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- PDB-8sbl: Structure of HLA-A*24:02 in complex with peptide, LYLPVRVLI -

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Basic information

Entry
Database: PDB / ID: 8sbl
TitleStructure of HLA-A*24:02 in complex with peptide, LYLPVRVLI
Components
  • Beta-2-microglobulin
  • LEU-TYR-LEU-PRO-VAL-ARG-VAL-LEU-ILE
  • MHC class I antigen
KeywordsIMMUNE SYSTEM / Major Histocompatibility Complex (MHC)
Function / homology
Function and homology information


negative regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / transferrin transport / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / peptide antigen assembly with MHC class II protein complex / cellular response to iron(III) ion ...negative regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / transferrin transport / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / peptide antigen assembly with MHC class II protein complex / cellular response to iron(III) ion / MHC class II protein complex / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / regulation of erythrocyte differentiation / HFE-transferrin receptor complex / response to molecule of bacterial origin / MHC class I peptide loading complex / T cell mediated cytotoxicity / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / MHC class I protein complex / positive regulation of T cell activation / peptide antigen binding / positive regulation of receptor-mediated endocytosis / negative regulation of neurogenesis / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / multicellular organismal-level iron ion homeostasis / specific granule lumen / phagocytic vesicle membrane / recycling endosome membrane / Interferon gamma signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / MHC class II protein complex binding / Modulation by Mtb of host immune system / late endosome membrane / sensory perception of smell / positive regulation of cellular senescence / tertiary granule lumen / DAP12 signaling / T cell differentiation in thymus / negative regulation of neuron projection development / ER-Phagosome pathway / protein refolding / early endosome membrane / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / endoplasmic reticulum lumen / Amyloid fiber formation / Golgi membrane / lysosomal membrane / external side of plasma membrane / focal adhesion / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / endoplasmic reticulum / Golgi apparatus / 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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsMallik, L. / Young, M.C. / Sgourakis, N.G.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)5R01AI143997 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5R35GM125034 United States
Citation
Journal: Sci Immunol / Year: 2023
Title: Structural principles of peptide-centric chimeric antigen receptor recognition guide therapeutic expansion.
Authors: Sun, Y. / Florio, T.J. / Gupta, S. / Young, M.C. / Marshall, Q.F. / Garfinkle, S.E. / Papadaki, G.F. / Truong, H.V. / Mycek, E. / Li, P. / Farrel, A. / Church, N.L. / Jabar, S. / Beasley, M. ...Authors: Sun, Y. / Florio, T.J. / Gupta, S. / Young, M.C. / Marshall, Q.F. / Garfinkle, S.E. / Papadaki, G.F. / Truong, H.V. / Mycek, E. / Li, P. / Farrel, A. / Church, N.L. / Jabar, S. / Beasley, M.D. / Kiefel, B.R. / Yarmarkovich, M. / Mallik, L. / Maris, J.M. / Sgourakis, N.G.
#1: Journal: Sci Immunol / Year: 2023
Title: The chilling origin of germinal centers.
Authors: Boehm, T.
History
DepositionApr 3, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 6, 2023Provider: repository / Type: Initial release
Revision 1.1Dec 13, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 16, 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
B: Beta-2-microglobulin
C: LEU-TYR-LEU-PRO-VAL-ARG-VAL-LEU-ILE
D: MHC class I antigen
E: Beta-2-microglobulin
F: LEU-TYR-LEU-PRO-VAL-ARG-VAL-LEU-ILE
G: MHC class I antigen
H: Beta-2-microglobulin
I: LEU-TYR-LEU-PRO-VAL-ARG-VAL-LEU-ILE
J: MHC class I antigen
K: Beta-2-microglobulin
L: LEU-TYR-LEU-PRO-VAL-ARG-VAL-LEU-ILE


Theoretical massNumber of molelcules
Total (without water)181,73012
Polymers181,73012
Non-polymers00
Water00
1
A: MHC class I antigen
B: Beta-2-microglobulin
C: LEU-TYR-LEU-PRO-VAL-ARG-VAL-LEU-ILE


