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- PDB-4d8p: Structural and functional studies of the trans-encoded HLA-DQ2.3 ... -

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Basic information

Entry
Database: PDB / ID: 4d8p
TitleStructural and functional studies of the trans-encoded HLA-DQ2.3 (DQA1*03:01/DQB1*02:01) molecule
Components
  • HLA-DQA1 protein
  • Peptide from Gamma-gliadin,HLA class II histocompatibility antigen, DQ beta 1 chain
KeywordsIMMUNE SYSTEM / class II MHC
Function / homology
Function and homology information


nutrient reservoir activity / antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / MHC class II protein complex / adaptive immune response / endosome membrane / lysosomal membrane / metal ion binding
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 / Immunoglobulins / Roll / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
HLA class II histocompatibility antigen DQ alpha chain / HLA class II histocompatibility antigen DQ beta chain / Gamma-gliadin
Similarity search - Component
Biological speciesHomo sapiens (human)
Triticum aestivum (bread wheat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.05 Å
AuthorsKim, C.-Y. / Hotta, K. / Mathews, I.I. / Chen, X.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Structural and functional studies of trans-encoded HLA-DQ2.3 (DQA1*03:01/DQB1*02:01) protein molecule
Authors: Tollefsen, S. / Hotta, K. / Chen, X. / Simonsen, B. / Swaminathan, K. / Mathews, I.I. / Sollid, L.M. / Kim, C.-Y.
History
DepositionJan 11, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 14, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 12, 2014Group: Database references
Revision 1.2Jun 21, 2017Group: Database references / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.pdbx_description / _entity.pdbx_mutation ..._entity.pdbx_description / _entity.pdbx_mutation / _struct_ref.db_code / _struct_ref.pdbx_db_accession / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq_dif.details / _struct_ref_seq_dif.pdbx_seq_db_accession_code
Revision 1.3Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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-DQA1 protein
B: Peptide from Gamma-gliadin,HLA class II histocompatibility antigen, DQ beta 1 chain
C: HLA-DQA1 protein
D: Peptide from Gamma-gliadin,HLA class II histocompatibility antigen, DQ beta 1 chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,0246
Polymers103,8404
Non-polymers1842
Water1086
1
A: HLA-DQA1 protein
B: Peptide from Gamma-gliadin,HLA class II histocompatibility antigen, DQ beta 1 chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,1044
Polymers51,9202
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6510 Å2
ΔGint-27 kcal/mol
Surface area18160 Å2
MethodPISA
2
C: HLA-DQA1 protein
D: Peptide from Gamma-gliadin,HLA class II histocompatibility antigen, DQ beta 1 chain


Theoretical massNumber of molelcules
Total (without water)51,9202
Polymers51,9202
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6140 Å2
ΔGint-27 kcal/mol
Surface area17910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.890, 114.920, 138.030
Angle α, β, γ (deg.)90.00, 103.36, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein HLA-DQA1 protein / MHC class II antigen


Mass: 23854.559 Da / Num. of mol.: 2 / Fragment: UNP residues 24-217
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DQA1 / Plasmid: pRmHa3 / Cell (production host): SCHNEIDER 2(S2) / Production host: DROSOPHILA MELANOGASTER (fruit fly) / References: UniProt: L8E864
#2: Protein Peptide from Gamma-gliadin,HLA class II histocompatibility antigen, DQ beta 1 chain / / MHC class II antigen


Mass: 28065.299 Da / Num. of mol.: 2 / Mutation: Q26E, Q23E
Source method: isolated from a genetically manipulated source
Details: Chimera protein of peptide from Gamma-gliadin (residues 68-81 in Uniprot Q94G94), linker, MHC class II antigen (residues 33-230 in uniprot Q5Y7D3)
Source: (gene. exp.) Triticum aestivum (bread wheat), (gene. exp.) Homo sapiens (human)
Plasmid: pRmHa3 / Gene: HLA-DQB1 / Cell (production host): SCHNEIDER 2(S2) / Production host: DROSOPHILA MELANOGASTER (fruit fly) / References: UniProt: Q94G94, UniProt: Q5Y7D3
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 2.78 Å3/Da / Density % sol: 55.8 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2M Li2So4, 0.1M Tris, 30% PEG 4000, 8% Glycerol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.9795 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Dec 16, 2009 / Details: Mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.05→29.31 Å / Num. all: 21713 / Num. obs: 21713 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 16.4
Reflection shellResolution: 3.05→3.13 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.851 / Mean I/σ(I) obs: 1.9 / Num. unique all: 1629 / % possible all: 99.6

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
REFMAC5.5.0109refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1JK8 and 1S9V

1jk8

1s9v


Resolution: 3.05→29.31 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.897 / SU B: 55.62 / SU ML: 0.441 / Cross valid method: THROUGHOUT / ESU R Free: 0.479 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28321 1086 5 %RANDOM
Rwork0.21045 ---
obs0.21398 20626 100 %-
all-21713 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 91.852 Å2
Baniso -1Baniso -2Baniso -3
1-4.86 Å20 Å2-9.39 Å2
2---1.81 Å20 Å2
3----7.39 Å2
Refinement stepCycle: LAST / Resolution: 3.05→29.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6102 0 12 6 6120
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0226286
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3931.9448573
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3635745
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.63623.812320
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.73315990
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7521546
X-RAY DIFFRACTIONr_chiral_restr0.090.2938
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214892
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5521.53777
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.0326178
X-RAY DIFFRACTIONr_scbond_it1.04732509
X-RAY DIFFRACTIONr_scangle_it1.8644.52395
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.05→3.129 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.416 81 -
Rwork0.382 1530 -
obs--100 %
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)
10.75770.7196-0.31241.1959-1.62043.6345-0.2598-0.1698-0.10140.1723-0.06750.2385-0.7809-0.06570.32730.17170.02310.0230.1864-0.05970.272112.453910.744952.4295
2-0.12951.10571.12151.6354-0.02992.52650.10950.0467-0.0038-0.22520.08060.03480.50660.3329-0.19010.13170.08860.05460.21890.06710.184919.7702-2.17644.6958
30.1081-1.10931.35842.461-1.79633.75780.022-0.3458-0.098-0.3609-0.00980.2914-0.1213-0.6568-0.01220.0576-0.0177-0.00620.3024-0.11970.2272-9.4289-3.2524.132
40.55890.55150.00061.083-0.97712.25190.03350.0342-0.059-0.0442-0.1148-0.04510.03910.12460.08130.142-0.01350.01020.1586-0.01390.15946.9284-5.593721.0325
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 182
2X-RAY DIFFRACTION2B3 - 190
3X-RAY DIFFRACTION3C1 - 181
4X-RAY DIFFRACTION4D3 - 190

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