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- PDB-6u9s: Crystal structure of human CD81 large extracellular loop in compl... -

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Basic information

Entry
Database: PDB / ID: 6u9s
TitleCrystal structure of human CD81 large extracellular loop in complex with 5A6 Fab
Components
  • 5A6 FAB Heavy Chain
  • 5A6 FAB Light Chain
  • CD81 antigen
KeywordsCELL ADHESION / tetraspanin / antibody
Function / homology
Function and homology information


positive regulation of adaptive immune memory response / positive regulation of protein catabolic process in the vacuole / macrophage fusion / CD4-positive, alpha-beta T cell costimulation / positive regulation of B cell receptor signaling pathway / osteoclast fusion / myoblast fusion involved in skeletal muscle regeneration / positive regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / positive regulation of inflammatory response to antigenic stimulus / regulation of macrophage migration ...positive regulation of adaptive immune memory response / positive regulation of protein catabolic process in the vacuole / macrophage fusion / CD4-positive, alpha-beta T cell costimulation / positive regulation of B cell receptor signaling pathway / osteoclast fusion / myoblast fusion involved in skeletal muscle regeneration / positive regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / positive regulation of inflammatory response to antigenic stimulus / regulation of macrophage migration / transferrin receptor binding / immunological synapse formation / tetraspanin-enriched microdomain / positive regulation of T-helper 2 cell cytokine production / positive regulation of protein exit from endoplasmic reticulum / protein localization to lysosome / humoral immune response mediated by circulating immunoglobulin / MHC class II protein binding / positive regulation of CD4-positive, alpha-beta T cell proliferation / cholesterol binding / positive regulation of T cell receptor signaling pathway / cellular response to low-density lipoprotein particle stimulus / immunological synapse / positive regulation of receptor clustering / positive regulation of B cell proliferation / basal plasma membrane / Regulation of Complement cascade / protein localization to plasma membrane / regulation of protein stability / receptor internalization / integrin binding / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / MHC class II protein complex binding / virus receptor activity / basolateral plasma membrane / vesicle / positive regulation of MAPK cascade / focal adhesion / positive regulation of transcription by RNA polymerase II / extracellular exosome / membrane / plasma membrane / cytosol
Similarity search - Function
Cd81 Antigen, Extracellular Domain; Chain: A / Tetraspanin / Tetraspanin, conserved site / Transmembrane 4 family signature. / Tetraspanin, animals / Tetraspanin, EC2 domain superfamily / Tetraspanin/Peripherin / Tetraspanin family / Immunoglobulins / Immunoglobulin-like ...Cd81 Antigen, Extracellular Domain; Chain: A / Tetraspanin / Tetraspanin, conserved site / Transmembrane 4 family signature. / Tetraspanin, animals / Tetraspanin, EC2 domain superfamily / Tetraspanin/Peripherin / Tetraspanin family / Immunoglobulins / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsSusa, K.J. / Seegar, T.C.M. / Blacklow, S.C.B. / Kruse, A.C.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R35 CA220340 United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)F31 HL147459 United States
CitationJournal: Elife / Year: 2020
Title: A dynamic interaction between CD19 and the tetraspanin CD81 controls B cell co-receptor trafficking.
Authors: Susa, K.J. / Seegar, T.C. / Blacklow, S.C. / Kruse, A.C.
History
DepositionSep 9, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 13, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 5A6 FAB Heavy Chain
B: 5A6 FAB Light Chain
C: CD81 antigen
D: 5A6 FAB Heavy Chain
E: 5A6 FAB Light Chain
F: CD81 antigen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,5969
Polymers119,3196
Non-polymers2763
Water6,449358
1
A: 5A6 FAB Heavy Chain
B: 5A6 FAB Light Chain
C: CD81 antigen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,8445
Polymers59,6603
Non-polymers1842
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6170 Å2
ΔGint-36 kcal/mol
Surface area23680 Å2
MethodPISA
2
D: 5A6 FAB Heavy Chain
E: 5A6 FAB Light Chain
F: CD81 antigen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,7524
Polymers59,6603
Non-polymers921
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5590 Å2
ΔGint-35 kcal/mol
Surface area23930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.003, 96.858, 297.091
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