Theoretical massNumber of molelcules
Total (without water)45,4333
Polymers45,4333
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4550 Å2
ΔGint-25 kcal/mol
Surface area18460 Å2
MethodPISA
2
D: MHC class I antigen
E: Beta-2-microglobulin
F: LEU-TYR-LEU-PRO-VAL-ARG-VAL-LEU-ILE


Theoretical massNumber of molelcules
Total (without water)45,4333
Polymers45,4333
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4380 Å2
ΔGint-27 kcal/mol
Surface area18700 Å2
MethodPISA
3
G: MHC class I antigen
H: Beta-2-microglobulin
I: LEU-TYR-LEU-PRO-VAL-ARG-VAL-LEU-ILE


Theoretical massNumber of molelcules
Total (without water)45,4333
Polymers45,4333
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4330 Å2
ΔGint-24 kcal/mol
Surface area18770 Å2
MethodPISA
4
J: MHC class I antigen
K: Beta-2-microglobulin
L: LEU-TYR-LEU-PRO-VAL-ARG-VAL-LEU-ILE


Theoretical massNumber of molelcules
Total (without water)45,4333
Polymers45,4333
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4420 Å2
ΔGint-25 kcal/mol
Surface area18660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.512, 76.193, 111.779
Angle α, β, γ (deg.)90.00, 109.76, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
MHC class I antigen


Mass: 32466.869 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-A / Production host: Escherichia coli (E. coli) / References: UniProt: A0A411J078
#2: Protein
Beta-2-microglobulin


Mass: 11879.356 Da / Num. of mol.: 4 / Fragment: UNP residues 21-119
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
LEU-TYR-LEU-PRO-VAL-ARG-VAL-LEU-ILE


Mass: 1086.390 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
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: 2.45 Å3/Da / Density % sol: 49.84 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.05M MES monohydrate pH 6.5, 22.5% Polyethylene Glycol w/v 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jan 27, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 3→105.19 Å / Num. obs: 34967 / % possible obs: 99.8 % / Redundancy: 3.5 % / Biso Wilson estimate: 36.83 Å2 / CC1/2: 0.877 / R split: 0.341 / Rmerge(I) obs: 0.388 / Rpim(I) all: 0.244 / Rrim(I) all: 0.459 / Χ2: 0.46 / Net I/σ(I): 2.8
Reflection shellResolution: 3.05→3.21 Å / Redundancy: 3.5 % / Rmerge(I) obs: 1.203 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 4832 / CC1/2: 0.419 / Rpim(I) all: 0.746 / Rrim(I) all: 1.418 / Χ2: 0.47 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→105.19 Å / SU ML: 0.49 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2695 2007 5.74 %
Rwork0.1932 --
obs0.1976 34967 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3→105.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12604 0 0 0 12604
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00912944
X-RAY DIFFRACTIONf_angle_d1.17717548
X-RAY DIFFRACTIONf_dihedral_angle_d7.311732
X-RAY DIFFRACTIONf_chiral_restr0.0611796
X-RAY DIFFRACTIONf_plane_restr0.0152308
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.080.36641460.29632346X-RAY DIFFRACTION100
3.08-3.160.35341450.27272337X-RAY DIFFRACTION100
3.16-3.250.32771390.2492320X-RAY DIFFRACTION100
3.25-3.360.32351410.24872336X-RAY DIFFRACTION100
3.36-3.480.30811420.2382369X-RAY DIFFRACTION100
3.48-3.620.29681450.22642331X-RAY DIFFRACTION100
3.62-3.780.30731440.21382342X-RAY DIFFRACTION100
3.78-3.980.24651420.18372348X-RAY DIFFRACTION100
3.98-4.230.2561440.17152363X-RAY DIFFRACTION100
4.23-4.550.25271410.15052336X-RAY DIFFRACTION100
4.55-5.010.2251390.14242361X-RAY DIFFRACTION100
5.01-5.740.2181480.14832361X-RAY DIFFRACTION100
5.74-7.230.23581430.17312387X-RAY DIFFRACTION100
7.23-105.190.20421480.14982423X-RAY DIFFRACTION99

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