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- PDB-7sg0: W316 TCR in complex with HLA-DQ2-omega1 -

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Basic information

Entry
Database: PDB / ID: 7sg0
TitleW316 TCR in complex with HLA-DQ2-omega1
Components
  • (T-cell receptor, w316, ...) x 2
  • DQ2-glia-omega1 peptide
  • HLA class II histocompatibility antigen, DQ alpha 1 chain
  • MHC class II HLA-DQ-beta-1
KeywordsIMMUNE SYSTEM / TCR-pHLA complex / Celiac disease
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 / lumenal side of endoplasmic reticulum membrane ...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 / lumenal side of endoplasmic reticulum membrane / peptide antigen assembly with MHC class II protein complex / 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 / positive regulation of T cell activation / peptide antigen binding / 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
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: 3 Å
AuthorsCiacchi, L. / Farenc, C. / Petersen, J. / Reid, H.H. / Rossjohn, J.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia) Australia
CitationJournal: J.Biol.Chem. / Year: 2022
Title: Structural basis of T cell receptor specificity and cross-reactivity of two HLA-DQ2.5-restricted gluten epitopes in celiac disease.
Authors: Ciacchi, L. / Farenc, C. / Dahal-Koirala, S. / Petersen, J. / Sollid, L.M. / Reid, H.H. / Rossjohn, J.
History
DepositionOct 4, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 23, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Dec 20, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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
Revision 1.3Nov 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: HLA class II histocompatibility antigen, DQ alpha 1 chain
B: MHC class II HLA-DQ-beta-1
C: DQ2-glia-omega1 peptide
D: T-cell receptor, w316, alpha chain
E: T-cell receptor, w316, beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,14210
Polymers95,5135
Non-polymers6295
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14090 Å2
ΔGint-59 kcal/mol
Surface area37630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)194.889, 73.248, 77.894
Angle α, β, γ (deg.)90.000, 95.230, 90.000
Int Tables number5
Space group name H-MC121

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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 / Cell line (production host): High Five / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P01909
#2: Protein MHC class II HLA-DQ-beta-1


Mass: 23700.586 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DQB1 / Cell line (production host): High Five / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: O19712

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T-cell receptor, w316, ... , 2 types, 2 molecules DE

#4: Protein T-cell receptor, w316, alpha chain


Mass: 22880.271 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
#5: Protein T-cell receptor, w316, beta chain


Mass: 26937.852 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)

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Protein/peptide / Sugars / Non-polymers , 3 types, 6 molecules C

#3: Protein/peptide DQ2-glia-omega1 peptide


Mass: 1311.437 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): High Five / Production host: Trichoplusia ni (cabbage looper)
#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
#7: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2

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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: 2.77 Å3/Da / Density % sol: 55.6 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: 24% PEG3350, 0.25 M (NH4)2SO4 and 0.1 M Tris/HCl at pH 8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 16, 2020
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 3→48.52 Å / Num. obs: 22108 / % possible obs: 99.8 % / Redundancy: 2 % / CC1/2: 0.919 / Net I/σ(I): 5.3
Reflection shellResolution: 3→3.1 Å / Redundancy: 2 % / Mean I/σ(I) obs: 1.7 / Num. unique obs: 2177 / CC1/2: 0.384

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6MFF, 6CUG, 4OZH

6mff

6cug

4ozh


Resolution: 3→48.52 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 22.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2301 1106 5 %
Rwork0.1908 20992 -
obs0.1927 22098 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 154.86 Å2 / Biso mean: 55.2196 Å2 / Biso min: 20 Å2
Refinement stepCycle: final / Resolution: 3→48.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6406 0 40 0 6446
Biso mean--74.33 --
Num. residues----805
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
3-3.140.30621380.285226092747
3.14-3.30.26861350.249425822717
3.3-3.510.30461380.223526032741
3.51-3.780.24311370.20326312768
3.78-4.160.23121390.180726242763
4.16-4.760.19371370.153826052742
4.76-60.20221400.160126462786
6-48.520.20681420.182626922834
Refinement TLS params.Method: refined / Origin x: 63.2724 Å / Origin y: -71.0908 Å / Origin z: 21.0647 Å
111213212223313233
T0.2915 Å20.0302 Å20.0137 Å2-0.2987 Å20.0143 Å2--0.208 Å2
L0.9522 °20.5025 °20.1131 °2-0.6132 °20.1497 °2--0.3479 °2
S-0.0394 Å °0.022 Å °0.0465 Å °-0.0262 Å °0.0234 Å °0.0028 Å °0.0147 Å °0.017 Å °0.0157 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 181
2X-RAY DIFFRACTION1allA182
3X-RAY DIFFRACTION1allB3 - 191
4X-RAY DIFFRACTION1allC0 - 10
5X-RAY DIFFRACTION1allD1 - 303
6X-RAY DIFFRACTION1allE5 - 301

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