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Components

#1: Antibody 5A6 FAB Heavy Chain


Mass: 24620.676 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): Expi293F / Production host: Homo sapiens (human)
#2: Antibody 5A6 FAB Light Chain


Mass: 24186.023 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): Expi293F / Production host: Homo sapiens (human)
#3: Protein CD81 antigen / 26 kDa cell surface protein TAPA-1 / Target of the antiproliferative antibody 1 / Tetraspanin-28 / Tspan-28


Mass: 10852.978 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD81, TAPA1, TSPAN28 / Cell line (production host): Expi293F / Production host: Homo sapiens (human) / References: UniProt: P60033
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 358 / 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: 2.5 Å3/Da / Density % sol: 50.81 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 4
Details: 0.2 Magnesium formate dihydrate, 0.1 M sodium acetate trihydrate pH 4.0, 18% w/v PEG MME 5000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 5, 2018
RadiationMonochromator: Cryo-Cooled double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.4→49.52 Å / Num. obs: 46501 / % possible obs: 99.1 % / Redundancy: 6.3 % / Biso Wilson estimate: 42.71 Å2 / CC1/2: 0.995 / Net I/σ(I): 7.94
Reflection shellResolution: 2.4→2.54 Å / Num. unique obs: 7210 / CC1/2: 0.166

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
PHENIX1.16_3549refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4S1D, 5TCX

