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

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ID or keywords:

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Basic information

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


MHC class II receptor activity / antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / transport vesicle membrane / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / Generation of second messenger molecules / Co-inhibition by PD-1 / MHC class II antigen presentation / trans-Golgi network membrane / peptide antigen assembly with MHC class II protein complex ...MHC class II receptor activity / antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / transport vesicle membrane / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / Generation of second messenger molecules / Co-inhibition by PD-1 / MHC class II antigen presentation / trans-Golgi network membrane / peptide antigen assembly with MHC class II protein complex / lumenal side of endoplasmic reticulum membrane / MHC class II protein complex / clathrin-coated endocytic vesicle membrane / 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 T cell activation / Interferon gamma signaling / MHC class II protein complex binding / endocytic vesicle membrane / late endosome membrane / Downstream TCR signaling / adaptive immune response / endosome membrane / immune response / Golgi membrane / lysosomal membrane / membrane / plasma membrane
Similarity search - Function
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 ...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 / FORMIC ACID / MHC class II HLA-DQ-beta-1 / HLA class II histocompatibility antigen, DQ alpha 1 chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsLim, J.J. / Loh, T.J. / Reid, H.H. / Rossjohn, J.
Funding support1items
OrganizationGrant numberCountry
Other private
CitationJournal: Nat Commun / Year: 2025
Title: A naturally selected alpha beta T cell receptor binds HLA-DQ2 molecules without co-contacting the presented peptide.
Authors: Lim, J.J. / Jones, C.M. / Loh, T.J. / Dao, H.T. / Tran, M.T. / Tye-Din, J.A. / La Gruta, N.L. / 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
Revision 1.2May 21, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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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
C: glia-omega 1 peptide
D: G9 T cell receptor alpha chain
E: G9 T cell receptor beta chain
B: MHC class II HLA-DQ-beta-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,83717
Polymers94,8035
Non-polymers1,03412
Water8,881493
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)92.947, 43.359, 257.586
Angle α, β, γ (deg.)90.000, 90.103, 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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Protein , 2 types, 2 molecules AB

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


Mass: 20683.141 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DQA1 / Production host: Homo sapiens (human) / References: UniProt: P01909
#5: Protein MHC class II HLA-DQ-beta-1


Mass: 22670.547 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

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

#3: 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)
#4: 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/peptide / Sugars , 2 types, 3 molecules C

#2: Protein/peptide glia-omega 1 peptide


Mass: 1311.437 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Baculovirus expression vector pFastBac1-HM
#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 , 4 types, 503 molecules

#7: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: CH2O2
#8: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#9: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 493 / 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: 55.07 %
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: Jun 28, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95373 Å / Relative weight: 1
ReflectionResolution: 2.2→45.09 Å / Num. obs: 52980 / % possible obs: 100 % / Redundancy: 5.6 % / Biso Wilson estimate: 32.68 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.122 / Net I/σ(I): 9.6
Reflection shellResolution: 2.2→2.27 Å / Num. unique obs: 4583 / CC1/2: 0.83

