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- PDB-9ejh: Peptide-independent T cell receptor recognition of HLA-DQ2 -

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Basic information

Entry
Database: PDB / ID: 9ejh
TitlePeptide-independent T cell receptor recognition of HLA-DQ2
Components
  • (G9 T cell receptor ...) x 2
  • (HLA class II histocompatibility ...) x 2
  • MHC class II HLA-DQ-beta-1
KeywordsIMMUNE SYSTEM / T cell receptor / immune receptor / human leukocyte antigen
Function / homology
Function and homology information


negative regulation of peptide secretion / macrophage migration inhibitory factor signaling pathway / NOS2-CD74 complex / MHC class II protein binding, via antigen binding groove / antigen processing and presentation of endogenous antigen / positive regulation of dendritic cell antigen processing and presentation / negative regulation of T cell differentiation / macrophage migration inhibitory factor binding / positive regulation of macrophage migration inhibitory factor signaling pathway / protein trimerization ...negative regulation of peptide secretion / macrophage migration inhibitory factor signaling pathway / NOS2-CD74 complex / MHC class II protein binding, via antigen binding groove / antigen processing and presentation of endogenous antigen / positive regulation of dendritic cell antigen processing and presentation / negative regulation of T cell differentiation / macrophage migration inhibitory factor binding / positive regulation of macrophage migration inhibitory factor signaling pathway / protein trimerization / macrophage migration inhibitory factor receptor complex / positive regulation of cytokine-mediated signaling pathway / T cell activation involved in immune response / positive regulation of prostaglandin biosynthetic process / T cell selection / positive regulation of type 2 immune response / negative thymic T cell selection / host-mediated suppression of symbiont invasion / MHC class II receptor activity / MHC class II protein binding / antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / negative regulation of mature B cell apoptotic process / positive regulation of kinase activity / positive thymic T cell selection / CD4 receptor binding / positive regulation of monocyte differentiation / vacuole / positive regulation of chemokine (C-X-C motif) ligand 2 production / cytokine receptor activity / positive regulation of neutrophil chemotaxis / prostaglandin biosynthetic process / positive regulation of macrophage cytokine production / positive regulation of T cell differentiation / nitric-oxide synthase binding / regulation of macrophage activation / transport vesicle membrane / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / antigen processing and presentation / cytokine binding / negative regulation of DNA damage response, signal transduction by p53 class mediator / immunoglobulin mediated immune response / : / Generation of second messenger molecules / response to type II interferon / Co-inhibition by PD-1 / positive regulation of chemokine production / positive regulation of B cell proliferation / MHC class II antigen presentation / protein folding chaperone / multivesicular body / lysosomal lumen / negative regulation of cell migration / trans-Golgi network membrane / positive regulation of interleukin-8 production / Cell surface interactions at the vascular wall / lumenal side of endoplasmic reticulum membrane / intracellular protein transport / peptide antigen assembly with MHC class II protein complex / clathrin-coated endocytic vesicle membrane / MHC class II protein complex / ER to Golgi transport vesicle membrane / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / peptide antigen binding / positive regulation of interleukin-6 production / positive regulation of T cell activation / positive regulation of fibroblast proliferation / Interferon gamma signaling / MHC class II protein complex binding / endocytic vesicle membrane / late endosome membrane / Downstream TCR signaling / late endosome / amyloid-beta binding / protein-containing complex assembly / positive regulation of canonical NF-kappaB signal transduction / adaptive immune response / positive regulation of MAPK cascade / positive regulation of ERK1 and ERK2 cascade / positive regulation of protein phosphorylation / lysosome / positive regulation of viral entry into host cell / protein stabilization / endosome membrane / immune response / Golgi membrane / lysosomal membrane / external side of plasma membrane / positive regulation of gene expression / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / cell surface / protein-containing complex / extracellular exosome / identical protein binding / nucleus / membrane / plasma membrane
Similarity search - Function
MHC class II-associated invariant chain, trimerisation / MHC class II-associated invariant chain/CLIP, MHC II-interacting / MHC class II-associated invariant chain / MHC class II-associated invariant chain, trimerisation domain superfamily / HLA class II histocompatibility antigen, gamma subunit / Class II MHC-associated invariant chain trimerisation domain / CLIP, MHC2 interacting / : / Thyroglobulin type-1 repeat signature. / Thyroglobulin type-1 ...MHC class II-associated invariant chain, trimerisation / MHC class II-associated invariant chain/CLIP, MHC II-interacting / MHC class II-associated invariant chain / MHC class II-associated invariant chain, trimerisation domain superfamily / HLA class II histocompatibility antigen, gamma subunit / Class II MHC-associated invariant chain trimerisation domain / CLIP, MHC2 interacting / : / Thyroglobulin type-1 repeat signature. / Thyroglobulin type-1 / Thyroglobulin type-1 superfamily / Thyroglobulin type-1 repeat / Thyroglobulin type-1 domain profile. / Thyroglobulin type I repeats. / MHC class II, beta chain, N-terminal / Class II histocompatibility antigen, beta domain / Class II histocompatibility antigen, beta domain / MHC class II, alpha chain, N-terminal / Class II histocompatibility antigen, alpha domain / Class II histocompatibility antigen, alpha domain / MHC class II, alpha/beta chain, N-terminal / 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
Similarity search - Domain/homology
ACETATE ION / MHC class II HLA-DQ-beta-1 / HLA class II histocompatibility antigen, DQ alpha 1 chain / HLA class II histocompatibility antigen gamma chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsLim, J.J. / Loh, T.J. / Reid, H.H. / Rossjohn, J.
Funding support1items
OrganizationGrant numberCountry
Other private
CitationJournal: To Be Published
Title: WITHHELD AT REQUEST OF AUTHORS
Authors: Lim, J.J. / Loh, T.J. / Rossjohn, J.
History
DepositionNov 27, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 26, 2025Provider: repository / Type: Initial release
Revision 1.1Apr 2, 2025Group: Database references / Category: citation / Item: _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HLA class II histocompatibility antigen, DQ alpha 1 chain
B: MHC class II HLA-DQ-beta-1
C: HLA class II histocompatibility antigen gamma chain
D: G9 T cell receptor alpha chain
E: G9 T cell receptor beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,53012
Polymers94,7595
Non-polymers7717
Water5,350297
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)92.974, 43.272, 257.958
Angle α, β, γ (deg.)90.000, 90.312, 90.000
Int Tables number5
Space group name H-MI121
Space group name HallC2y(x,y,-x+z)
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z+1/2
#4: -x+1/2,y+1/2,-z+1/2