4s1d

5tcx


Resolution: 2.4→49.52 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 32.2686
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2808 1747 4.29 %
Rwork0.2144 38998 -
obs0.2172 40745 87.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 78.23 Å2
Refinement stepCycle: LAST / Resolution: 2.4→49.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7974 0 18 358 8350
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00288166
X-RAY DIFFRACTIONf_angle_d0.537311133
X-RAY DIFFRACTIONf_chiral_restr0.0421287
X-RAY DIFFRACTIONf_plane_restr0.00361429
X-RAY DIFFRACTIONf_dihedral_angle_d14.25262892
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.470.55091030.45152442X-RAY DIFFRACTION66.16
2.47-2.550.44151150.40622524X-RAY DIFFRACTION69.19
2.55-2.640.46811240.38012761X-RAY DIFFRACTION74.95
2.64-2.740.4091340.34392917X-RAY DIFFRACTION79.6
2.74-2.870.34141370.3093086X-RAY DIFFRACTION83.2
2.87-3.020.39351430.28933245X-RAY DIFFRACTION88.64
3.02-3.210.32651520.2563396X-RAY DIFFRACTION92.11
3.21-3.460.27961580.22573529X-RAY DIFFRACTION94.83
3.46-3.80.26441650.18583664X-RAY DIFFRACTION98.03
3.8-4.350.2321680.1563727X-RAY DIFFRACTION98.78
4.35-5.480.20981710.14833763X-RAY DIFFRACTION98.67
5.48-49.520.23441770.18153944X-RAY DIFFRACTION98.03
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)
12.417189629091.26627726333-2.013074001855.77909343758-1.484900240844.79301375197-0.2654230962580.0587034315998-0.3907399303160.115269587748-0.02428638735220.1136945355620.68985359237-0.07454219938970.2805066843320.339853862106-0.01033066709290.1113523629780.272307903215-0.04337076725720.561948917627-17.8198610571-21.4942298665-54.8634410664
23.55978304862-3.20183332358-3.286992883059.30805128722-0.4508994927232.76531329373-0.145961435636-0.8955164091350.5171371884250.6737939334520.389148460521-0.6315875447771.094746371670.03244066966380.1862441824250.392900318494-0.06576999773370.01230253014460.763839805504-0.1029070811850.728426918959-36.6417105029-22.6926903059-21.7392052035
39.593974072042.67717120005-1.558538722277.46658789755-2.05311656323.45133368563-0.2938315382360.2971919273810.0421168976785-0.5325325876750.2142816784960.5391808592610.579300924474-0.6236112440850.1827477247470.482684660361-0.04769739626390.0005037979994260.5561965016590.04750725232090.431185955779-39.9266105241-19.5544373067-26.4204034934
44.809677107081.0328163222-0.6892806582451.42530714202-1.446828637314.888867665680.414569606536-0.688131506937-0.3586847573030.396502939017-0.431535000836-0.278318492184-0.1257939821040.7105628618930.07688066998680.391009907968-0.0912858369103-0.09216582256930.5329345344130.03914385754280.533000672764-8.79695886817-2.80594448118-37.9568363017
54.775427992040.7423008348863.501324646547.18829637711-3.709077653482.07744764722-0.432153023662-0.2882177233310.21074854483-0.036591349967-0.194647882353-1.160913996860.1463372087231.254422726960.6163493434880.2526923995450.0760126614654-0.06046293100780.7704778415760.05431297054370.8145762996061.83781184962-3.80962359428-56.5449024122
63.131425421171.49951298008-2.742293729292.77324920374-1.433891640455.014729967920.19283509981-0.3164425354210.2813861228180.303098033681-0.128131298357-0.0355495359927-0.3144061710240.249007282579-0.1355198989110.294494680357-0.00463231312791-0.03502443664240.337530941923-0.02301487716310.458850977466-14.0410486219-2.23489463875-44.1177636276
73.766458818132.07761487916-1.36296812219.54512598889-5.492555888288.838933342670.251606518528-1.55007844339-0.3940305745920.541560832594-0.634293745342-0.475460399270.06233696947251.19217574130.3578498938570.448206738858-0.01008365155740.05937380848321.077906762860.05352642847110.471399988332-27.4851426646-18.907699473-14.6039646022
89.565685885692.76251025115-5.922883581023.88919839026-1.904600797068.136220078150.781942545365-0.3949595103441.345590678350.463570761331-0.007493886079990.0652430735716-1.056337934760.240384438331-0.7054186628980.331862136884-0.00224257385155-0.002696168306380.303733881695-0.01451152629270.733066191969-4.9309118027713.4148034827-73.798691603
