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- PDB-9l47: Crystal structure of HLA-C*12:03-MY9 -

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Basic information

Entry
Database: PDB / ID: 9l47
TitleCrystal structure of HLA-C*12:03-MY9
Components
  • Beta-2-microglobulin
  • MHC class I antigen
  • MY9
KeywordsIMMUNE SYSTEM / HLA-C*12:03 / Complex
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 / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / peptide antigen assembly with MHC class II protein complex ...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 / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / peptide antigen assembly with MHC class II protein complex / lumenal side of endoplasmic reticulum membrane / 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 / peptide antigen binding / positive regulation of T cell activation / 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
Beta-2-microglobulin / MHC class I antigen
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsYang, M. / Zhong, P.L. / Wei, P.C.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32000611 China
CitationJournal: Int.J.Biol.Macromol. / Year: 2025
Title: Biochemical and structural insights into position 97 micropolymorphisms in human leukocyte antigen (HLA)-C*12 allotypes and their differential disease associations.
Authors: Yang, M. / Zhong, P. / Liu, Q. / Jiao, H. / Lei, J. / Wei, P.
History
DepositionDec 20, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Mar 19, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MHC class I antigen
B: Beta-2-microglobulin
C: MY9
D: MHC class I antigen
E: Beta-2-microglobulin
F: MY9


Theoretical massNumber of molelcules
Total (without water)89,0546
Polymers89,0546
Non-polymers00
Water00
1
A: MHC class I antigen
B: Beta-2-microglobulin
C: MY9


Theoretical massNumber of molelcules
Total (without water)44,5273
Polymers44,5273
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4160 Å2
ΔGint-18 kcal/mol
Surface area18760 Å2
MethodPISA
2
D: MHC class I antigen
E: Beta-2-microglobulin
F: MY9


Theoretical massNumber of molelcules
Total (without water)44,5273
Polymers44,5273
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3900 Å2
ΔGint-17 kcal/mol
Surface area19160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.490, 136.770, 68.920
Angle α, β, γ (deg.)90.000, 107.770, 90.000
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

#1: Protein MHC class I antigen


Mass: 31703.779 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-C / Production host: Escherichia coli (E. coli) / References: UniProt: Q2UV93
#2: Protein Beta-2-microglobulin


Mass: 11676.032 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 (E. coli) / References: UniProt: P61769
#3: Protein/peptide MY9


Mass: 1147.303 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
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: 2.36 Å3/Da / Density % sol: 47.96 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Lithium sulfate 0.1M Tris pH8.5 30% w/v PEG4,000

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9785 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 1, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.8→47.34 Å / Num. obs: 18891 / % possible obs: 93.4 % / Redundancy: 5.9 % / CC1/2: 0.989 / Rmerge(I) obs: 0.0694 / Rpim(I) all: 0.0694 / Rrim(I) all: 0.09815 / Net I/σ(I): 9.88
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.2727 / Num. unique obs: 1857 / CC1/2: 0.797 / Rpim(I) all: 0.2727 / Rrim(I) all: 0.3857 / % possible all: 92.2

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→44.27 Å / SU ML: 0.3646 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.5825
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2646 1894 10.04 %
Rwork0.207 16979 -
obs0.2128 18873 93.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.36 Å2
Refinement stepCycle: LAST / Resolution: 2.8→44.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6112 0 0 0 6112
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026285
X-RAY DIFFRACTIONf_angle_d0.44368535
X-RAY DIFFRACTIONf_chiral_restr0.0377858
X-RAY DIFFRACTIONf_plane_restr0.00451123
X-RAY DIFFRACTIONf_dihedral_angle_d4.105838
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.870.32941320.27541194X-RAY DIFFRACTION91.2
2.87-2.950.39771430.25911204X-RAY DIFFRACTION93.28
2.95-3.030.33341270.25941199X-RAY DIFFRACTION94.44
3.03-3.130.29531350.24521265X-RAY DIFFRACTION95.5
3.13-3.240.31591400.22471205X-RAY DIFFRACTION94.85
3.24-3.370.27741390.22681243X-RAY DIFFRACTION95.11
3.37-3.530.27011270.21841208X-RAY DIFFRACTION93.62
3.53-3.710.28581300.19641181X-RAY DIFFRACTION91.23
3.71-3.950.2541430.20131239X-RAY DIFFRACTION94.72
3.95-4.250.23931390.18541230X-RAY DIFFRACTION94.35
4.25-4.680.20791370.16681222X-RAY DIFFRACTION94.18
4.68-5.350.21941330.17171175X-RAY DIFFRACTION91.4
5.35-6.740.23541320.20181198X-RAY DIFFRACTION91.16
6.74-44.270.22271370.191216X-RAY DIFFRACTION91.98
Refinement TLS params.Method: refined / Origin x: -9.89634796917 Å / Origin y: -16.3342467941 Å / Origin z: -18.8619203877 Å
111213212223313233
T0.0725138326652 Å2-0.0387859392553 Å2-0.0093196176327 Å2-0.06893310556 Å2-0.018583865012 Å2--0.0884765719623 Å2
L0.0232999878821 °2-0.162565532093 °20.0848343824751 °2-0.0228607576107 °2-0.225758655794 °2--0.251443272129 °2
S-0.0340813881072 Å °-0.0326268016538 Å °0.0342543413829 Å °-0.0414415978827 Å °0.0178682283346 Å °-0.0295648318836 Å °0.0593301118818 Å °-0.00214953050894 Å °-0.000682388433501 Å °
Refinement TLS groupSelection details: all

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