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- PDB-6mfg: HLA-DQ2-glia-alpha1 -

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Basic information

Entry
Database: PDB / ID: 6mfg
TitleHLA-DQ2-glia-alpha1
Components
  • HLA class II histocompatibility antigen, DQ alpha 1 chain
  • MHC class II HLA-DQ-beta-1 - DQ2-glia-alpha1 chimeric protein
KeywordsIMMUNE SYSTEM / Immune complex / Gliadin epitope / Celiac Disease / 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 / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / Interferon gamma signaling / endocytic vesicle membrane / 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
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 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
Revision 1.4Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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
C: HLA class II histocompatibility antigen, DQ alpha 1 chain
E: MHC class II HLA-DQ-beta-1 - DQ2-glia-alpha1 chimeric protein
A: HLA class II histocompatibility antigen, DQ alpha 1 chain
F: MHC class II HLA-DQ-beta-1 - DQ2-glia-alpha1 chimeric protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,6545
Polymers94,4334
Non-polymers2211
Water8,881493
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16440 Å2
ΔGint-76 kcal/mol
Surface area33300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.226, 101.968, 70.528
Angle α, β, γ (deg.)90.00, 91.78, 90.00
Int Tables number4
Space group name H-MP1211

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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.: 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: P01909
#2: Protein MHC class II HLA-DQ-beta-1 - DQ2-glia-alpha1 chimeric protein


Mass: 25799.783 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
#3: 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.: 1
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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 493 / Source method: isolated from a natural source / Formula: H2O
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: 2.25 Å3/Da / Density % sol: 45.43 %
Crystal growTemperature: 293.15 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: Aug 9, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2→70.49 Å / Num. obs: 56391 / % possible obs: 99.7 % / Redundancy: 3.8 % / CC1/2: 0.999 / Rpim(I) all: 0.044 / Net I/σ(I): 13.5
Reflection shellResolution: 2→2.11 Å / Redundancy: 3.7 % / CC1/2: 0.751 / Rpim(I) all: 0.393 / % possible all: 97.3

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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→59.198 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.2
RfactorNum. reflection% reflection
Rfree0.222 1739 3.09 %
Rwork0.1867 --
obs0.1877 56343 99.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2→59.198 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6011 0 14 493 6518
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026193
X-RAY DIFFRACTIONf_angle_d0.5688451
X-RAY DIFFRACTIONf_dihedral_angle_d16.5453695
X-RAY DIFFRACTIONf_chiral_restr0.044939
X-RAY DIFFRACTIONf_plane_restr0.0051091
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.05890.33781420.28214522X-RAY DIFFRACTION100
2.0589-2.12540.30971470.25084547X-RAY DIFFRACTION100
2.1254-2.20130.281320.22834561X-RAY DIFFRACTION100
2.2013-2.28950.26651650.22174506X-RAY DIFFRACTION100
2.2895-2.39370.27761420.22244551X-RAY DIFFRACTION100
2.3937-2.51990.24291360.21954556X-RAY DIFFRACTION100
2.5199-2.67770.21461500.21514564X-RAY DIFFRACTION100
2.6777-2.88450.22261410.20224541X-RAY DIFFRACTION100
2.8845-3.17480.23251620.19654545X-RAY DIFFRACTION100
3.1748-3.63410.22841400.17144567X-RAY DIFFRACTION100
3.6341-4.57830.16741470.14824555X-RAY DIFFRACTION99
4.5783-59.22340.18711350.15684589X-RAY DIFFRACTION98
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)
14.09950.3216-1.32693.52650.03943.1031-0.0742-0.1945-0.25060.0641-0.0555-0.05690.31860.220.12460.23680.0515-0.00120.18780.00840.1975197.8292-187.721313.1891
22.51870.7983-1.45752.5879-1.24053.95940.1637-0.7435-0.1160.5873-0.1839-0.0174-0.25790.62350.00790.3309-0.00720.00720.37030.02770.2207192.779-180.050634.1391
31.08020.0015-1.2691.6580.04873.66180.02380.1771-0.0389-0.2866-0.00160.015-0.0788-0.1429-0.03260.27480.0462-0.02330.16960.00320.2708192.81-181.32243.0559
45.1058-0.2882-1.76884.05950.0332.60540.17280.12660.49260.62560.2351.0084-0.25-0.7963-0.13320.37920.12050.21570.44560.18050.5425167.9214-174.969231.9571
53.0756-0.4383-0.86621.99-0.06964.39490.0534-0.46220.2670.1939-0.01810.0232-0.21170.1324-0.02710.18890.0089-0.0030.2287-0.04290.1879187.9744-144.568923.7576
63.29390.925-1.15732.5184-1.16672.7933-0.0853-0.2909-0.30210.0418-0.1395-0.4178-0.00890.3760.22060.15880.0209-0.01520.17320.01440.2444208.0869-152.279315.6188
73.6732-0.0474-2.20691.3613-0.20770.9064-0.1117-0.0344-0.18750.21730.04830.223-0.0303-0.14560.04360.22430.01120.00210.2002-0.02080.2606177.4573-151.457520.8319
83.1775-0.6136-1.70974.32330.69586.21330.0380.6829-0.1138-0.8956-0.1318-0.25940.398-0.23880.0460.3879-0.0120.06360.2814-0.01270.232201.4531-157.5726-8.8729
98.1094.4768-5.8055.4401-3.98454.4531-0.0207-0.587-0.29860.3737-0.41620.14330.1130.55370.48710.32080.0530.00540.2745-0.01640.3041177.677-144.864526.714
105.80725.4371-5.86245.1912-5.59316.1342-0.6661-0.4344-0.2266-0.93730.06130.18190.68640.4460.55940.37190.05670.08780.3002-0.02410.4374198.3005-188.29732.4734
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN C AND RESID 1:83 )C1 - 83
2X-RAY DIFFRACTION2( CHAIN C AND RESID 84:181 )C84 - 181
3X-RAY DIFFRACTION3( CHAIN E AND RESID 39:132 )E39 - 132
4X-RAY DIFFRACTION4( CHAIN E AND RESID 133:226 )E133 - 226
5X-RAY DIFFRACTION5( CHAIN A AND RESID 1:83 )A1 - 83
6X-RAY DIFFRACTION6( CHAIN A AND RESID 84:181 )A84 - 181
7X-RAY DIFFRACTION7( CHAIN F AND RESID 39:132 )F39 - 132
8X-RAY DIFFRACTION8( CHAIN F AND RESID 133:226 )F133 - 226
9X-RAY DIFFRACTION9( CHAIN E AND RESID 0:10 )E0 - 10
10X-RAY DIFFRACTION10( CHAIN F AND RESID 0:10 )F0 - 10

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