94.652645737031.47268352367-1.183686315874.042940466950.9272469709336.5114616482-0.087187611875-0.1822686954750.533369335406-0.248537708797-0.1090670335720.06090679617180.0727200575095-1.094284845050.1517742476780.183467916732-0.003067203861340.00695300610720.463543919042-0.01651668096780.593123151242-12.81372660613.98145293221-73.550725126
102.589130988993.830128998392.809072482959.09079587643-0.2360963296668.14863588394-0.351983062480.330154481852-0.188679342748-0.5274274075030.197707152239-0.4908098209470.4344068944820.2188008230970.1233673080560.219241960760.003710950471340.05821447096820.3506544667950.006206424431060.430670791428-10.5131552022-4.31785288789-66.3303075094
114.067446842043.39959045107-4.064813295898.049049306481.438661175629.16491163882-1.04684776868-0.357428511919-1.375550018470.139581944406-0.212339104422-0.565543564357-0.05264880513991.916943096511.015086244790.262924294712-0.0443574625875-0.01655618603010.7473118697020.1510029913120.6702755472122.837136892574.92135539273-73.0310677036
126.678989289342.06247297159-0.2588810843747.16367644648-2.943339378939.92178906052-0.658173297147-0.34437745027-0.9841181224950.3119918682310.180436768050.08774354908622.02601769467-0.5138825590640.4809183941820.880926171193-0.01299195657860.2387763086050.497243100617-0.04691854544540.652320968223-12.6068467897-65.1193167014-39.3852906432
134.383453069980.288917954879-2.41720498840.644054969548-0.7713217562376.99120877882-0.677024697025-0.526612482031-1.02472509920.2135650541280.117322132483-0.3118301675112.31561996757-0.6555295461690.6062869890611.14755993408-0.1434606634330.2101970958190.7072683627310.09900450320040.717041673459-16.1353140238-66.1020326371-33.1726707762
147.955694636210.218288782158-4.858294481745.175465145560.2541772764668.794769603-0.708486509081-0.553076006246-0.3359482775660.179491454150.4490246405470.7586876241820.665204445916-1.568311833750.2450211134120.8290874381170.01192882258950.01890236633991.848558713850.1774612786010.648556627928-33.7936211466-57.1635533582-9.45742243416
154.90470594866-0.836066815109-0.4176881144890.517118738143-0.8071631879591.86155231981-0.168625808158-0.763756281472-0.4946527468840.608728819291-0.306061557098-0.06982056915320.50979972350.6760348909840.2844381305810.6991181215940.304603963726-0.1319848375262.02988741166-0.2485704346920.68908494203-1.38468339171-49.0429115804-25.4471010484
162.90856519859-0.0625919285751-0.5932279697382.66728071403-1.367642331495.30588698182-0.470068776583-1.380917512170.6157722297170.4776697165920.426393256666-0.585187134008-0.3849067370421.621776669710.122906563340.4575657570390.174258287843-0.1532551485441.30338017587-0.26119527680.7814412953752.16525396133-44.8083483319-36.2735565992
170.14048456156-1.03617810758-0.4538168521896.466869055140.4738302178617.59677748865-0.230959979695-0.69235625320.3824910334820.4155240426820.303480802925-0.190864985075-0.1951484801360.191853324613-0.03726560887030.318543826590.0924310448830.006081882171880.804824051467-0.1866109949860.5427235041-7.37523513605-43.4496710747-35.9079123178
186.325799652017.28089210336-1.484027513598.808446543190.7637485163378.759403505960.172391457967-1.266674165790.8757124280671.3590717843-0.3456681420231.27783131656-0.1531591259230.1015650243970.1181350856330.4957640393730.131646260736-0.006685482215620.812815657533-0.157290650170.529331337729-11.051973209-43.0244753157-29.4694598696
191.2751655355-0.898873386222-1.832493649521.859776796460.1089649423577.45253171685-0.187487346359-1.340563150160.4108293318480.5663947056670.704072143224-0.1116989454390.207334834582-0.257867791991-0.4535378754690.7035142277940.399262863248-0.07861362638761.72468813317-0.04613416538160.441048258478-16.9947624309-52.8283430803-13.8466700491
201.558676297541.467795311972.167422193659.260467419054.333508252433.657466848710.34924491253-0.829507223578-0.3996239804620.448394316084-0.2425754291560.100623516434-0.524395578135-0.0764953213883-0.2155763304860.5958305778530.222088487554-0.005041882221181.66826560376-0.07865453889550.628413022573-19.9294861229-50.8834179473-4.43735703385
