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- PDB-6py2: HLA-TCR complex -

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Basic information

Entry
Database: PDB / ID: 6py2
TitleHLA-TCR complex
Components
  • (HLA class II histocompatibility antigen DQ ...) x 2
  • (T-cell receptor, T594, ...) x 2
  • DQ2.2-glut-L1
KeywordsIMMUNE SYSTEM / HLA / MHC / TCR / Gluten
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
AAI/SS protein, conserved domain / 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) ...AAI/SS protein, conserved domain / 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 beta chain / T-cell receptor, sp3.4 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: 2.82543430029 Å
AuthorsTing, Y.T. / Peteren, J. / 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 28, 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: Data collection / Database references / Category: chem_comp / citation
Item: _chem_comp.type / _citation.journal_volume ..._chem_comp.type / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _entity.pdbx_description ..._chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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, T594, alpha chain,T-cell receptor, T594, alpha chain
E: T-cell receptor, T594, beta chain,T-cell receptor, T594, beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,95210
Polymers109,1045
Non-polymers8485
Water37821
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14260 Å2
ΔGint-52 kcal/mol
Surface area37120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.280, 275.140, 141.550
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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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, T594, ... , 2 types, 2 molecules DE

#4: Protein T-cell receptor, T594, alpha chain,T-cell receptor, T594, alpha chain /


Mass: 22702.121 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: K7N5N2
#5: Protein T-cell receptor, T594, beta chain,T-cell receptor, T594, beta chain /


Mass: 27423.689 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: K7N5M4

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Protein/peptide / Sugars , 2 types, 4 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: 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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
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 , 2 types, 23 molecules

#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 21 / 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: 3.36 Å3/Da / Density % sol: 69.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1 M MES, pH 6.5, 5% v/v MPD, 15% w/v PEG6000

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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: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 20, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.82→45.86 Å / Num. obs: 35664 / % possible obs: 85 % / Redundancy: 2 % / Biso Wilson estimate: 62.1477047536 Å2 / CC1/2: 0.998 / Net I/σ(I): 10.95
Reflection shellResolution: 2.82→2.93 Å / Num. unique obs: 462 / CC1/2: 0.854

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Processing

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

4ozh


Resolution: 2.82543430029→45.8566666667 Å / SU ML: 0.309354034075 / Cross valid method: FREE R-VALUE / σ(F): 1.36288831066 / Phase error: 27.5167505887
RfactorNum. reflection% reflection
Rfree0.244164779274 1570 5.16600309302 %
Rwork0.215876274303 --
obs0.2173823465 30391 84.9741367258 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 65.7357577549 Å2
Refinement stepCycle: LAST / Resolution: 2.82543430029→45.8566666667 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6382 0 54 21 6457
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003541003183276607
X-RAY DIFFRACTIONf_angle_d0.7460259674739001
X-RAY DIFFRACTIONf_chiral_restr0.0442249628139995
X-RAY DIFFRACTIONf_plane_restr0.003956281156911164
X-RAY DIFFRACTIONf_dihedral_angle_d17.86409569343914
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.82543430029-2.91660.51140.37373X-RAY DIFFRACTION11.97
2.9166-3.02080.349336960075890.3104419473851339X-RAY DIFFRACTION44.7929736512
3.0208-3.14180.3888714760111330.2979861648612493X-RAY DIFFRACTION81.8578553616
3.1418-3.28470.2545543496451550.2721588521093007X-RAY DIFFRACTION98.6275733001
3.2847-3.45780.3163976976431360.2541972835063036X-RAY DIFFRACTION98.9086373558
3.4578-3.67440.2946973329341750.2422032092993000X-RAY DIFFRACTION99.0021827253
3.6744-3.95790.2682933609411470.2157638224713112X-RAY DIFFRACTION99.6331397126
3.9579-4.3560.2264845571551870.1825444564423027X-RAY DIFFRACTION99.4430693069
4.356-4.98560.1876255351131660.162077697743087X-RAY DIFFRACTION99.7546764796
4.9856-6.27880.2121929785641910.1982376319933116X-RAY DIFFRACTION99.9093655589
6.2788-45.85666666670.2257064999791770.2228751952743231X-RAY DIFFRACTION99.3296415039
Refinement TLS params.Method: refined / Origin x: 33.828583974 Å / Origin y: 38.4639294037 Å / Origin z: 2.28464849524 Å
111213212223313233
T0.275077645186 Å20.0477640169517 Å2-0.0633528113139 Å2-0.4726983716 Å20.0244650146853 Å2--0.249420217425 Å2
L0.892910773254 °20.102034378773 °2-0.0508929682214 °2-4.62779404923 °2-0.393763777616 °2--0.481712656347 °2
S-0.0280658192995 Å °0.190579738744 Å °0.216186974111 Å °-0.236731768664 Å °0.045158347783 Å °0.2281128901 Å °0.0471809222957 Å °-0.0891617594442 Å °-0.0193448988103 Å °
Refinement TLS groupSelection details: all

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