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- PDB-8gvi: The complex between H25-11 TCR and HLA-A24 bound to HIV-1 Nef138-... -

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Basic information

Entry
Database: PDB / ID: 8gvi
TitleThe complex between H25-11 TCR and HLA-A24 bound to HIV-1 Nef138-8 peptide
Components
  • 8-mer peptide from Protein Nef
  • Beta-2-microglobulin
  • H25-11 TCR alpha chain
  • H25-11 TCR beta chain
  • MHC class I antigen
KeywordsIMMUNE SYSTEM / Complex structure / Public TCRs / T cell immunity / Nef138-8 epitope
Function / homology
Function and homology information


negative regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / transferrin transport / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / peptide antigen assembly with MHC class II protein complex / cellular response to iron(III) ion ...negative regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / transferrin transport / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / peptide antigen assembly with MHC class II protein complex / cellular response to iron(III) ion / MHC class II protein complex / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / regulation of erythrocyte differentiation / HFE-transferrin receptor complex / response to molecule of bacterial origin / MHC class I peptide loading complex / T cell mediated cytotoxicity / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / MHC class I protein complex / positive regulation of T cell activation / peptide antigen binding / positive regulation of receptor-mediated endocytosis / negative regulation of neurogenesis / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / multicellular organismal-level iron ion homeostasis / specific granule lumen / phagocytic vesicle membrane / recycling endosome membrane / Interferon gamma signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / MHC class II protein complex binding / Modulation by Mtb of host immune system / late endosome membrane / sensory perception of smell / positive regulation of cellular senescence / tertiary granule lumen / DAP12 signaling / T cell differentiation in thymus / negative regulation of neuron projection development / ER-Phagosome pathway / protein refolding / early endosome membrane / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / endoplasmic reticulum lumen / Amyloid fiber formation / Golgi membrane / lysosomal membrane / external side of plasma membrane / focal adhesion / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / endoplasmic reticulum / Golgi apparatus / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane / cytosol
Similarity search - Function
MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / MHC classes I/II-like antigen recognition protein / : ...MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / MHC classes I/II-like antigen recognition protein / : / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
MHC class I antigen / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
HIV whole-genome vector AA1305#18 (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsGao, G.F. / Shi, Y. / Tan, S. / Ma, K. / Chai, Y. / Qi, J. / Kawana-Tachikawa, A. / Iwamoto, A. / Dong, T. / Guan, J.
Funding support China, 1items
OrganizationGrant numberCountry
Chinese Academy of Sciences2021YFC2300700 China
CitationJournal: J Immunol. / Year: 2022
Title: Molecular Basis for the Recognition of HIV Nef138-8 Epitope by a Pair of Human Public T Cell Receptors.
Authors: Ma, K. / Chai, Y. / Guan, J. / Tan, S. / Qi, J. / Kawana-Tachikawa, A. / Dong, T. / Iwamoto, A. / Shi, Y. / Gao, G.F.
History
DepositionSep 15, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 19, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 26, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: H25-11 TCR alpha chain
B: H25-11 TCR beta chain
H: MHC class I antigen
L: Beta-2-microglobulin
P: 8-mer peptide from Protein Nef


Theoretical massNumber of molelcules
Total (without water)96,0475
Polymers96,0475
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11040 Å2
ΔGint-54 kcal/mol
Surface area38490 Å2
Unit cell
Length a, b, c (Å)70.524, 70.524, 384.253
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z

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Components

#1: Protein H25-11 TCR alpha chain


Mass: 23174.695 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#2: Protein H25-11 TCR beta chain


Mass: 28269.469 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#3: Protein MHC class I antigen


Mass: 31683.086 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-A / Production host: Escherichia coli (E. coli) / References: UniProt: F6IQZ4
#4: Protein Beta-2-microglobulin


Mass: 11879.356 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Production host: Escherichia coli (E. coli) / References: UniProt: P61769
#5: Protein/peptide 8-mer peptide from Protein Nef


Mass: 1040.195 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) HIV whole-genome vector AA1305#18 (others)
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: 2.87 Å3/Da / Density % sol: 57.17 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Potassium chloride, 0.1 M tris (pH 8.0), 15% PEG2000 MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 11, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 3.3→50 Å / Num. obs: 17740 / % possible obs: 99.5 % / Redundancy: 16.1 % / Biso Wilson estimate: 64.33 Å2 / Rmerge(I) obs: 0.161 / Rsym value: 0.161 / Net I/σ(I): 18.477
Reflection shellResolution: 3.3→3.42 Å / Rmerge(I) obs: 2.033 / Mean I/σ(I) obs: 1.406 / Num. unique obs: 17740

