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- PDB-6u3o: JR51 DQ2-p.aeru-alpha2a complex -

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Basic information

Entry
Database: PDB / ID: 6u3o
TitleJR51 DQ2-p.aeru-alpha2a complex
Components
  • (MHC class II HLA-DQ- ...) x 2
  • (T-CELL RECEPTOR, JR5.1 ...) x 2
  • Peptide
KeywordsIMMUNE SYSTEM / Immune Complex / Celiac disease / Gliadin epitope / TCR cross-reactivity
Function / homology
Function and homology information


antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / transmembrane transport / MHC class II protein complex / adaptive immune response / membrane => GO:0016020 / endosome membrane / lysosomal membrane / membrane
Similarity search - Function
Oligopeptide transporter OPT / Oligopeptide transporter, OPT superfamily / OPT oligopeptide transporter protein / Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 / Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 / 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 ...Oligopeptide transporter OPT / Oligopeptide transporter, OPT superfamily / OPT oligopeptide transporter protein / Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 / Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 / 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 / Immunoglobulins / Roll / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
MHC class II HLA-DQ-alpha chain / MHC class II HLA-DQ-beta-1 / Uncharacterized protein
Similarity search - Component
Biological speciesHomo sapiens (human)
Pseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.743 Å
AuthorsPetersen, J. / Rossjohn, J.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC)CE140100011 Australia
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2020
Title: T cell receptor cross-reactivity between gliadin and bacterial peptides in celiac disease.
Authors: Petersen, J. / Ciacchi, L. / Tran, M.T. / Loh, K.L. / Kooy-Winkelaar, Y. / Croft, N.P. / Hardy, M.Y. / Chen, Z. / McCluskey, J. / Anderson, R.P. / Purcell, A.W. / Tye-Din, J.A. / Koning, F. ...Authors: Petersen, J. / Ciacchi, L. / Tran, M.T. / Loh, K.L. / Kooy-Winkelaar, Y. / Croft, N.P. / Hardy, M.Y. / Chen, Z. / McCluskey, J. / Anderson, R.P. / Purcell, A.W. / Tye-Din, J.A. / Koning, F. / Reid, H.H. / Rossjohn, J.
History
DepositionAug 22, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 1, 2020Group: Data collection / Database references / Category: chem_comp / citation / citation_author
Item: _chem_comp.type / _citation.country ..._chem_comp.type / _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
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _chem_comp.name / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
G: T-CELL RECEPTOR, JR5.1 alpha
H: T-CELL RECEPTOR, JR5.1 beta
A: T-CELL RECEPTOR, JR5.1 alpha
B: T-CELL RECEPTOR, JR5.1 beta
C: MHC class II HLA-DQ-alpha chain
D: MHC class II HLA-DQ-beta-1
E: MHC class II HLA-DQ-alpha chain
F: MHC class II HLA-DQ-beta-1
I: Peptide
J: Peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)194,91812
Polymers194,07010
Non-polymers8492
Water1,18966
1
G: T-CELL RECEPTOR, JR5.1 alpha
H: T-CELL RECEPTOR, JR5.1 beta
E: MHC class II HLA-DQ-alpha chain
F: MHC class II HLA-DQ-beta-1
I: Peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,4596
Polymers97,0355
Non-polymers4241
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: T-CELL RECEPTOR, JR5.1 alpha
B: T-CELL RECEPTOR, JR5.1 beta
C: MHC class II HLA-DQ-alpha chain
D: MHC class II HLA-DQ-beta-1
J: Peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,4596
Polymers97,0355
Non-polymers4241
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.057, 157.650, 106.100
Angle α, β, γ (deg.)90.000, 96.530, 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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T-CELL RECEPTOR, JR5.1 ... , 2 types, 4 molecules GAHB

#1: Protein T-CELL RECEPTOR, JR5.1 alpha /


Mass: 22567.066 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#2: Protein T-CELL RECEPTOR, JR5.1 beta /


Mass: 27229.176 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)

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MHC class II HLA-DQ- ... , 2 types, 4 molecules CEDF

#3: Protein MHC class II HLA-DQ-alpha chain


Mass: 21501.840 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DQA1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: O19705
#4: Protein MHC class II HLA-DQ-beta-1


Mass: 23703.496 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DQB1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: O19712

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Protein/peptide / Sugars / Non-polymers , 3 types, 70 molecules IJ

#5: Protein/peptide Peptide /


Mass: 2033.178 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9HX82*PLUS
#6: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 66 / 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: 2.95 Å3/Da / Density % sol: 58.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 23%PEG3350, 0.01mM Na-Acetate, 0.1 M Tris pH8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95372 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 2.743→47.03 Å / Num. obs: 58874 / % possible obs: 99.26 % / Redundancy: 3.6 % / Rpim(I) all: 0.04437 / Net I/σ(I): 13.4
Reflection shellResolution: 2.743→2.841 Å / Num. unique obs: 5791 / Rpim(I) all: 0.3744

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Processing

Software
NameClassification
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.743→47.03 Å / Cross valid method: FREE R-VALUE /
Num. reflection% reflection
obs58558 99.26 %
Refinement stepCycle: LAST / Resolution: 2.743→47.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12766 0 56 66 12888

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