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- PDB-7wt3: Crystal structure of HLA-A*2402 complexed with 4-mer lipopeptide -

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Basic information

Entry
Database: PDB / ID: 7wt3
TitleCrystal structure of HLA-A*2402 complexed with 4-mer lipopeptide
Components
  • 4-mer lipopeptide
  • Beta-2-microglobulin
  • MHC class I antigen
KeywordsIMMUNE SYSTEM / MHC class I / antigen presentation
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-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 / : ...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
ACETATE ION / MHC class I antigen / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88765498464 Å
AuthorsAsa, M. / Morita, D. / Sugita, M.
Funding support Japan, 9items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)18K07172 Japan
Japan Society for the Promotion of Science (JSPS)21K07078 Japan
Japan Society for the Promotion of Science (JSPS)20J23335 Japan
Japan Society for the Promotion of Science (JSPS)19H04805 Japan
Japan Society for the Promotion of Science (JSPS)21H02968 Japan
Japan Society for the Promotion of Science (JSPS)20K21615 Japan
Japan Society for the Promotion of Science (JSPS)19H04805 Japan
Japan Society for the Promotion of Science (JSPS)18K19563 Japan
Japan Society for the Promotion of Science (JSPS)18H02852 Japan
CitationJournal: J.Biol.Chem. / Year: 2022
Title: Crystal structures of N-myristoylated lipopeptide-bound HLA class I complexes indicate reorganization of B-pocket architecture upon ligand binding.
Authors: Asa, M. / Morita, D. / Kuroha, J. / Mizutani, T. / Mori, N. / Mikami, B. / Sugita, M.
History
DepositionFeb 3, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 22, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 6, 2022Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Jul 13, 2022Group: Source and taxonomy / Category: pdbx_entity_src_syn
Item: _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific
Revision 1.3Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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: 4-mer lipopeptide
D: MHC class I antigen
E: Beta-2-microglobulin
F: 4-mer lipopeptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,36450
Polymers88,5726
Non-polymers2,79244
Water7,260403
1
A: MHC class I antigen
B: Beta-2-microglobulin
C: 4-mer lipopeptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,27134
Polymers44,2863
Non-polymers1,98531
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: MHC class I antigen
E: Beta-2-microglobulin
F: 4-mer lipopeptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,09316
Polymers44,2863
Non-polymers80713
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)87.069, 46.41, 142.67
Angle α, β, γ (deg.)90.0, 104.873, 90.0
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Protein , 2 types, 4 molecules ADBE

#1: Protein MHC class I antigen


Mass: 31849.191 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-A / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosseta2 / References: UniProt: A0A411J078
#2: Protein Beta-2-microglobulin / hB2m


Mass: 11819.238 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosseta2 / References: UniProt: P61769

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Protein/peptide , 1 types, 2 molecules CF

#3: Protein/peptide 4-mer lipopeptide


Mass: 617.777 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 5 types, 447 molecules

#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#7: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 37 / Source method: obtained synthetically / Formula: C2H6O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 403 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 3.15 Å3/Da / Density % sol: 60.9 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 2mM ZnCL2, 100mM Tris, 20% PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Dec 7, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.88765498464→50 Å / Num. obs: 89133 / % possible obs: 99.6 % / Redundancy: 3.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.057 / Net I/σ(I): 14.42
Reflection shellResolution: 1.89→2 Å / Rmerge(I) obs: 0.448 / Num. unique obs: 14275 / CC1/2: 0.87

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Processing

Software
NameVersionClassification
PHENIX1.9_1692+SVNrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4F7T

4f7t


Resolution: 1.88765498464→42.0759698716 Å / SU ML: 0.221366445189 / Cross valid method: FREE R-VALUE / σ(F): 1.34760405114 / Phase error: 23.0331605078
RfactorNum. reflection% reflection
Rfree0.235061256255 4456 4.99983169328 %
Rwork0.199287283702 84667 -
obs0.201054993769 89123 99.6823514937 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 37.0662604233 Å2
Refinement stepCycle: LAST / Resolution: 1.88765498464→42.0759698716 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5556 0 171 403 6130
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008131654585745949
X-RAY DIFFRACTIONf_angle_d1.243289712087971
X-RAY DIFFRACTIONf_chiral_restr0.0525987244526794
X-RAY DIFFRACTIONf_plane_restr0.006767021857231041
X-RAY DIFFRACTIONf_dihedral_angle_d14.0277559352221
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8877-1.90910.3297304003771450.3128536278312759X-RAY DIFFRACTION98.0087748903
1.9091-1.93160.2760343001211510.2620372836822868X-RAY DIFFRACTION100
1.9316-1.95510.2996146578511450.2426796077942755X-RAY DIFFRACTION99.9655291279
1.9551-1.97990.3254704213671480.2336330527342806X-RAY DIFFRACTION100
1.9799-2.00590.2510770809881480.2206093948152807X-RAY DIFFRACTION99.9661705007
2.0059-2.03340.2704190130891470.2195466550482800X-RAY DIFFRACTION100
2.0334-2.06240.2354134116451460.2146090937382764X-RAY DIFFRACTION99.8284734134
2.0624-2.09320.2561392656391490.2174336388122844X-RAY DIFFRACTION100
2.0932-2.12590.2575785617761490.2083001088582819X-RAY DIFFRACTION100
2.1259-2.16080.2671528750951450.210616400562772X-RAY DIFFRACTION99.9314833847
2.1608-2.1980.2489862103561510.2052859852752858X-RAY DIFFRACTION99.9335768848
2.198-2.2380.2301006798141470.2004164164142795X-RAY DIFFRACTION99.9660210669
2.238-2.28110.2304009463911470.1976314110952786X-RAY DIFFRACTION100
2.2811-2.32760.2336316421021490.2039331072232833X-RAY DIFFRACTION99.9664767013
2.3276-2.37820.2461901885311470.2026753267812801X-RAY DIFFRACTION100
2.3782-2.43350.2343873098481500.2047521474532846X-RAY DIFFRACTION99.9666333
2.4335-2.49440.2579682086171480.2041823345082817X-RAY DIFFRACTION99.9662845583
2.4944-2.56180.2452667955271490.2065237738842819X-RAY DIFFRACTION99.9326599327
2.5618-2.63720.2390184947911460.1946255951862779X-RAY DIFFRACTION99.761255116
2.6372-2.72230.2591264581611510.2112564582282876X-RAY DIFFRACTION99.7692814766
2.7223-2.81960.2423008963091470.2026273851242788X-RAY DIFFRACTION99.6604414261
2.8196-2.93240.2266063432441480.2057455521632819X-RAY DIFFRACTION99.5637583893
2.9324-3.06590.224164359591490.2026855259542829X-RAY DIFFRACTION99.7320830543
3.0659-3.22750.2345782710821480.2012653208832802X-RAY DIFFRACTION99.0930466913
3.2275-3.42960.2497171630321490.2015138096542839X-RAY DIFFRACTION99.6332110704
3.4296-3.69420.2434389109131490.1867201189942836X-RAY DIFFRACTION99.6661101836
3.6942-4.06570.2009374806251510.1733528653292870X-RAY DIFFRACTION99.6372031662
4.0657-4.65340.2044923002041510.1646220704692853X-RAY DIFFRACTION99.1092048829
4.6534-5.86030.1763031255861510.183702757672873X-RAY DIFFRACTION99.0501146413
5.8603-42.07590.2676250528481550.2209158722842954X-RAY DIFFRACTION98.5732403297

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