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Processing

Software
NameVersionClassification
REFMAC5refinement
PHENIX1.19.2_4158refinement
xia2data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VXM

3vxm


Resolution: 3.3→47.81 Å / SU ML: 0.5048 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.7303
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3135 793 4.99 %
Rwork0.2865 15110 -
obs0.2879 15903 89.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 73.11 Å2
Refinement stepCycle: LAST / Resolution: 3.3→47.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6666 0 0 0 6666
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00246842
X-RAY DIFFRACTIONf_angle_d0.54539279
X-RAY DIFFRACTIONf_chiral_restr0.0409965
X-RAY DIFFRACTIONf_plane_restr0.00441220
X-RAY DIFFRACTIONf_dihedral_angle_d15.15412508
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3-3.510.3684610.42011212X-RAY DIFFRACTION44.09
3.51-3.780.45491370.3782582X-RAY DIFFRACTION95.27
3.78-4.150.32831290.33042803X-RAY DIFFRACTION99.52
4.16-4.760.29231680.26062725X-RAY DIFFRACTION99.21
4.76-5.990.30631280.25462822X-RAY DIFFRACTION99.23
5.99-47.810.25871700.23812966X-RAY DIFFRACTION98.83
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)
1-0.00139322556827-0.067943293449-0.0675410266104-0.0598891464473-0.0376373006496-0.04948591318090.347659967123-0.171846183611-0.1449941982510.108682275210.0592793104986-0.07605828676310.249600707105-0.1323306662071.13139762753E-9-3.53677599612.443074020540.593817353355-1.36592125097-0.432442378427-0.763153830474-13.6040453871-8.8803283062910.9608636353
20.00644938718883-0.0089249767749-0.001935772043050.02359946722670.003240987730280.02427031017050.08879234272570.0218507987230.00492233107634-0.00426328529746-0.00337859678671-0.0294705449252-0.0986682673325-0.00716671085261-9.83258164945E-110.6105077106020.3823560109060.05479386631920.5558858073080.1892441084480.738864483672-6.448019765916.5228893669-13.1176126633
30.00105935988534-0.000193079038106-0.005331620207830.000897014440090.006115543279990.000886678120488-0.002677416710230.007778079982590.015183921838-0.007556906494170.000987467980914-0.000385847668806-0.04530046367180.0207171403321-3.3349271188E-70.3833979473820.0299368962810.06209495550380.423926521257-0.02656934667520.426003644079-11.471324853817.126989533223.3488589398
40.002387058132750.006256586582930.007295255432970.0128757967442-0.004393471271670.0117476649202-0.0496632748355-0.02657461202530.0575308471362-0.00105197909286-0.01068752056610.029650840934-0.09284531117280.01913979795918.84300335745E-80.01818013685990.07171910328850.06274092413590.5564487579060.08736456415430.209024971506-15.05989263064.6124747807526.8566978789
50.0008805666464260.002993174519180.0002286312709220.0006824762495080.01051809137220.00465020598259-0.00351673107146-0.00490201235821-0.001544903915010.0562361666441-0.03911532296640.00999970308718-0.0293922384880.03402354285873.25966496127E-80.2732901930470.02971381533050.07821003027810.581085811692-0.06468990029190.467276250731-11.8665086995.3595893703835.7803227789
6-0.0002756745292170.00396346667664-0.00104021435254-0.0004530618692730.00166964589404-0.00125849374723-0.017937554196-0.0004890450625680.03379436349770.029808393729-0.01814997353850.00298168223737-0.0195216067260.0319236842901-8.30486620885E-70.548484969183-0.1041722294460.1194772948150.5919294731070.01756878787270.424564889784-6.2998519693413.830908363529.729588833
70.00812872084074-0.004433205928870.005804074083360.000373290194621-0.0025165203780.00813738592098-0.079245256680.00279857074418-0.09273759716110.00113855338471-0.03646943200650.0700282460774-0.08152066221450.0155884152739-3.09790793677E-70.09208633688980.3373186303940.09114205542460.3891571782880.008476547018050.48077958314-20.812696092-1.7947369080424.8763690492
8-0.004091316254790.00651912047908-0.01233892872970.0001308458246660.00459099340908-0.0146324704932-0.09455154195710.02580301882640.07597143508390.006507479128-0.0752499781988-0.0440278438158-0.09969614013240.0421791044836-3.3022430424E-70.202033134724-0.05515241196310.01789114980250.216474419869-3.0717040879E-50.196161917433-5.2555333342520.30089113617.6606841792