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Components

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HLA class II histocompatibility ... , 2 types, 2 molecules AC

#1: Protein HLA class II histocompatibility antigen, DQ alpha 1 chain / DC-1 alpha chain / DC-alpha / HLA-DCA / MHC class II DQA1


Mass: 20667.074 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DQA1 / Production host: Baculovirus expression vector pFastBac1-HM / References: UniProt: P01909
#3: Protein/peptide HLA class II histocompatibility antigen gamma chain / HLA-DR antigens-associated invariant chain / Ia antigen-associated invariant chain / Ii


Mass: 1313.628 Da / Num. of mol.: 1 / Fragment: UNP residues 110-122
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD74, DHLAG / Production host: Baculovirus expression vector pFastBac1-HM / References: UniProt: P04233

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G9 T cell receptor ... , 2 types, 2 molecules DE

#4: Protein G9 T cell receptor alpha chain


Mass: 22841.359 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli BL21(DE3) (bacteria)
#5: Protein G9 T cell receptor beta chain


Mass: 27296.340 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli BL21(DE3) (bacteria)

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Protein / Sugars , 2 types, 3 molecules B

#2: Protein MHC class II HLA-DQ-beta-1


Mass: 22640.520 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DQB1 / Production host: Baculovirus expression vector pFastBac1-HM / References: UniProt: O19712
#6: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 302 molecules

#7: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#8: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 297 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.74 Å3/Da / Density % sol: 55.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 8% Tacsimate, pH 8.0, 20-24% w/v PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95373 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 15, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95373 Å / Relative weight: 1
ReflectionResolution: 2.45→45.22 Å / Num. obs: 38503 / % possible obs: 100 % / Redundancy: 4.4 % / Biso Wilson estimate: 37.35 Å2 / CC1/2: 0.988 / Net I/σ(I): 7.1
Reflection shellResolution: 2.45→2.55 Å / Mean I/σ(I) obs: 2.2 / Num. unique obs: 4311 / CC1/2: 0.735

