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- PDB-6px6: HLA-TCR complex -

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Basic information

Entry
Database: PDB / ID: 6px6
TitleHLA-TCR complex
Components
  • (HLA class II histocompatibility antigen DQ ...) x 2
  • (T-cell receptor, T1005.2.56, ...) x 2
  • DQ2.2-glut-L1
KeywordsIMMUNE SYSTEM / HLA / MHC / TCR / Complex / Celiac Disease
Function / homology
Function and homology information


nutrient reservoir activity / antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / MHC class II protein complex / adaptive immune response / endosome membrane / lysosomal membrane
Similarity search - Function
Gliadin/LMW glutenin / Cys-rich Gliadin N-terminal / Plant lipid transfer protein / seed storage protein / trypsin-alpha amylase inhibitor domain family / Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain / Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain superfamily / : / T-cell receptor alpha chain, constant domain / Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 / Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 / Domain of unknown function (DUF1968) ...Gliadin/LMW glutenin / Cys-rich Gliadin N-terminal / Plant lipid transfer protein / seed storage protein / trypsin-alpha amylase inhibitor domain family / Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain / Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain superfamily / : / T-cell receptor alpha chain, constant domain / Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 / Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 / Domain of unknown function (DUF1968) / 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 / Immunoglobulin V-Type / Immunoglobulin V-set domain / MHC classes I/II-like antigen recognition protein / Immunoglobulin V-set domain / : / Immunoglobulin subtype / Immunoglobulin / 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 / Immunoglobulins / Roll / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
HLA class II histocompatibility antigen DQ beta chain / Human nkt tcr alpha chain / Glutenin, low molecular weight subunit PTDUCD1 / HLA class II histocompatibility antigen DQ alpha chain
Similarity search - Component
Biological speciesHomo sapiens (human)
Triticum aestivum (bread wheat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.00000337881 Å
AuthorsTing, Y.T. / Reid, H.H. / Rossjohn, J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: A molecular basis for the T cell response in HLA-DQ2.2 mediated celiac disease.
Authors: Ting, Y.T. / Dahal-Koirala, S. / Kim, H.S.K. / Qiao, S.W. / Neumann, R.S. / Lundin, K.E.A. / Petersen, J. / Reid, H.H. / Sollid, L.M. / Rossjohn, J.
History
DepositionJul 24, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 15, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 22, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation_author.name
Revision 1.2Feb 5, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3Feb 26, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Nov 13, 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: HLA class II histocompatibility antigen DQ alpha chain
B: HLA class II histocompatibility antigen DQ beta chain
C: DQ2.2-glut-L1
D: T-cell receptor, T1005.2.56, alpha chain,Human nkt tcr alpha chain
E: T-cell receptor, T1005.2.56, beta chain


Theoretical massNumber of molelcules
Total (without water)111,4155
Polymers111,4155
Non-polymers00
Water45025
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13090 Å2
ΔGint-68 kcal/mol
Surface area35640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.534, 99.416, 72.565
Angle α, β, γ (deg.)90.000, 118.264, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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HLA class II histocompatibility antigen DQ ... , 2 types, 2 molecules AB

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


Mass: 27962.971 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DQA1 / Plasmid: pFastBac1-HM / Production host: Baculovirus expression vector pFastBac1-HM / References: UniProt: Q08AS3
#2: Protein HLA class II histocompatibility antigen DQ beta chain / MHC class II antigen


Mass: 29714.135 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DQB1 / Plasmid: pFastBac1-HM / Production host: Baculovirus expression vector pFastBac1-HM / References: UniProt: A0A0U5IHY9

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T-cell receptor, T1005.2.56, ... , 2 types, 2 molecules DE

#4: Protein T-cell receptor, T1005.2.56, alpha chain,Human nkt tcr alpha chain / Human nkt tcr beta chain


Mass: 23798.406 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: K7N5M3
#5: Protein T-cell receptor, T1005.2.56, beta chain


Mass: 28637.789 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli BL21 (bacteria)

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Protein/peptide / Non-polymers , 2 types, 26 molecules C

#3: Protein/peptide DQ2.2-glut-L1


Mass: 1301.400 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Triticum aestivum (bread wheat) / References: UniProt: P16315*PLUS
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.07 Å3/Da / Density % sol: 40.53 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M MOPS/HEPES, pH 7.5, 12.5% v/v PEG1000, 12.5% v/v MPD, 12.5% w/v PEG3350, 0.04 M NPS mixture

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953728973866 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 11, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953728973866 Å / Relative weight: 1
ReflectionResolution: 3→39.24 Å / Num. obs: 18263 / % possible obs: 99.9 % / Redundancy: 3.5 % / Biso Wilson estimate: 62.1477047332 Å2 / Net I/σ(I): 4.21
Reflection shellResolution: 3→3.18 Å / Num. unique obs: 18263

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4OZH

4ozh


Resolution: 3.00000337881→39.2378503996 Å / SU ML: 0.39014417998 / Cross valid method: FREE R-VALUE / σ(F): 1.35017227076 / Phase error: 24.264618814
RfactorNum. reflection% reflection
Rfree0.257016907768 950 5.20291363163 %
Rwork0.204891061514 --
obs0.207648302688 18259 99.9452624665 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 38.1893751348 Å2
Refinement stepCycle: LAST / Resolution: 3.00000337881→39.2378503996 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6266 0 0 25 6291
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002454656108866428
X-RAY DIFFRACTIONf_angle_d0.5950191751498768
X-RAY DIFFRACTIONf_chiral_restr0.043144153081975
X-RAY DIFFRACTIONf_plane_restr0.003870378519411145
X-RAY DIFFRACTIONf_dihedral_angle_d18.73516608343828
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.00000337881-3.15810.302672899321410.2492269672522466X-RAY DIFFRACTION99.9233422767
3.1581-3.35590.3263643612551130.2405265232942447X-RAY DIFFRACTION99.8829496684
3.3559-3.61480.256506106651350.2229718428432483X-RAY DIFFRACTION100
3.6148-3.97830.2804514540031610.2128276563322442X-RAY DIFFRACTION99.9232245681
3.9783-4.55320.2852667168731140.1813535127972492X-RAY DIFFRACTION100
4.5532-5.73370.2192938664421650.1776546300282438X-RAY DIFFRACTION100
5.7337-39.23785039960.2035344528531210.1995653982262541X-RAY DIFFRACTION99.8874296435
Refinement TLS params.Method: refined / Origin x: 10.1690814046 Å / Origin y: 8.94899136936 Å / Origin z: -1.83344289454 Å
111213212223313233
T0.177434355922 Å20.0143949600881 Å2-0.00689541472787 Å2-0.171233587855 Å20.0511620191853 Å2--0.277017342422 Å2
L0.265233599027 °20.177028912079 °20.497806039044 °2-0.545282772194 °20.873477519331 °2--2.96610621928 °2
S-0.0152232548807 Å °0.0259406150327 Å °-0.0209521409602 Å °-0.0013546968971 Å °0.0130914402731 Å °-0.0471399051533 Å °0.0956299814975 Å °0.0985775996023 Å °-0.00475504545218 Å °
Refinement TLS groupSelection details: all

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