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- PDB-7wj3: Crystal structure of HLA-C*1402 complexed with 4-mer lipopeptide -

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Basic information

Entry
Database: PDB / ID: 7wj3
TitleCrystal structure of HLA-C*1402 complexed with 4-mer lipopeptide
Components
  • 4-mer lipopeptide
  • Beta-2-microglobulin
  • MHC class I protein
KeywordsIMMUNE SYSTEM / MHC class I / antigen presentation
Function / homology
Function and homology information


antigen processing and presentation of peptide antigen via MHC class I / 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 ...antigen processing and presentation of peptide antigen via MHC class I / 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 / 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
MYRISTIC ACID / MHC class I protein / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5634361884 Å
AuthorsKuroha, J. / Morita, D. / Asa, M. / Sugita, M.
Funding support Japan, 4items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)18K07172 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
DepositionJan 5, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 22, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2022Group: Database references / Source and taxonomy / Category: citation / pdbx_entity_src_syn
Item: _citation.journal_volume / _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MHC class I protein
B: Beta-2-microglobulin
C: 4-mer lipopeptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,50722
Polymers44,1623
Non-polymers1,34619
Water4,089227
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3760 Å2
ΔGint-10 kcal/mol
Surface area19610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.050, 77.508, 60.637
Angle α, β, γ (deg.)90.000, 120.934, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein MHC class I protein


Mass: 32012.070 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-C / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosseta2 / References: UniProt: A0A890UPS4
#2: Protein Beta-2-microglobulin / hB2m


Mass: 11819.238 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 BL21(DE3) (bacteria) / Variant (production host): Rosseta2 / References: UniProt: P61769

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Protein/peptide , 1 types, 1 molecules C

#3: Protein/peptide 4-mer lipopeptide


Mass: 330.380 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 3 types, 246 molecules

#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-MYR / MYRISTIC ACID


Mass: 228.371 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H28O2 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 227 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 2.08 Å3/Da / Density % sol: 40.81 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.7
Details: 200 mM ammonium acetate, 100 mM sodium acetate, 5 % ethylene glycol, 25 % PEG Smear Low

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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: RAYONIX MX-225 / Detector: CCD / Date: Oct 20, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.56→50 Å / Num. obs: 50958 / % possible obs: 99.2 % / Redundancy: 7.4 % / Biso Wilson estimate: 16.918141935 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.044 / Net I/σ(I): 49.5
Reflection shellResolution: 1.56→1.59 Å / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 4.8 / Num. unique obs: 2167 / CC1/2: 0.933

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-2000data reduction
HKL-2000data scaling
HKL-2000data collection
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5W6A

5w6a


Resolution: 1.5634361884→38.754 Å / SU ML: 0.132671293175 / Cross valid method: FREE R-VALUE / σ(F): 1.35016818549 / Phase error: 18.9703082307
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.187470436472 2584 5.07104168302 %
Rwork0.170024397513 48372 -
obs0.170925152586 50956 99.8080463823 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.0129903354 Å2
Refinement stepCycle: LAST / Resolution: 1.5634361884→38.754 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3123 0 72 227 3422
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008604489956413370
X-RAY DIFFRACTIONf_angle_d0.9172439504914549
X-RAY DIFFRACTIONf_chiral_restr0.0646523262507450
X-RAY DIFFRACTIONf_plane_restr0.00626580340987603
X-RAY DIFFRACTIONf_dihedral_angle_d28.56101371251267
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5635-1.59350.2141803729711390.1825181971142586X-RAY DIFFRACTION97.0096119616
1.5935-1.6260.2038204378711460.1860796814172680X-RAY DIFFRACTION99.9292786421
1.626-1.66140.2466282337521400.1809061817352714X-RAY DIFFRACTION99.9649737303
1.6614-1.70.2087336246261480.1753877467222662X-RAY DIFFRACTION100
1.7-1.74260.2131725632581460.1728130555022651X-RAY DIFFRACTION100
1.7426-1.78970.2005073663191300.1746005679672716X-RAY DIFFRACTION100
1.7897-1.84230.2026536430321370.1774224741152688X-RAY DIFFRACTION100
1.8423-1.90180.2084280905931450.1666459503032673X-RAY DIFFRACTION100
1.9018-1.96980.2302429200121300.1649486720972713X-RAY DIFFRACTION100
1.9698-2.04860.1798151656671580.1609269864722655X-RAY DIFFRACTION100
2.0486-2.14190.1999090612691490.1638581865772708X-RAY DIFFRACTION100
2.1419-2.25480.2017087111941200.1691976600432687X-RAY DIFFRACTION100
2.2548-2.3960.1973516497671600.1792557556692708X-RAY DIFFRACTION100
2.396-2.5810.1808271251831220.176646347422702X-RAY DIFFRACTION100
2.581-2.84060.2024944374741400.1818920489232707X-RAY DIFFRACTION100
2.8406-3.25150.1904195012031560.1736555933082679X-RAY DIFFRACTION100
3.2515-4.09580.1737464045171510.1647122474812705X-RAY DIFFRACTION100
4.0958-38.7540.1605554001571670.1605554001572738X-RAY DIFFRACTION99.6227709191

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