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- PDB-7sg2: XPA5 TCR in complex with HLA-DQ2-omega1 -

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Basic information

Entry
Database: PDB / ID: 7sg2
TitleXPA5 TCR in complex with HLA-DQ2-omega1
Components
  • (T-cell receptor, xpa5, ...) 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 / 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 / PD-1 signaling / 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 / PD-1 signaling / MHC class II antigen presentation / trans-Golgi network membrane / lumenal side of endoplasmic reticulum membrane / clathrin-coated endocytic vesicle membrane / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / endocytic vesicle membrane / Interferon gamma signaling / positive regulation of immune response / positive regulation of T cell activation / Downstream TCR signaling / MHC class II protein complex binding / late endosome membrane / 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 / 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: 3.1 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 1.1Sep 13, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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 1.2Oct 18, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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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
F: HLA class II histocompatibility antigen, DQ alpha 1 chain
G: MHC class II HLA-DQ-beta-1
D: T-cell receptor, xpa5, alpha chain
E: T-cell receptor, xpa5, beta chain
C: DQ2-glia-omega1 peptide
H: DQ2-glia-omega1 peptide
I: T-cell receptor, xpa5, alpha chain
J: T-cell receptor, xpa5, beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)192,57119
Polymers191,74410
Non-polymers8279
Water1267
1
A: HLA class II histocompatibility antigen, DQ alpha 1 chain
B: MHC class II HLA-DQ-beta-1
D: T-cell receptor, xpa5, alpha chain
E: T-cell receptor, xpa5, beta chain
C: DQ2-glia-omega1 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,29510
Polymers95,8725
Non-polymers4225
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
F: HLA class II histocompatibility antigen, DQ alpha 1 chain
G: MHC class II HLA-DQ-beta-1
H: DQ2-glia-omega1 peptide
I: T-cell receptor, xpa5, alpha chain
J: T-cell receptor, xpa5, beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,2769
Polymers95,8725
Non-polymers4044
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)137.245, 75.108, 216.431
Angle α, β, γ (deg.)90.000, 103.160, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 3 through 180 or resid 201))
21(chain F and (resid 3 through 180 or resid 201))
12chain B
22(chain G and (resid 3 through 163 or resid 169 through 190))
13chain C
23chain H
14(chain D and (resid 4 through 143 or resid 149 through 195 or resid 200 through 203))
24(chain I and (resid 4 through 162 or resid 169 through 203))
15(chain E and (resid 2 through 192 or resid 199 through 255))
25(chain J and resid 2 through 255)

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 3 through 180 or resid 201))A0
211(chain F and (resid 3 through 180 or resid 201))F0
112chain BB3 - 190
212(chain G and (resid 3 through 163 or resid 169 through 190))G3 - 163
222(chain G and (resid 3 through 163 or resid 169 through 190))G169 - 190
113chain CC0 - 12
213chain HH0 - 12
114(chain D and (resid 4 through 143 or resid 149 through 195 or resid 200 through 203))D4 - 143
124(chain D and (resid 4 through 143 or resid 149 through 195 or resid 200 through 203))D149 - 195
134(chain D and (resid 4 through 143 or resid 149 through 195 or resid 200 through 203))D200 - 203
214(chain I and (resid 4 through 162 or resid 169 through 203))I4 - 162
224(chain I and (resid 4 through 162 or resid 169 through 203))I169 - 203
115(chain E and (resid 2 through 192 or resid 199 through 255))E2 - 192
125(chain E and (resid 2 through 192 or resid 199 through 255))E199 - 255
215(chain J and resid 2 through 255)J2 - 255

NCS ensembles :
ID
1
2
3
4
5

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Components

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Protein , 2 types, 4 molecules AFBG

#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.: 2
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: 23556.455 Da / Num. of mol.: 2
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, xpa5, ... , 2 types, 4 molecules DIEJ

#3: Protein T-cell receptor, xpa5, alpha chain


Mass: 22661.199 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
#4: Protein T-cell receptor, xpa5, beta chain


