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- PDB-6mff: HLA-DQ2-glia-omega1 -

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Basic information

Entry
Database: PDB / ID: 6mff
TitleHLA-DQ2-glia-omega1
Components
  • HLA class II histocompatibility antigen, DQ alpha 1 chain
  • MHC class II HLA-DQ-beta-1 - DQ2-glia-omega1 chimeric protein
KeywordsIMMUNE SYSTEM / Immune Complex / Celiac disease / Gliadin epitope / TCR cross-reactivity
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 / endocytic vesicle membrane / antigen processing and presentation of exogenous peptide antigen via MHC class II / 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 / lysosomal membrane / Golgi membrane / membrane / plasma membrane
Similarity search - Function
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 ...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-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: 2.6 Å
AuthorsPetersen, J. / Ciacchi, L. / Rossjohn, J.
CitationJournal: J. Biol. Chem. / Year: 2019
Title: Discriminative T-cell receptor recognition of highly homologous HLA-DQ2-bound gluten epitopes.
Authors: Dahal-Koirala, S. / Ciacchi, L. / Petersen, J. / Risnes, L.F. / Neumann, R.S. / Christophersen, A. / Lundin, K.E.A. / Reid, H.H. / Qiao, S.W. / Rossjohn, J. / Sollid, L.M.
History
DepositionSep 10, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 21, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 12, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_DOI ..._citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jan 30, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Jul 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 / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
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
A: HLA class II histocompatibility antigen, DQ alpha 1 chain
C: MHC class II HLA-DQ-beta-1 - DQ2-glia-omega1 chimeric protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,6584
Polymers47,2162
Non-polymers4422
Water45025
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6170 Å2
ΔGint-23 kcal/mol
Surface area18020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.870, 96.610, 107.050
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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


Mass: 21416.803 Da / Num. of mol.: 1
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: P01909
#2: Protein MHC class II HLA-DQ-beta-1 - DQ2-glia-omega1 chimeric protein


Mass: 25798.754 Da / Num. of mol.: 1
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
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2 / Source method: isolated from a natural 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
#4: Water ChemComp-HOH / water / Water


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

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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: 2.53 Å3/Da / Density % sol: 51.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 23% PEG3350 and 0.1 M NaH2PO4, pH 6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jun 14, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.6→67.32 Å / Num. obs: 15331 / % possible obs: 100 % / Redundancy: 12.5 % / CC1/2: 0.998 / Rpim(I) all: 0.044 / Net I/σ(I): 13.4
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 12.7 % / Mean I/σ(I) obs: 2.3 / Num. unique obs: 2200 / CC1/2: 0.719 / Rpim(I) all: 0.366 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→46.935 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.52
RfactorNum. reflection% reflection
Rfree0.2503 771 5.04 %
Rwork0.2086 --
obs0.2107 15303 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.6→46.935 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2999 0 28 25 3052
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033113
X-RAY DIFFRACTIONf_angle_d0.5754251
X-RAY DIFFRACTIONf_dihedral_angle_d13.2121850
X-RAY DIFFRACTIONf_chiral_restr0.051476
X-RAY DIFFRACTIONf_plane_restr0.004548
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6001-2.7630.42071510.36562355X-RAY DIFFRACTION100
2.763-2.97630.32771220.27942381X-RAY DIFFRACTION100
2.9763-3.27580.30581380.26282385X-RAY DIFFRACTION100
3.2758-3.74960.28351200.21132442X-RAY DIFFRACTION100
3.7496-4.72340.22071240.1672412X-RAY DIFFRACTION100
4.7234-46.94270.16621160.17462557X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
17.9837-2.3892-2.10668.2285-2.85732.3727-1.25851.31831.41990.1466-0.23190.1223-1.65090.66591.08311.1748-0.1464-0.38010.5248-0.0120.5766-17.773917.416820.754
24.9917-1.4910.21326.44570.04983.2421-0.293-0.26630.46140.43290.01450.294-0.7423-0.06930.28130.5588-0.0254-0.11210.3808-0.060.3365-24.05898.806622.3053
33.30121.89490.51465.8855-0.49363.4893-0.23050.27920.1697-0.9190.26020.95740.1852-0.595-0.07950.4809-0.0131-0.14870.42820.03170.3934-34.5319-10.354215.496
43.00880.9343-0.46875.4358-0.7292.515-0.18140.19760.4549-0.1656-0.082-0.2293-0.8250.34840.22190.6932-0.1502-0.17170.53740.05760.3769-14.29513.478414.0581
53.2507-1.6317-0.56729.13560.70484.52620.11320.1544-0.6202-0.6162-0.1624-1.01491.53710.59020.04240.90950.23010.10610.48920.14080.5782-13.6356-24.961211.1349
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'C' and (resid 1 through 10 )
2X-RAY DIFFRACTION2chain 'A' and (resid 2 through 80 )
3X-RAY DIFFRACTION3chain 'A' and (resid 81 through 180 )
4X-RAY DIFFRACTION4chain 'C' and (resid 39 through 129 )
5X-RAY DIFFRACTION5chain 'C' and (resid 130 through 226 )

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