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- PDB-7yg3: Crystal structure of HLA-B*13:01 -

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Basic information

Entry
Database: PDB / ID: 7yg3
TitleCrystal structure of HLA-B*13:01
Components
  • ARG-GLN-ASP-ILE-LEU-ASP-LEU-TRP-ILE
  • Beta-2-microglobulin
  • MHC class I antigen
KeywordsIMMUNE SYSTEM / HLA-B*13:01 / T cell receptor / drug-induced hypersensitivity syndrome
Function / homology
Function and homology information


positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / negative regulation of receptor binding / DAP12 interactions / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / cellular response to iron ion ...positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / negative regulation of receptor binding / DAP12 interactions / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / negative regulation of forebrain neuron differentiation / regulation of erythrocyte differentiation / peptide antigen assembly with MHC class I protein complex / ER to Golgi transport vesicle membrane / regulation of iron ion transport / response to molecule of bacterial origin / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / MHC class I protein complex / negative regulation of neurogenesis / positive regulation of receptor-mediated endocytosis / peptide antigen assembly with MHC class II protein complex / multicellular organismal-level iron ion homeostasis / MHC class II protein complex / cellular response to nicotine / specific granule lumen / positive regulation of cellular senescence / positive regulation of T cell mediated cytotoxicity / recycling endosome membrane / phagocytic vesicle membrane / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / negative regulation of epithelial cell proliferation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of immune response / Interferon gamma signaling / Modulation by Mtb of host immune system / positive regulation of T cell activation / sensory perception of smell / negative regulation of neuron projection development / positive regulation of protein binding / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / late endosome membrane / iron ion transport / ER-Phagosome pathway / T cell differentiation in thymus / early endosome membrane / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / lysosomal membrane / Golgi membrane / external side of plasma membrane / signaling receptor binding / focal adhesion / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / Golgi apparatus / endoplasmic reticulum / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane / cytosol
Similarity search - Function
MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / MHC classes I/II-like antigen recognition protein / : / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. ...MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / 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 / Immunoglobulin-like fold
Similarity search - Domain/homology
MHC class I antigen / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
Human immunodeficiency virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsWang, H.S. / Ouyang, S.Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)81371751, 81972950, 31770948, 82103748 and 81773477 China
CitationJournal: J.Biomed.Sci. / Year: 2022
Title: Functional and structural characteristics of HLA-B*13:01-mediated specific T cells reaction in dapsone-induced drug hypersensitivity.
Authors: Jiang, H. / Wang, C.W. / Wang, Z. / Dai, Y. / Zhu, Y. / Lee, Y.S. / Cao, Y. / Chung, W.H. / Ouyang, S. / Wang, H.
History
DepositionJul 11, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 26, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MHC class I antigen
C: Beta-2-microglobulin
B: ARG-GLN-ASP-ILE-LEU-ASP-LEU-TRP-ILE


Theoretical massNumber of molelcules
Total (without water)44,8873
Polymers44,8873
Non-polymers00
Water11,584643
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4360 Å2
ΔGint-14 kcal/mol
Surface area19280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.297, 82.768, 110.442
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein MHC class I antigen


Mass: 31966.363 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-B / Production host: Escherichia coli (E. coli) / References: UniProt: F4YTC6
#2: Protein Beta-2-microglobulin


Mass: 11748.160 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M / Production host: Escherichia coli (E. coli) / References: UniProt: P61769
#3: Protein/peptide ARG-GLN-ASP-ILE-LEU-ASP-LEU-TRP-ILE


Mass: 1172.354 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 643 / 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: 2.56 Å3/Da / Density % sol: 51.97 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop / Details: 0.1 M HEPES pH 6.5, 20% PEG 4000, 0.2 M NaCl

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Data collection

DiffractionMean temperature: 298.15 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.987 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 2150046 / % possible obs: 99.8 % / Redundancy: 6.5 % / Biso Wilson estimate: 17.29 Å2 / CC1/2: 0.992 / Net I/σ(I): 3.5
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 12.5 % / Num. unique obs: 2837 / CC1/2: 0.932 / % possible all: 98.2

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Processing

Software
NameVersionClassification
HKL-20001.18.2_3874data collection
PHENIX1.18.2_3874phasing
PHENIX1.18.2_3874refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4JQX

4jqx


Resolution: 1.5→45.94 Å / SU ML: 0.1383 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 18.8338
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1949 3761 5.04 %
Rwork0.175 70821 -
obs0.176 74582 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21 Å2
Refinement stepCycle: LAST / Resolution: 1.5→45.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3164 0 0 643 3807
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00653250
X-RAY DIFFRACTIONf_angle_d1.10894416
X-RAY DIFFRACTIONf_chiral_restr0.1681456
X-RAY DIFFRACTIONf_plane_restr0.0072580
X-RAY DIFFRACTIONf_dihedral_angle_d13.5644433
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.520.2181420.19522475X-RAY DIFFRACTION95.37
1.52-1.540.20651470.18972585X-RAY DIFFRACTION100
1.54-1.560.23251320.17812578X-RAY DIFFRACTION99.96
1.56-1.580.24471340.1752612X-RAY DIFFRACTION99.89
1.58-1.60.1931400.16622571X-RAY DIFFRACTION99.93
1.6-1.630.18461290.17222633X-RAY DIFFRACTION99.93
1.63-1.660.24571060.18012595X-RAY DIFFRACTION99.89
1.66-1.690.21671220.17722641X-RAY DIFFRACTION100
1.69-1.720.17661440.17662571X-RAY DIFFRACTION100
1.72-1.750.21151350.17922603X-RAY DIFFRACTION99.96
1.75-1.780.21371260.1772628X-RAY DIFFRACTION100
1.78-1.820.23671320.18122597X-RAY DIFFRACTION100
1.82-1.870.1911540.17742627X-RAY DIFFRACTION100
1.87-1.910.18331390.17732580X-RAY DIFFRACTION100
1.91-1.960.24951390.17272622X-RAY DIFFRACTION100
1.96-2.020.20151420.1732613X-RAY DIFFRACTION99.93
2.02-2.090.18611280.17262630X-RAY DIFFRACTION99.89
2.09-2.160.18441340.17772634X-RAY DIFFRACTION100
2.16-2.250.20261470.17162617X-RAY DIFFRACTION99.96
2.25-2.350.1821550.17852590X-RAY DIFFRACTION100
2.35-2.470.21211440.18652651X-RAY DIFFRACTION100
2.47-2.630.21121460.19182640X-RAY DIFFRACTION99.96
2.63-2.830.21741570.19362640X-RAY DIFFRACTION99.93
2.83-3.120.20751380.18812663X-RAY DIFFRACTION100
3.12-3.570.1821460.17412684X-RAY DIFFRACTION100
3.57-4.50.16831400.14822705X-RAY DIFFRACTION100
4.5-45.940.17651630.1692836X-RAY DIFFRACTION99.87

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