90.0108729604678-0.006764752574150.002696626189360.0177630239558-0.002407387018150.004391661261660.0281121193293-0.001279141684450.002805763323150.031970880791-0.0520880228130.0360203833956-0.022653895518-0.0399313060805-3.65863516448E-70.5172401230430.434357877341-0.09641649450480.3480021661870.2705856845760.64747069362-14.283248977522.445918148-5.50793339597
100.00111690006233-0.005567989380170.003605526737820.0133660575101-0.001657020977470.0003647455986980.02485192672510.009949484623390.006262597930270.0428734998944-0.011471963541-0.0425719101497-0.057223572206-0.0263472571817-2.36595933519E-70.6228769059850.2270099387380.001216867414010.557007105360.1353147465610.878744942525-9.444914846318.92348580951.83062133563
110.003110345482570.000472883243798-0.002415707582930.00693292242667-0.006516806378410.0001188325093340.0452461411289-0.004437796597670.04681554747690.039581938436-0.09818281709450.085583750239-0.0357183458184-0.07106144458516.0949444147E-70.5060701361890.511063828138-0.09727380832010.4613969593340.3460425645090.737086897145-21.339421620923.1531166183-6.76204391921
120.0008263678625730.001136424324870.000446041028166-0.000198176089190.0007027981421570.00129108479625-0.02235144540620.002773140662870.01671325848150.002476689851570.001996907183370.00134720565679-0.0258664889686-0.001412334041172.37980943975E-71.15698651812-0.127186762902-0.01658884816231.151297155740.07732727042791.12255515895-8.2230090458731.76631628419.2422657475
130.000622913925822-0.0018223608160.0007604054577856.85115608827E-50.00145457661441-6.66238779567E-50.02423583596820.018666636558-3.5693532884E-5-0.00288065810643-0.0336700755280.0181045408219-0.0169353788534-0.0119955082255-2.3966864034E-60.6631173236370.319331471524-0.03604062651990.5831788451510.02935182252170.808224071881-20.320537744730.1005045913-3.41192800682
140.03804134278730.01136370102790.008349549479210.0693115750523-0.07676999256580.07239120651740.11776523589-0.0553460345869-0.02802912880570.288066839394-0.06966223398520.206007471291-0.0007398566173490.1421584574582.32880995695E-9-0.8751598861360.1127802046980.07721721939940.707620790580.136671781719-0.018800750577-21.1778520897-16.238899709742.0112333706
150.0360852180898-0.06537351748960.0219357394528-0.00592216041974-0.0387137910853-0.008717035974080.440694407261-0.0327561486144-0.230176472628-0.0883352528968-0.188689238116-0.07246195641620.19590682177-0.1412767400819.70936408889E-9-0.2676674587850.279631661784-0.5039487517290.9072460168740.5441740731430.275258078536-10.6131812615-40.671274074861.6314897364
160.00169704942108-0.000547958575927-0.005806828317350.003348559886510.0007482586738630.00908218296684-0.01913487386780.00547989979991-0.00239855200012-0.0191574659398-0.008050975522430.02232976203830.00128918755650.00050155447393-2.2812220074E-70.1803661814950.138433122502-0.01074548550930.5852796320760.02577194045980.278731017934-22.0445402728-24.587964222964.7203137307
170.001685979008350.000200041184476-0.00066794184666-0.0003546140241921.73601933177E-50.00171981739171-0.00531401955832-0.00398261541940.00905493824311-0.000919971134139-0.00382048091765-0.00996295884979-0.00781023643987-0.00401898265975-1.81990458823E-60.57817141465-0.00947936966633-0.03159539570590.6849483990650.0836440803870.6523799486610.52400179626-28.676934761971.8800854224
180.004315902150120.0049193966658-0.007387916774150.00177286493564-0.007004181434390.008496687657260.0363397395823-0.00339724377760.03916936501160.0362021444080.0589429697501-0.008166635603-0.0257479222452-0.0006394886361023.10578611288E-70.2766275816590.237802630467-0.03561749040540.7914335441930.191688082740.406226744959-15.6264650245-19.013401620966.0965658942
