122
20.0009917699271870.00757165173799-0.0114990049510.038661996474-0.05835923929070.07284954247390.0851539381824-0.3557557100990.6366058160450.133885139153-0.138270624394-0.510729479340.1831818593740.115846372424-0.01330002228670.310764251727-0.03644057531470.1335042366750.3344510298250.02537759057140.5575108936418.90591167166-3.51250962846-9.93890055062
30.421967704127-0.5227446545210.5175002300571.05459851089-0.6515637110890.619170396374-0.0314388108098-0.0747142396755-0.1250223987430.4039521720410.0690887614502-0.10704523533-0.453122484060.125595905256-0.01647131942530.230534660936-0.008901169594750.0251972657810.1904998149170.003512440057490.231570861735-1.67493854762-7.64766456319-8.07948075435
40.228190996172-0.1987083443690.2370801033890.296942536392-0.4358561701950.6432574341850.2510666929690.671556083025-0.201405657499-0.500459951415-0.238364852014-0.1110241919410.008164468548570.455357209383-0.04473134756690.5793818073050.0482563307007-0.1691116556380.496251834560.02671500604280.125687710247-3.78210159755-9.33481658618-22.1181742469
51.279016945350.7296829295442.216328826530.9775799097030.4281767309595.1776050244-0.335299922535-0.3129323500441.44224249915-0.286250303529-0.22138507370.0889364000179-1.45726929402-0.763479170083-0.366576841570.585943884410.0112175138506-0.13199677540.135227485914-0.04246606823150.521161280081-8.31331519044.77157274976-8.4214509391
65.90013801168-0.811000882082-0.9324900021540.408078828525-0.4064329223831.13764743539-0.009963707898440.512081082516-1.29838243641-0.1716394046370.3848855917150.6480695521680.392523952927-0.3046708725551.050558553830.2574471583490.0977419941548-0.03823305811450.09181586615110.02910655920510.29662700791-10.8479321653-7.40269066888-7.79548200155
71.72234386284-1.2561221767-3.13987070130.9727424894862.278571161595.80853793545-0.4550217083560.32315898092-0.8964830175640.407933199882-0.1584215702230.006153830269760.9626333300610.0602496707605-0.4349661006250.303331330304-0.051740403238-0.08522885911440.392127994909-0.1045414467960.618733649424-4.74039833646-24.8817435828-12.3445699225
80.944760196658-0.14326828529-1.070353862690.9658170386921.763146364634.00514241695-0.4245117010670.118551995989-0.1593212274090.4195711423450.662295506473-0.6193623046590.5090236074350.708524507944-0.008415710641840.177567244651-0.0407854359922-0.1267621059910.216885296720.01720251350530.26122720451114.2101014688-22.0847470137-4.97446311332
90.693422071417-0.1329391335470.5176162414160.4560039918050.138705657750.948227258336-0.389410405368-0.324674262021-0.0599071489610.405570582042-0.01792357966430.1526262351040.0767224835414-0.280851017108-0.4566783644930.453679960901-0.0975043857915-0.1174872609080.202037140948-0.1893752306170.7275889323255.27273823163-37.3564323529-8.85672239299
100.114289734748-0.2464285716680.08186394109360.3656328246380.1208012330430.830413102229-0.0212412389660.131032678260.1926381019760.34106090825-0.047574701192-0.245677096750.0982232395684-0.0732825585011-0.001124504367560.2525502872230.0112930671064-0.01988212649010.29612593536-0.005339997085130.27859930150913.1086416413-30.3664304854-14.6811336551
110.3520966052760.0963655963086-0.07608520549040.1284567941530.06675133398710.07820454083580.118926880712-0.523709263992-0.294555227437-0.1155892753640.170188420391-0.136902082660.7228876805230.3965049539110.01713018423160.5575297414650.141400721106-0.09269806029360.3826707426240.001345680125740.35355580393115.0042938378-41.2779001976-18.0930138408
126.656484032710.3406538695482.7565716022.41649943472-1.70769158142.622079312330.556588531395-0.8355672020870.06131885983970.246684795605-0.1337044158960.529868839915-0.903212796941-0.6713557198130.5107861159980.524767872830.0904974777236-0.0291673042970.276836471432-0.157987264650.2874413387374.17914294106-31.318978459-26.5093382391
130.101310933001-0.115696724605-0.06065408914680.575339657917-0.1193317312790.3755424533780.2826529977090.486695383931-0.0977763223988-0.815211555201-0.257769256663-0.8274605143351.227395415030.375172041698-0.01892771454590.6902722862460.163842910912-0.03092173496740.352351636233-0.02915728477140.55915502579418.2684784693-45.1234097754-21.3798174076
140.194390766089-0.2901448147680.1380837838971.165292205220.796495037381.71973336170.2288922890290.3718435472870.435850381423-0.2885636988040.0487596752199-0.849215206394-0.6028795463390.4871194892650.1634716490090.2427355721980.110869980735-0.02032032558270.36521356544-0.05935531472040.35293412137519.6681556676-33.0334819518-22.5444001297
151.21227770788-0.4019083890570.1726794668950.4682475220910.5337695232861.060687032630.3955459684940.1054137061510.8301244852580.116878957285-0.744279748523-0.211597418792-0.435456199961-0.887696907589-0.07827816004160.366921923258-0.02629082362610.108357740060.5332252586880.01959434199080.36065700136312.0503572286-15.7559041418-20.2077134688
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 107 through 127 )AA107 - 1271 - 21
22chain 'A' and (resid 128 through 134 )AA128 - 13422 - 28
33chain 'A' and (resid 135 through 176 )AA135 - 17629 - 70
44chain 'A' and (resid 177 through 191 )AA177 - 19171 - 85
55chain 'A' and (resid 192 through 205 )AA192 - 20586 - 98
66chain 'A' and (resid 206 through 215 )AA206 - 21599 - 108
77chain 'A' and (resid 216 through 228 )AA216 - 228109 - 121
88chain 'B' and (resid 109 through 127 )BB109 - 1271 - 19
99chain 'B' and (resid 128 through 134 )BB128 - 13420 - 26
1010chain 'B' and (resid 135 through 165 )BB135 - 16527 - 57
1111chain 'B' and (resid 166 through 176 )BB166 - 17658 - 68
1212chain 'B' and (resid 177 through 191 )BB177 - 19169 - 82
1313chain 'B' and (resid 192 through 205 )BB192 - 20583 - 95
1414chain 'B' and (resid 206 through 215 )BB206 - 21596 - 105
1515chain 'B' and (resid 216 through 228 )BB216 - 228106 - 118

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