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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: 2.2→45.09 Å / SU ML: 0.2254 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.8209
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2248 2693 5.09 %
Rwork0.1953 50264 -
obs0.1968 52957 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.47 Å2
Refinement stepCycle: LAST / Resolution: 2.2→45.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6295 0 67 493 6855
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00396515
X-RAY DIFFRACTIONf_angle_d0.71648869
X-RAY DIFFRACTIONf_chiral_restr0.0463992
X-RAY DIFFRACTIONf_plane_restr0.0071150
X-RAY DIFFRACTIONf_dihedral_angle_d14.56892278
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.240.26531540.23972584X-RAY DIFFRACTION99.78
2.24-2.280.27841700.25072617X-RAY DIFFRACTION99.68
2.28-2.330.3081190.2372620X-RAY DIFFRACTION100
2.33-2.380.26771230.23492624X-RAY DIFFRACTION99.96
2.38-2.440.28071480.23982626X-RAY DIFFRACTION99.96
2.44-2.50.26281530.22292599X-RAY DIFFRACTION99.93
2.5-2.560.24771480.22082662X-RAY DIFFRACTION100
2.56-2.640.23631380.20852579X-RAY DIFFRACTION100
2.64-2.720.22291110.21372691X-RAY DIFFRACTION99.93
2.72-2.820.23681170.20542634X-RAY DIFFRACTION100
2.82-2.940.22751500.20412608X-RAY DIFFRACTION99.89
2.94-3.070.19091400.20052660X-RAY DIFFRACTION100
3.07-3.230.2221490.18872628X-RAY DIFFRACTION99.93
3.23-3.430.20391400.17582645X-RAY DIFFRACTION99.96
3.43-3.70.18911370.16932649X-RAY DIFFRACTION99.93
3.7-4.070.18681190.17582698X-RAY DIFFRACTION99.96
4.07-4.660.21241440.16552680X-RAY DIFFRACTION100
4.66-5.870.21981590.18152670X-RAY DIFFRACTION100
5.87-45.090.24231740.21622790X-RAY DIFFRACTION99.8
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)
10.01343469468490.0211216601855-0.02173285668510.0264057923679-0.01243699165480.0512510371977-0.0337951617932-0.07736457743110.008020861688520.0857659021257-0.0499111299924-0.0367268580583-0.16562536543-0.2619747349271.15934251216E-70.1764889005110.104804849271-0.04764112372990.204889723922-0.04726590505430.175729661573-1.6073384575820.782622979248.3389869109
2-0.00101478549408-0.0027093238949-0.000233618308820.007880698664420.000895630152240.002324317528410.0172424157190.006347985226980.0777155286565-0.00117462981104-0.02556555083740.094318803938-0.123298653417-0.03504935630277.75780403943E-70.5026745107090.0806320516964-0.07970941865210.223686523991-0.04322913067750.3364795801671.1120514980332.322048277253.0063931289
30.01850679602070.009093695382650.0205618059889-0.00361683966483-0.01097569667580.01090971221060.02750997044630.0298447715321-0.0507231097981-0.0138897245431-0.1166772388110.0717614335716-0.167337972495-0.3373585851768.91056443599E-80.3124414076850.0845501367899-0.07419768606320.428886101501-0.02047628588070.26496822956-12.0577560918.690013318538.4819590156
40.005105702974770.0054314542388-0.00805295837551-0.0026963976374-0.0005102339928420.00257207769243-0.0314011189322-0.06987446622060.005908940434210.08307897033110.05049441768520.00374764810581-0.00461439344147-0.00325712219671-1.53608015469E-60.2100889154830.06170537848220.0431703307490.51782041187-0.002382535326390.22794625941-3.9361077834812.827284716173.0092927317
50.0209197388880.0147913973652-0.03018038316890.00379538185490.01834174790340.00298167790516-0.254634233075-0.303888123915-0.09188682000270.0686393390484-0.01112803130840.110992143229-0.0133717025635-0.5270466283563.96672068244E-8-1.259272949940.4203907847070.4823606218560.600360549655-0.1087760644050.119188316891-11.861563204614.763654088663.9349717362