213.672992138432.50889910408-0.7398503279993.592117079190.8008516894621.18764697059-0.722154557006-1.53276866773-0.1998782431560.8331599867851.41544304587-0.2093737238130.19733242931-1.87205693695-0.651178548260.9207168404580.463743102284-0.05126608405921.81282010225-0.0629600296960.659122784245-18.4987347634-53.8500291975-3.50014061458
229.0832550977-1.811075238390.9972226366998.372473107977.657373015727.91208398155-0.154025578533-1.67433924593-1.373362812422.682582266460.8104555409261.775726020010.598117105745-1.91090492285-0.9021666356251.03515938970.1026772763020.06135597323452.125072522810.2407889035340.68424572742-22.1920419234-61.38360477180.274385107906
234.713334199742.09154942904-1.805058489489.06067567474-1.462782410064.39422767195-0.159858618117-1.61240543407-0.1413570751311.571758366810.4435641315040.120347889990.701095866840.453982679097-0.3038235702941.255321509180.28924121639-0.01143414749322.3910681154-0.01726318807110.669415593824-21.00036499-52.49551532767.83655954943
249.378616566454.79630297955-5.038741793054.69149065568-3.655555350579.087052022130.2347724936910.2724121250840.3936539213590.4651461536210.269468525988-0.329798519683-0.977085579681-0.153706407669-0.4686373704580.24716432483-0.06082342505730.04562172778540.382248845672-0.1894088100740.81939596627-0.858667228713-33.7901945856-63.4494908528
254.4215689484-1.10813004251.805609092365.589257528171.082427067978.85874096085-0.260597940123-0.690220357379-0.1497749176630.04344867655320.1748534826720.1792367373030.00732773804791-0.6826692107620.04448649250920.233282271675-0.03050730095080.05825038233490.482801383284-0.1134585653510.57699307622-7.98254887342-43.3185241728-60.3107409648
263.206109243093.923932307452.024577198539.41061187155-2.005105526485.55518908371-0.8142175192970.329697099097-0.239667305631-0.04825514362760.6251463372330.01771312485640.9240710933860.04897150523220.1606572739670.4106879091440.04458083620090.1279742408260.765813973207-0.1224495858790.556097461522-5.67919591468-51.6631702554-53.6305394369
272.066538864858.53058752865-7.906359685327.98328101762-3.1234991942.16377330008-0.631482840293-0.721561365759-0.5312217444260.249816641907-0.162041820639-0.7827059434010.2709010500430.9445983356020.7609737348050.2780506389450.0550085807719-0.003253962949310.687462817765-0.02766156990620.7218551357437.62668475694-42.4642895173-61.8441535283
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 117 )
2X-RAY DIFFRACTION2chain 'A' and (resid 118 through 151 )
3X-RAY DIFFRACTION3chain 'A' and (resid 152 through 221 )
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 25 )
5X-RAY DIFFRACTION5chain 'B' and (resid 26 through 38 )
6X-RAY DIFFRACTION6chain 'B' and (resid 39 through 118 )
7X-RAY DIFFRACTION7chain 'B' and (resid 119 through 219 )
8X-RAY DIFFRACTION8chain 'C' and (resid 111 through 136 )
9X-RAY DIFFRACTION9chain 'C' and (resid 137 through 162 )
10X-RAY DIFFRACTION10chain 'C' and (resid 163 through 189 )
11X-RAY DIFFRACTION11chain 'C' and (resid 190 through 202 )
12X-RAY DIFFRACTION12chain 'D' and (resid 1 through 64 )
13X-RAY DIFFRACTION13chain 'D' and (resid 65 through 130 )
14X-RAY DIFFRACTION14chain 'D' and (resid 131 through 219 )
15X-RAY DIFFRACTION15chain 'E' and (resid 1 through 13 )
16X-RAY DIFFRACTION16chain 'E' and (resid 14 through 38 )
17X-RAY DIFFRACTION17chain 'E' and (resid 39 through 81 )
18X-RAY DIFFRACTION18chain 'E' and (resid 82 through 96 )
19X-RAY DIFFRACTION19chain 'E' and (resid 97 through 133 )
20X-RAY DIFFRACTION20chain 'E' and (resid 134 through 151 )
21X-RAY DIFFRACTION21chain 'E' and (resid 152 through 177 )
22X-RAY DIFFRACTION22chain 'E' and (resid 178 through 191 )
23X-RAY DIFFRACTION23chain 'E' and (resid 192 through 218 )
24X-RAY DIFFRACTION24chain 'F' and (resid 112 through 136 )
25X-RAY DIFFRACTION25chain 'F' and (resid 137 through 165 )
26X-RAY DIFFRACTION26chain 'F' and (resid 166 through 189 )
27X-RAY DIFFRACTION27chain 'F' and (resid 190 through 202 )

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