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- PDB-1s9v: Crystal structure of HLA-DQ2 complexed with deamidated gliadin peptide -

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Basic information

Entry
Database: PDB / ID: 1s9v
TitleCrystal structure of HLA-DQ2 complexed with deamidated gliadin peptide
Components
  • HLA class II histocompatibility antigen, DQ(1) beta chain
  • HLA class II histocompatibility antigen, DQ(3) alpha chain
  • alpha-I gliadin
KeywordsIMMUNE SYSTEM / HLA-DQ2
Function / homology
Function and homology information


MHC class II receptor activity / 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 ...MHC class II receptor activity / 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 / MHC class II protein complex / clathrin-coated endocytic vesicle membrane / ER to Golgi transport vesicle membrane / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / positive regulation of T cell activation / peptide antigen binding / 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 / 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 / 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 / HLA class II histocompatibility antigen, DQ beta 1 chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.22 Å
AuthorsKim, C.-Y. / Quarsten, H. / Bergseng, E. / Khosla, C. / Sollid, L.M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2004
Title: Structural basis for HLA-DQ2-mediated presentation of gluten epitopes in celiac disease
Authors: Kim, C.-Y. / Quarsten, H. / Bergseng, E. / Khosla, C. / Sollid, L.M.
History
DepositionFeb 5, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 2, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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(3) alpha chain
B: HLA class II histocompatibility antigen, DQ(1) beta chain
C: alpha-I gliadin
D: HLA class II histocompatibility antigen, DQ(3) alpha chain
E: HLA class II histocompatibility antigen, DQ(1) beta chain
F: alpha-I gliadin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,63810
Polymers92,3906
Non-polymers2484
Water6,377354
1
A: HLA class II histocompatibility antigen, DQ(3) alpha chain
B: HLA class II histocompatibility antigen, DQ(1) beta chain
C: alpha-I gliadin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,3195
Polymers46,1953
Non-polymers1242
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6970 Å2
ΔGint-26 kcal/mol
Surface area17780 Å2
MethodPISA
2
D: HLA class II histocompatibility antigen, DQ(3) alpha chain
E: HLA class II histocompatibility antigen, DQ(1) beta chain
F: alpha-I gliadin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,3195
Polymers46,1953
Non-polymers1242
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7070 Å2
ΔGint-33 kcal/mol
Surface area17460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.11, 93.75, 102.72
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 HLA class II histocompatibility antigen, DQ(3) alpha chain / HLA-DQ2 alpha chain / HLA-DQA1*0501 / DC-alpha / HLA-DCA


Mass: 21752.373 Da / Num. of mol.: 2 / Fragment: residues (-1)-191
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P01909
#2: Protein HLA class II histocompatibility antigen, DQ(1) beta chain / HLA-DQ2 beta chain / DQB1*0201 / DC-3 beta chain


Mass: 23114.023 Da / Num. of mol.: 2 / Fragment: residues 1-198
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P01918, UniProt: P01920*PLUS
#3: Protein/peptide alpha-I gliadin


Mass: 1328.509 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: chemically synthesized
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 354 / 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: 2.37 Å3/Da / Density % sol: 48.16 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 3.5
Details: sodium acetate, ammonium acetate, ammonium sulfate, ethylene glycol, PEG 3350, pH 3.5, VAPOR DIFFUSION, HANGING DROP, temperature 300K
Crystal grow
*PLUS
pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
12-4 mg/mlprotein1drop
225 mMTris-HCl1droppH8.0
350 mMsodium acetate1reservoirpH3.5
4200 mMammonium acetate1reservoir
540 mMammonium sulfate1reservoir
64 %ethylene gylcol1reservoir
726 %PEG33501reservoir

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 15, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→69 Å / Num. obs: 44458
Reflection
*PLUS
Lowest resolution: 40 Å / % possible obs: 93.9 % / Num. measured all: 288797 / Rmerge(I) obs: 0.092
Reflection shell
*PLUS
% possible obs: 76.5 % / Num. unique obs: 1677 / Num. measured obs: 4689 / Rmerge(I) obs: 0.351 / Mean I/σ(I) obs: 2.182

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Processing

Software
NameVersionClassification
Blu-Icedata collection
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.22→69 Å /
RfactorNum. reflection
Rfree0.283 -
Rwork0.221 -
obs-44458
Refinement stepCycle: LAST / Resolution: 2.22→69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5960 0 16 354 6330
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d26.2
X-RAY DIFFRACTIONc_improper_angle_d0.8
Refinement
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 40 Å / Num. reflection obs: 38843
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg26.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.8
LS refinement shell
*PLUS
Rfactor Rfree: 0.348 / Rfactor Rwork: 0.294

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