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- PDB-8xke: The structure of HLA-A/14-3-D -

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Basic information

Entry
Database: PDB / ID: 8xke
TitleThe structure of HLA-A/14-3-D
Components
  • Beta-2-microglobulin
  • GLU-VAL-ASP-ASN-ALA-THR-ARG-PHE-ALA-SER-VAL-TYR
  • HLA class I heavy chain
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / Complex / Peptide presentation / Immune system / VIRAL PROTEIN-IMMUNE SYSTEM complex
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 / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC ...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 / 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 / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / MHC class I protein complex / multicellular organismal-level iron ion homeostasis / negative regulation of neurogenesis / positive regulation of receptor-mediated endocytosis / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / specific granule lumen / recycling endosome membrane / phagocytic vesicle membrane / peptide antigen binding / positive regulation of cellular senescence / negative regulation of epithelial cell proliferation / antigen processing and presentation of exogenous peptide antigen via MHC class II / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / positive regulation of immune response / 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 / early endosome membrane / late endosome membrane / iron ion transport / ER-Phagosome pathway / T cell differentiation in thymus / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / Amyloid fiber formation / Golgi membrane / endoplasmic reticulum lumen / external side of plasma membrane / lysosomal membrane / 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
Beta-2-Microglobulin / : / 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
Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
Severe acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 Å
AuthorsZhang, J.N. / Yue, C. / Liu, J. / Sun, Z.Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Immunohorizons / Year: 2024
Title: Uncommon P1 Anchor-featured Viral T Cell Epitope Preference within HLA-A*2601 and HLA-A*0101 Individuals.
Authors: Zhang, J. / Yue, C. / Lin, Y. / Tian, J. / Guo, Y. / Zhang, D. / Guo, Y. / Ye, B. / Chai, Y. / Qi, J. / Zhao, Y. / Gao, G.F. / Sun, Z. / Liu, J.
History
DepositionDec 23, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 10, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HLA class I heavy chain
B: Beta-2-microglobulin
M: GLU-VAL-ASP-ASN-ALA-THR-ARG-PHE-ALA-SER-VAL-TYR


Theoretical massNumber of molelcules
Total (without water)44,8893
Polymers44,8893
Non-polymers00
Water3,333185
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4500 Å2
ΔGint-15 kcal/mol
Surface area18770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.170, 67.250, 122.470
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 HLA class I heavy chain


Mass: 31636.955 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#2: Protein Beta-2-microglobulin


Mass: 11879.356 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Production host: Escherichia coli (E. coli) / References: UniProt: P61769
#3: Protein/peptide GLU-VAL-ASP-ASN-ALA-THR-ARG-PHE-ALA-SER-VAL-TYR


Mass: 1372.460 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Severe acute respiratory syndrome coronavirus 2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 185 / 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: 2.44 Å3/Da / Density % sol: 49.57 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.1M Bis-Tris, 20%w/v Polyethylene glycol monomethyl ether 5000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.979183 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 24, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979183 Å / Relative weight: 1
ReflectionResolution: 1.92→29.47 Å / Num. obs: 34186 / % possible obs: 99.51 % / Redundancy: 12.3 % / Biso Wilson estimate: 32.08 Å2 / Rmerge(I) obs: 0.129 / Net I/σ(I): 10.3
Reflection shellResolution: 2.13→61.07 Å / Num. unique obs: 25142 / Rrim(I) all: 0.134

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487model building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4NQV

4nqv


Resolution: 1.92→29.47 Å / SU ML: 0.2373 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.6701
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2513 1738 5.09 %
Rwork0.2087 32421 -
obs0.2109 34159 99.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.98 Å2
Refinement stepCycle: LAST / Resolution: 1.92→29.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3160 0 0 185 3345
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083244
X-RAY DIFFRACTIONf_angle_d1.00524396
X-RAY DIFFRACTIONf_chiral_restr0.0575446
X-RAY DIFFRACTIONf_plane_restr0.0096582
X-RAY DIFFRACTIONf_dihedral_angle_d6.5821435
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.92-1.980.40251430.36722634X-RAY DIFFRACTION97.92
1.98-2.040.36241490.28512665X-RAY DIFFRACTION99.93
2.04-2.110.35871380.28162618X-RAY DIFFRACTION98.36
2.11-2.20.24981610.23512655X-RAY DIFFRACTION99.93
2.2-2.30.3491360.26972660X-RAY DIFFRACTION99.08
2.3-2.420.29811370.23242709X-RAY DIFFRACTION99.93
2.42-2.570.29361280.23642688X-RAY DIFFRACTION99.86
2.57-2.770.28011510.23742675X-RAY DIFFRACTION99.82
2.77-3.050.24131410.23192728X-RAY DIFFRACTION99.97
3.05-3.490.27571390.20672745X-RAY DIFFRACTION99.97
3.49-4.390.22221540.16822760X-RAY DIFFRACTION100
4.39-29.470.18651610.16632884X-RAY DIFFRACTION99.77

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