Mass: 27515.707 Da / Num. of mol.: 2
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 , 2 types, 4 molecules CH

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


Mass: 1455.567 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
#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, 14 molecules

#7: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#8: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#9: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.72 Å3/Da / Density % sol: 54.73 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: Mother liquor: 16-18% PEG3350, 0.12-0.14 M CaOAc, 0.1 M Tris/HCl at pH 8.0, Additives: 2 mM reduced and oxidised Glutathione

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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: Mar 6, 2020
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 3.1→45.44 Å / Num. obs: 39351 / % possible obs: 99.8 % / Redundancy: 1.9 % / CC1/2: 0.982 / Net I/σ(I): 7.4
Reflection shellResolution: 3.1→3.2 Å / Redundancy: 1.9 % / Mean I/σ(I) obs: 1.8 / Num. unique obs: 3913 / CC1/2: 0.661 / % possible all: 99.9

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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, 4OZI

6mff

4ozi


Resolution: 3.1→45.44 Å / SU ML: 0.44 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2588 1956 4.97 %
Rwork0.2178 37375 -
obs0.2198 39331 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 195.84 Å2 / Biso mean: 73.1761 Å2 / Biso min: 30 Å2
Refinement stepCycle: final / Resolution: 3.1→45.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12494 0 50 7 12551
Biso mean--89.85 46.34 -
Num. residues----1569
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1655X-RAY DIFFRACTION8.173TORSIONAL
12F1655X-RAY DIFFRACTION8.173TORSIONAL
21B1700X-RAY DIFFRACTION8.173TORSIONAL
22G1700X-RAY DIFFRACTION8.173TORSIONAL
31C128X-RAY DIFFRACTION8.173TORSIONAL
32H128X-RAY DIFFRACTION8.173TORSIONAL
41D1505X-RAY DIFFRACTION8.173TORSIONAL
42I1505X-RAY DIFFRACTION8.173TORSIONAL
51E2190X-RAY DIFFRACTION8.173TORSIONAL
52J2190X-RAY DIFFRACTION8.173TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.1-3.180.37871250.317626652790100
3.18-3.260.30211590.286926782837100
3.26-3.360.35271340.26525922726100
3.36-3.470.2921420.256626742816100
3.47-3.590.3151420.242926422784100
3.59-3.740.27521420.24326592801100
3.74-3.910.32751360.237726552791100
3.91-4.110.25011360.207426702806100
4.11-4.370.23541370.193426582795100
4.37-4.710.20321440.168426602804100
4.71-5.180.19591400.172126542794100
5.18-5.930.23431400.195326952835100
5.93-7.460.26671370.235727012838100
7.46-45.440.24861420.21762772291499
Refinement TLS params.Method: refined / Origin x: -36.0845 Å / Origin y: 25.8572 Å / Origin z: 53.8266 Å
111213212223313233
T0.4668 Å2-0.0326 Å20.1036 Å2-0.4169 Å20.0304 Å2--0.3767 Å2
L1.5069 °20.0679 °21.4472 °2-0.2914 °20.0578 °2--1.4934 °2
S-0.0779 Å °-0.3179 Å °-0.005 Å °0.1211 Å °0.015 Å °-0.015 Å °-0.1868 Å °-0.3783 Å °0.0621 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA2 - 180
2X-RAY DIFFRACTION1allA201 - 204
3X-RAY DIFFRACTION1allB3 - 190
4X-RAY DIFFRACTION1allF3 - 180
5X-RAY DIFFRACTION1allF201 - 301
6X-RAY DIFFRACTION1allG3 - 190
7X-RAY DIFFRACTION1allD3 - 217
8X-RAY DIFFRACTION1allE2 - 255
9X-RAY DIFFRACTION1allC0 - 12
10X-RAY DIFFRACTION1allH0 - 12
11X-RAY DIFFRACTION1allI4 - 203
12X-RAY DIFFRACTION1allJ2 - 301
13X-RAY DIFFRACTION1allW2 - 10
14X-RAY DIFFRACTION1allK1 - 2

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