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.45→45.22 Å / SU ML: 0.2559 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.3322
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2316 1954 5.08 %
Rwork0.1756 36532 -
obs0.1783 38486 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 41.82 Å2
Refinement stepCycle: LAST / Resolution: 2.45→45.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6291 0 50 297 6638
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00346493
X-RAY DIFFRACTIONf_angle_d0.57938844
X-RAY DIFFRACTIONf_chiral_restr0.0435996
X-RAY DIFFRACTIONf_plane_restr0.00441145
X-RAY DIFFRACTIONf_dihedral_angle_d13.72942270
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.45-2.510.33561430.24962564X-RAY DIFFRACTION99.89
2.51-2.580.27011270.22822610X-RAY DIFFRACTION99.89
2.58-2.660.27041440.20442558X-RAY DIFFRACTION100
2.66-2.740.26121210.19932579X-RAY DIFFRACTION99.93
2.74-2.840.2681660.2012564X-RAY DIFFRACTION99.96
2.84-2.950.30771420.18852590X-RAY DIFFRACTION99.93
2.95-3.090.27071530.18332601X-RAY DIFFRACTION100
3.09-3.250.23741520.17282540X-RAY DIFFRACTION99.93
3.25-3.450.23391630.1662597X-RAY DIFFRACTION99.96
3.45-3.720.19691390.15782607X-RAY DIFFRACTION99.96
3.72-4.090.2197960.15622669X-RAY DIFFRACTION100
4.09-4.690.18091430.14072616X-RAY DIFFRACTION99.96
4.69-5.90.19511330.16342658X-RAY DIFFRACTION99.96
5.9-45.220.23361320.20282779X-RAY DIFFRACTION99.79
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)
10.128289948761-0.0179501841622-0.1573905881740.04155081532980.07207083637260.213321697986-0.130682868385-0.0797988373228-0.2021835112370.0711617232320.1735394424990.0640792245214-0.0394173224527-0.2845623685240.0002063748636080.2370489228760.00574541221921-0.0488194292730.2710463881080.01934952602890.252478209314-1.8179370495416.846352227645.7272373108
20.09198785883990.09945018587830.1390225483070.09383661737140.05726358025280.11760768037-0.0626069260453-0.2153563630640.07777446563880.2885534848190.05129286624330.104954862625-0.133652308509-0.187886972412-6.65689628184E-50.2656673192460.08002751335650.01673815945120.259326406876-0.008265995555590.236779115504-0.3752345724428.22258102351.9907538602
30.5747876599320.317828338679-0.2299663121860.178912058157-0.146396417080.5395539988360.04977798241290.5845617125180.0432381961703-0.292892493869-0.009546281758230.234371418838-0.392096263224-0.4836118083640.1423673442680.2765363508610.118208727713-0.05262913892930.3944185656-0.006097940757130.278010706222-10.137895285524.117129059636.0430153553
40.458634949903-0.0400072430039-0.02007980462790.597716579167-0.1442508080890.539350618463-0.0657253041175-0.22803178729-0.1110469628720.07753307356330.0215208123090.123441275385-0.0353783218347-0.4926084280470.000263687133240.2181873984820.01835451367710.05353153195190.4897722802320.002731755221280.307810210465-11.58722712713.843048967263.2171337262
50.07667411608140.0844321173119-0.1687384577910.4232282967360.06654083854440.835249480680.02386568547190.06990100290780.0420940972176-0.110564031135-0.0397435279441-0.0157707739123-0.104031241394-0.138570728992-0.0009302181360220.1734344620420.0116468578852-0.01211852741560.179749638335-0.009594570016710.1950548742963.5136769087916.845869113636.6184464649
60.0357534724911-0.2394865131170.4108563683240.176128463533-0.3041147389011.208979965720.07971175815220.106392511494-0.09324218917890.0117693712845-0.03459789276260.0004870985054950.115576978620.135111730515-1.68294123028E-50.2560448438940.0130571869671-0.01293032567810.2649172582030.008112241765630.24845163852411.49118389266.8693698550374.0175635343
70.006977947778590.02047420188480.02934783648230.03453471112040.0718046187640.03802894119960.2062613814920.28070102525-0.05448410610420.1924918704420.129460046736-0.0177445821551-0.374975541514-0.01774678204656.19221421951E-50.3696517395950.0413536512472-0.03487354538070.3935234201410.009836559391890.3765667253481.0596384502426.273821130737.2757357448