190.00820148007111-0.015875908708-0.002271803868850.0003369586436830.007938769334390.00367299649581-0.01163455141640.05231027402830.005646312116440.114152385180.003774851313220.00356587440808-0.0722622888482-0.01881233209524.59442961594E-70.2056687112560.1505336567860.09371047672570.6618221501420.2388422930880.354896047994-15.493335025-17.558611518561.6256851009
200.002609795545210.000694789858922-0.00110836512557-0.00143599516206-0.000454023557730.00296220660788-0.0109280173132-0.0101389208718-0.003482138374410.0163824449748-0.00977707164983-0.0475302143666-0.002205685159670.0140015688316-3.66402079803E-60.3704707734970.08199366981280.034245353570.5674241358620.03976547535630.281566301451-7.04452967977-19.149948722966.7615748865
210.0009355462503030.000185555631824-0.000157750865255-0.000814778690957-9.06375537374E-50.0001530546799330.002426901703940.001809872794760.00313447022420.0112817572355-0.005704146465040.0145792690190.001166370651930.00934684693759-3.01757905506E-60.652982851055-0.0584517922064-0.05161090479960.7631157406270.1058821898510.713819313523-4.35898955294-23.991998787582.6197749344
220.0003327176680460.000537721764518-0.000910372197675-0.000665261242354-0.001471889985190.000961612550787-0.000833466464836-0.01130953016120.0167833967142-0.005041643216370.00846539629680.04560434691740.006189652246640.01131687117931.60151952812E-50.634413057550.0010095402549-0.03599501804330.7746562651450.06582498179260.696200217852-17.9284673044-17.565841429272.1021234012
230.000692747815266-0.000775793499827-0.000266616152421-7.92287215517E-60.0006433391369840.0002133589025070.00748638209891-0.002577456416710.0003094408883590.004183599237920.004673083706450.0122184225528-0.00555053442002-0.001628746886341.0756778462E-50.5841196244060.06829140955320.01393376610410.690747267655-0.00968470268130.45112158865-28.7397447272-16.734840601171.4422531687
240.00167394979205-0.001226607126470.0001893408499256.90098653048E-5-0.0007955354465060.001203418939520.009464318648670.0202428158145-0.02223358608230.007382476117770.0310320292041-0.01518140226980.00237872688021-0.0003195930912841.79690800174E-60.4828829167770.0560017495293-0.03969841591830.6206971829970.03713878191690.418494289484-13.6304598703-27.589283538375.8636187683
250.000620660896311-0.0002154245267660.0009893471761970.00495014463863-0.00125052841880.00647562729569-0.014507482975-0.0242255960044-0.01825619807340.0347429056165-0.00585303866967-0.0351064296136-0.00632014119535-0.02338521013226.73885880997E-70.1755017683230.1945522569590.07269249030980.5710201518160.0489453258340.306196049468-20.9963532539-13.450352847536.743573999
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 3 through 114 )AA3 - 1141 - 112
22chain 'A' and (resid 115 through 205 )AA115 - 205113 - 203
33chain 'B' and (resid 3 through 19 )BB3 - 191 - 17
44chain 'B' and (resid 20 through 51 )BB20 - 5118 - 49
55chain 'B' and (resid 52 through 74 )BB52 - 7450 - 72
66chain 'B' and (resid 75 through 89 )BB75 - 8973 - 87
77chain 'B' and (resid 90 through 106 )BB90 - 10688 - 104
88chain 'B' and (resid 107 through 125 )BB107 - 125105 - 123
99chain 'B' and (resid 126 through 163 )BB126 - 163124 - 161
1010chain 'B' and (resid 164 through 191 )BB164 - 191162 - 187
1111chain 'B' and (resid 192 through 216 )BB192 - 216188 - 212
1212chain 'B' and (resid 217 through 234 )BB217 - 234213 - 230
1313chain 'B' and (resid 235 through 245 )BB235 - 245231 - 241
1414chain 'H' and (resid 1 through 162 )HC1 - 1621 - 162
1515chain 'H' and (resid 163 through 274 )HC163 - 274163 - 274
1616chain 'L' and (resid 1 through 11 )LD1 - 111 - 11
1717chain 'L' and (resid 12 through 19 )LD12 - 1912 - 19
1818chain 'L' and (resid 20 through 41 )LD20 - 4120 - 41
1919chain 'L' and (resid 42 through 63 )LD42 - 6342 - 63
2020chain 'L' and (resid 64 through 71 )LD64 - 7164 - 71
2121chain 'L' and (resid 72 through 77 )LD72 - 7772 - 77
2222chain 'L' and (resid 78 through 84 )LD78 - 8478 - 84
2323chain 'L' and (resid 85 through 90 )LD85 - 9085 - 90
2424chain 'L' and (resid 91 through 99 )LD91 - 9991 - 99
2525chain 'P' and (resid 1 through 8 )PE1 - 81 - 8

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