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- PDB-2nna: Structure of the MHC class II molecule HLA-DQ8 bound with a deami... -

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Basic information

Entry
Database: PDB / ID: 2nna
TitleStructure of the MHC class II molecule HLA-DQ8 bound with a deamidated gluten peptide
Components
  • (MHC class II antigen) x 2
  • gluten peptide
KeywordsIMMUNE SYSTEM / Major Histocompatibility complex HLA-DQ8 / deamidated gluten peptide / post translational modification
Function / homology
Function and homology information


nutrient reservoir activity / 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 / humoral immune response / Generation of second messenger molecules / Co-inhibition by PD-1 / MHC class II antigen presentation ...nutrient reservoir activity / 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 / humoral immune response / Generation of second messenger molecules / Co-inhibition by PD-1 / MHC class II antigen presentation / trans-Golgi network membrane / lumenal side of endoplasmic reticulum membrane / peptide antigen assembly with MHC class II protein complex / clathrin-coated endocytic vesicle membrane / MHC class II protein complex / ER to Golgi transport vesicle membrane / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / peptide antigen binding / positive regulation of T cell activation / Interferon gamma signaling / MHC class II protein complex binding / endocytic vesicle membrane / late endosome membrane / Downstream TCR signaling / T cell receptor signaling pathway / adaptive immune response / endosome membrane / immune response / Golgi membrane / lysosomal membrane / membrane / plasma 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 / 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 ...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 / 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 / Roll / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
HLA class II histocompatibility antigen, DQ alpha 1 chain / HLA class II histocompatibility antigen, DQ beta 1 chain / Alpha/beta-gliadin MM1 / HLA class II histocompatibility antigen, DQ alpha 1 chain / HLA class II histocompatibility antigen DQ beta chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsHenderson, K.N. / Tye-Din, J.A. / Rossjohn, J. / Anderson, R.P.
CitationJournal: Immunity / Year: 2007
Title: A structural and immunological basis for the role of human leukocyte antigen DQ8 in celiac disease
Authors: Henderson, K.N. / Tye-Din, J.A. / Reid, H.H. / Chen, Z. / Borg, N.A. / Beissbarth, T. / Tatham, A. / Mannering, S.I. / Purcell, A.W. / Dudek, N.L. / van Heel, D.A. / McCluskey, J. / Rossjohn, J. / Anderson, R.P.
History
DepositionOct 24, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 4, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.2Oct 25, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MHC class II antigen
B: MHC class II antigen
C: gluten peptide


Theoretical massNumber of molelcules
Total (without water)46,8353
Polymers46,8353
Non-polymers00
Water5,603311
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7370 Å2
ΔGint-32 kcal/mol
Surface area18090 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)58.830, 92.520, 113.060
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein MHC class II antigen


Mass: 21047.453 Da / Num. of mol.: 1 / Fragment: residues in database 24-207
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pFastbacDual / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Hi5 cells / References: UniProt: Q5Y7F5, UniProt: P01909*PLUS
#2: Protein MHC class II antigen


Mass: 23779.551 Da / Num. of mol.: 1 / Fragment: residues in database 33-224
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pFastbacDual / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Hi5 cells / References: UniProt: Q5Y7F6, UniProt: P01920*PLUS
#3: Protein/peptide gluten peptide


Mass: 2008.019 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: The C terminus of chain C was linked to the N terminus of chain B with a flexible serine glycine linker. This flexible linker was cleaved with trypsin at an unknown point in the sequence ...Details: The C terminus of chain C was linked to the N terminus of chain B with a flexible serine glycine linker. This flexible linker was cleaved with trypsin at an unknown point in the sequence during the purification process.
References: UniProt: P18573
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 311 / 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: 3.28 Å3/Da / Density % sol: 62.5 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.05M mono-Pottasium dihydrogen phosphate, 19%(w/v) PEG 8000, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Sep 29, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→49.64 Å / Num. obs: 36603
Reflection shellResolution: 2.1→2.18 Å

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Processing

Software
NameClassification
CrystalCleardata collection
AMoREphasing
CNSrefinement
d*TREKdata reduction
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1JK8, with the insulin peptide removed

1jk8


Resolution: 2.1→49.64 Å / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflectionSelection details
Rfree0.2478 1473 RANDOM
Rwork0.217 --
obs-36603 -
Displacement parametersBiso mean: 37.8476 Å2
Refinement stepCycle: LAST / Resolution: 2.1→49.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3071 0 0 311 3382

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