81.00488115058-0.2172839080970.4959970003720.3664777417770.4929944339330.9411015884920.04807688184460.09773138186480.05088952144430.00301880987227-0.038175790393-0.01318621534390.132440176708-0.09720295263470.01243182073660.215095705876-0.022100919004-0.02026836345310.19449331017-0.0003483048661450.1880638572516.83987495115-1.842754965878.66100454323
90.3986291831820.07502295824440.009387770599690.2614203692940.05905420179290.7327298902850.3264728438970.292861722978-0.217673101448-0.311093871507-0.1919979687040.0997315983410.2406900106620.08402874842351.93402771001E-50.6104426693230.0505010680726-0.08415798770870.379689935617-0.05367070829940.35274643219625.0050349776-22.7381233098-9.18168619117
100.0875998503281-0.0757060299996-0.104159718970.04600235788580.05511645436130.07095644286010.09276383401180.1880078137530.198449059795-0.500450292593-0.0259598134741-0.203324602028-0.05637085070130.233195226232-0.0001063981362650.3024024691560.01722298795410.02907610302830.2324678649030.0008436927761450.34748200897730.5123746676-8.9674128443522.0820007407
110.183650027070.03642658211220.01312873843930.3508111607750.1725436654610.0858108323279-0.0467178472177-0.1052493050830.0862732944120.2414899076380.130139841996-0.189296727396-0.02930986167230.1525101559270.006469432644530.2748192373410.03354345977950.00061797175150.147412372384-0.001387887506770.2367056047426.9706128792-3.7897035714828.5995435793
120.3440894424420.0825701297681-0.1455718842980.354974988268-0.2861408030270.215490660097-0.0229074983213-0.0326246961488-0.1331491904620.02213100841850.08270725461430.01301766693550.0979457879346-0.0154920564-1.0562421211E-50.225541134081-0.0165799148978-0.008635572219990.155172018576-0.02149932498360.24229245355516.1339395868-5.1227620209429.6039691761
130.347345688296-0.0205433470011-0.129372270760.3126658553420.3115265860860.447544688929-0.0901968195829-0.00749439940940.0577266535566-0.07278938962220.107046484287-0.03416944914840.001769328516380.01444733670871.19679784965E-50.190685354512-0.00829459067679-0.002784817476760.1415528346480.01014227139030.19906802325821.9324616612-3.3900924616627.696549814
140.632306696897-0.235553031682-0.06147412979690.202047684327-0.1586589201090.1987375605450.05397927127450.106309140884-0.156144599552-0.101663421538-0.0490265843635-0.07646601588060.09269574685930.0421573595431-0.002458267303890.3016520052580.0823758470840.05580718782840.233994840117-0.02675840627670.25054643949733.1393352106-18.60565701273.80212268642
150.0600317308744-0.0756512507311-0.008967187946580.2944270828620.3384813336030.456538549740.1675259896380.2270270755490.025241924109-0.1766098489460.174863317831-0.0117002982550.0818606188656-0.331601795231-9.28202099582E-50.343360695291-0.0666884814121-0.002090521583330.365697021971-0.005431469010970.3624247403428.4608102928-18.08513085714.59320969337
160.382635150421-0.0886353830458-0.0197594107120.7205159188080.3137200104580.3521807949870.04221879808440.270365125612-0.077491367916-0.187946925710.0548954609617-0.3378289686680.1798231244950.289404287580.07524130470770.2532625835840.03307708301680.07696261785250.363326935164-0.01790872468790.32296164251639.3396878101-15.97777500133.6548286625
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 20 )AA1 - 201 - 21
22chain 'A' and (resid 21 through 57 )AA21 - 5722 - 57
33chain 'A' and (resid 58 through 78 )AA58 - 7858 - 78
44chain 'A' and (resid 79 through 182 )AA79 - 18279 - 182
55chain 'B' and (resid 3 through 88 )BC3 - 881 - 86
66chain 'B' and (resid 89 through 194 )BC89 - 19487 - 187
77chain 'C' and (resid -1 through 10 )CH-1 - 101 - 12
88chain 'D' and (resid 2 through 131 )DI2 - 1311 - 114
99chain 'D' and (resid 132 through 213 )DI132 - 213115 - 194
1010chain 'E' and (resid 3 through 14 )EJ3 - 141 - 12
1111chain 'E' and (resid 15 through 37 )EJ15 - 3713 - 28
1212chain 'E' and (resid 38 through 75 )EJ38 - 7529 - 61
1313chain 'E' and (resid 76 through 120 )EJ76 - 12062 - 105
1414chain 'E' and (resid 121 through 173 )EJ121 - 173106 - 158
1515chain 'E' and (resid 174 through 199 )EJ174 - 199159 - 184
1616chain 'E' and (resid 200 through 255 )EJ200 - 255185 - 240

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External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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