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- PDB-5hhq: Crystal Structure of HLA-A*0201 in complex with M1-L3W -

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Basic information

Entry
Database: PDB / ID: 5hhq
TitleCrystal Structure of HLA-A*0201 in complex with M1-L3W
Components
  • Beta-2-microglobulin
  • HLA class I histocompatibility antigen, A-2 alpha chain
  • M1-L3W, GIWGFVFTL
KeywordsIMMUNE SYSTEM / HLA A*0201 / influenza / M1 / TCR / T cell
Function / homology
Function and homology information


positive regulation of memory T cell activation / T cell mediated cytotoxicity directed against tumor cell target / TAP complex binding / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / positive regulation of CD8-positive, alpha-beta T cell proliferation / CD8 receptor binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / beta-2-microglobulin binding ...positive regulation of memory T cell activation / T cell mediated cytotoxicity directed against tumor cell target / TAP complex binding / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / positive regulation of CD8-positive, alpha-beta T cell proliferation / CD8 receptor binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / beta-2-microglobulin binding / endoplasmic reticulum exit site / TAP binding / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / protection from natural killer cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / detection of bacterium / T cell receptor binding / 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 / lumenal side of endoplasmic reticulum membrane / 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 / positive regulation of type II interferon production / 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 / Interferon alpha/beta signaling / Modulation by Mtb of host immune system / late endosome membrane / sensory perception of smell / positive regulation of cellular senescence / antibacterial humoral response / tertiary granule lumen / DAP12 signaling / T cell differentiation in thymus / T cell receptor signaling pathway / E3 ubiquitin ligases ubiquitinate target proteins / 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 / defense response to Gram-positive bacterium / immune response / endoplasmic reticulum lumen / Amyloid fiber formation / signaling receptor binding / Golgi membrane / lysosomal membrane / innate immune response / external side of plasma membrane / focal adhesion / Neutrophil degranulation / endoplasmic reticulum membrane / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / cell surface / endoplasmic reticulum / Golgi apparatus / protein homodimerization activity / extracellular space / RNA binding / extracellular exosome
Similarity search - Function
MHC class I, alpha chain, C-terminal / MHC_I C-terminus / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / 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 class I, alpha chain, C-terminal / MHC_I C-terminus / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / 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 / Immunoglobulins / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
HLA class I histocompatibility antigen, A alpha chain / HLA class I histocompatibility antigen, A alpha chain / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsGras, S. / Josephs, T.M. / Rossjohn, J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: Molecular basis for universal HLA-A*0201-restricted CD8+ T-cell immunity against influenza viruses.
Authors: Valkenburg, S.A. / Josephs, T.M. / Clemens, E.B. / Grant, E.J. / Nguyen, T.H. / Wang, G.C. / Price, D.A. / Miller, A. / Tong, S.Y. / Thomas, P.G. / Doherty, P.C. / Rossjohn, J. / Gras, S. / Kedzierska, K.
History
DepositionJan 11, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 23, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 30, 2016Group: Database references
Revision 1.2Apr 13, 2016Group: Database references
Revision 1.3May 4, 2016Group: Database references
Revision 1.4Sep 27, 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 / citation / database_2 / diffrn_source / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.5Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HLA class I histocompatibility antigen, A-2 alpha chain
B: Beta-2-microglobulin
C: M1-L3W, GIWGFVFTL


Theoretical massNumber of molelcules
Total (without water)44,6723
Polymers44,6723
Non-polymers00
Water3,135174
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4070 Å2
ΔGint-22 kcal/mol
Surface area18970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.651, 80.153, 57.608
Angle α, β, γ (deg.)90.000, 114.420, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein HLA class I histocompatibility antigen, A-2 alpha chain / MHC class I antigen A*2


Mass: 31753.139 Da / Num. of mol.: 1 / Fragment: UNP residues 25-298
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-A, HLAA / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P01892, UniProt: P04439*PLUS
#2: Protein Beta-2-microglobulin


Mass: 11879.356 Da / Num. of mol.: 1 / Fragment: UNP residues 21-119
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P61769
#3: Protein/peptide M1-L3W, GIWGFVFTL


Mass: 1039.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: GL biochem / Source: (synth.) synthetic construct (others)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 174 / 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: 2.53 Å3/Da / Density % sol: 51.43 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 18-22% PEG 3350, Na citrate pH 6.5, 0.1M MgCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 7, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.1→48.85 Å / Num. all: 26019 / Num. obs: 26019 / % possible obs: 100 % / Redundancy: 7.6 % / Biso Wilson estimate: 24.82 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.217 / Rpim(I) all: 0.084 / Rrim(I) all: 0.233 / Rsym value: 0.217 / Net I/σ(I): 11.7 / Num. measured all: 196977
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRsym value% possible all
2.1-2.217.61.3643.62859937760.6680.0230.059100
6.64-48.857.40.05927.363608540.9970.0250.06599.8

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Processing

Software
NameVersionClassification
SCALA3.3.21data scaling
PHENIX1.9_1692refinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3GSO

3gso


Resolution: 2.1→40.077 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2271 1322 5.09 %
Rwork0.17 24664 -
obs0.1729 25986 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 86.3 Å2 / Biso mean: 30.1618 Å2 / Biso min: 7.06 Å2
Refinement stepCycle: final / Resolution: 2.1→40.077 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3143 0 0 174 3317
Biso mean---35.34 -
Num. residues----382
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083333
X-RAY DIFFRACTIONf_angle_d1.0464544
X-RAY DIFFRACTIONf_chiral_restr0.043466
X-RAY DIFFRACTIONf_plane_restr0.005595
X-RAY DIFFRACTIONf_dihedral_angle_d12.3831235
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.1-2.18410.27331720.211926822854
2.1841-2.28350.29561160.217627712887
2.2835-2.40390.30841710.208327122883
2.4039-2.55450.25311520.199226962848
2.5545-2.75170.27841320.201427772909
2.7517-3.02850.25621440.192327212865
3.0285-3.46650.21221400.175927442884
3.4665-4.36660.19331430.135227682911
4.3666-40.08380.17411520.136327932945

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