60.00201472607917-0.002904970345050.002911869276070.002954543941890.001520286895560.0005179651744590.05852278313930.00516434633740.03156720697460.03396582616840.0295148911478-0.0363378966496-0.0541967998395-0.01737260005064.45059019102E-60.3887318779980.0676920713188-0.03797604587660.3429120570660.04712683891810.3814608617521.3668864051825.620480657837.1260821991
70.08520563854920.002525431142260.05417868988330.08074579093630.06795015441580.07095682191140.01690369132620.105541423630.02400152671620.0135189917753-0.05382853615160.001465647010860.193336216132-0.1966097343565.88397023393E-90.221062148717-0.0111178894124-0.01798847831950.220933856408-0.01922247061330.1628649506695.89152458986-0.2184223932319.39344271579
80.0450308825684-0.02231737680350.03614470375810.0422432218926-0.02443978039790.0097553285190.04824127753580.0619215862729-0.03163269356120.009925740970880.0340164315535-0.006765611936960.0364730641433-0.008236255645845.43956257598E-70.3391080539350.012306254702-0.04063189164460.222920687093-0.0723285390160.062498442090711.0351888644-7.493868945675.20046284098
90.00129752001173-0.006633264089750.002785385465370.01384705315970.008317391019980.01431671123160.0532637664931-0.0269881255093-0.142952605353-0.05870469314620.0153618946068-0.03671003540170.0689573183371-0.00682915156958-3.90334099551E-70.734082277120.161762816598-0.03780740836640.540630621849-0.1386204824030.47442383001326.4015831128-23.7835329881-8.88615744197
100.01584543507480.007119923576070.01011589624650.004418557490070.01994558014840.01969644890020.1730896192230.116200759456-0.09451068620730.04231883616490.0667162170983-0.09116574604930.0944011522720.01190160969273.09167764863E-70.6460713055410.0469863881143-0.0313829456370.365792986372-0.0219948395150.27921791541924.4449513283-15.2562483253-7.0294054061
11-0.002870797220310.001812592470020.002264802884290.003129334507840.005866438957550.00346476839677-0.01125255468240.0427563248484-0.05963234473320.03751220632290.04094688704320.02314934339860.0550523285335-0.01350279837342.56817378388E-60.9327214209020.0494183865918-0.08664468871910.662505849209-0.1881356421160.61809160911923.2810875134-29.3350757977-13.0255387406
120.009101762055080.00220284504803-0.003257088085010.001502456031590.006138284992640.003764915230640.0528613512730.05356930834550.0799812163758-0.01700883666980.0395877382985-0.00170288138504-0.00207510584470.0781763525902-3.14346774555E-60.2004206283650.01070500653970.04637398521110.12841115752-0.01771596290170.24948584105330.5048232219-9.0530315610421.8891530153
130.02803669038680.000781035457684-0.01742309661360.002603537350940.005527662942580.02199790358010.0362890756749-0.05829037771940.037930088510.03042865751630.0524951621811-0.0305389983294-0.03705852101860.159836447079-1.35345019646E-60.1975578627310.01020142987550.008232748305230.111828268499-0.006239699401850.21864837718626.963442013-3.8777932067828.475719259
140.01444044641210.00154850486248-0.006149962700720.00197682722519-0.01121113541310.0135807027316-0.0611342913382-0.04336788135870.0847562032481-0.00277149611940.01400886179730.0551984348404-0.000451650291907-0.08444043052352.81785851125E-70.173789456526-0.01094501716660.004941221610690.0967594750511-0.007913093034010.1855545163916.356833317-5.7198602323826.1269296642
150.0310657591158-0.0215357817316-0.008729693491170.0161420768345-0.01614310113330.0327185630991-0.0582135867718-0.190410909110.03824526004730.05265599747220.0797131808884-0.0716013092599-0.00160896319790.05018791545371.80253553499E-80.211301339660.0185510206750.004164533804080.12102255025-0.01601339197640.20682311923721.7031852909-6.487698257933.2366316253
160.01129669760780.0155914984303-0.003137723438180.009354117040290.002121910624970.01557401735640.0346571189935-0.02109826224050.117848029931-0.02907521641620.00220731805453-0.00242567602931-0.144840638033-0.0704573961085-7.70426883052E-80.1605548424650.002309721785020.01106306408330.06543996810480.02282797992720.15941304403718.72850641331.0271554475422.2945123996
170.036030496178-0.0343496783933-0.01719764566420.01964684898910.03525710816370.005418779247510.1214738387490.236330413237-0.247805056306-0.2254995271-0.084651466042-0.2007574231820.0393300932281-0.061933905538-2.65367735615E-90.4487320688450.247668759290.1580611562580.173553564725-0.04809038693440.22462065014732.9715212545-20.26529681982.30327049408
180.0218099830174-0.02828305469410.02587825868270.03997399482240.03319457986590.03267423508460.3461090891040.319128032995-0.0138818660449-0.1237770312870.0204903582187-0.1945733465710.147287197241-0.05049578657811.32657000013E-90.2610382913120.07367534314630.1336929574520.2895174850030.003522483460130.23685926851731.6579424124-15.88362089870.475412058577
190.00033614932965-0.00453056876057-0.001938393331940.006501634352830.001053657021830.002809864193770.02197303797780.2026219742210.059670084415-0.08484089606370.00265298165543-0.112009929378-0.03262874185810.08448400882293.35324481296E-60.1721079244270.05999890272310.3734003028070.2934593133580.00194978425380.23682556703340.0327011511-11.70334874851.02361790065
200.0326537093944-0.0264886094512-0.01319348129950.02163030471160.01470847890630.001603787592540.08561960061020.133503713598-0.07488008480640.05671269323190.0116638369454-0.2274955611590.09348224853860.08331714181493.01353463017E-80.1382992121660.1682943644030.1541990444480.3417602876630.06459294228090.46613800992742.3355178681-19.937853832712.5426637549
210.0378963318816-0.0301780910147-0.04071481738760.1719166667960.01303094759270.177919303651-0.0256049843455-0.0689068971253-0.0159081689519-0.0989241734803-0.0648150431583-0.0541805855257-0.259782776585-0.2450230251871.01287938824E-80.1453749029010.0127656121867-0.03329667415690.1465022781720.004468707016340.1556608156854.6857221862617.29614984639.0290247578
220.03265014629080.003574128616510.01718753632080.04117674757840.02063188848420.08728300097250.1425544796160.084623115318-0.110658885206-0.0195920034298-0.1204899211530.02804389250680.2331307611320.07776839278241.62466559058E-80.1858218224430.0159074270209-0.04117983129720.2288123368940.005643349605590.21009703845911.38303904264.9581086028375.5205299437
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 37 )AA3 - 371 - 36
22chain 'A' and (resid 38 through 57 )AA38 - 5737 - 55
33chain 'A' and (resid 58 through 89 )AA58 - 8956 - 87
44chain 'A' and (resid 90 through 103 )AA90 - 10388 - 101
55chain 'A' and (resid 104 through 182 )AA104 - 182102 - 180
66chain 'C' and (resid 0 through 9 )CC0 - 91 - 10
77chain 'D' and (resid 3 through 108 )DD3 - 1081 - 90
88chain 'D' and (resid 109 through 131 )DD109 - 13191 - 113
99chain 'D' and (resid 132 through 165 )DD132 - 165114 - 147
1010chain 'D' and (resid 166 through 190 )DD166 - 190148 - 172
1111chain 'D' and (resid 191 through 213 )DD191 - 213173 - 195
1212chain 'E' and (resid 3 through 14 )EE3 - 141 - 12
1313chain 'E' and (resid 15 through 37 )EE15 - 3713 - 28
1414chain 'E' and (resid 38 through 57 )EE38 - 5729 - 48
1515chain 'E' and (resid 58 through 99 )EE58 - 9949 - 84
1616chain 'E' and (resid 100 through 121 )EE100 - 12185 - 106
1717chain 'E' and (resid 122 through 152 )EE122 - 152107 - 137
1818chain 'E' and (resid 153 through 215 )EE153 - 215138 - 200
1919chain 'E' and (resid 216 through 227 )EE216 - 227201 - 212
2020chain 'E' and (resid 228 through 256 )EE228 - 255213 - 240
2121chain 'B' and (resid 3 through 97 )BG3 - 971 - 95
2222chain 'B' and (resid 98 through 194 )BG98 - 19496 - 189

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