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- PDB-9l4a: Crystal structure of HLA-C*12:02-MY9 -

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Basic information

Entry
Database: PDB / ID: 9l4a
TitleCrystal structure of HLA-C*12:02-MY9
Components
  • Beta-2-microglobulin
  • MHC class I antigen
  • MY9
KeywordsIMMUNE SYSTEM / HLA-C*12:02 / 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 / 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 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: 1.9 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

Downloads & links

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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)88,9966
Polymers88,9966
Non-polymers00
Water18,1771009
1
A: MHC class I antigen
B: Beta-2-microglobulin
C: MY9


Theoretical massNumber of molelcules
Total (without water)44,4983
Polymers44,4983
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4380 Å2
ΔGint-17 kcal/mol
Surface area18950 Å2
MethodPISA
2
D: MHC class I antigen
E: Beta-2-microglobulin
F: MY9


Theoretical massNumber of molelcules
Total (without water)44,4983
Polymers44,4983
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4460 Å2
ΔGint-17 kcal/mol
Surface area18890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.520, 96.400, 121.100
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein MHC class I antigen


Mass: 31674.764 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: S5DHS4
#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)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1009 / 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: 2.61 Å3/Da / Density % sol: 52.83 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop
Details: 0.2M Sodium formate 0.1M Bis-Tris propane pH8.5 20% w/v PEG3,350

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17UM / 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: 1.9→48.2 Å / Num. obs: 73658 / % possible obs: 99.6 % / Redundancy: 11.2 % / Biso Wilson estimate: 17.31 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.097 / Rpim(I) all: 0.031 / Rrim(I) all: 0.106 / Χ2: 0.99 / Net I/σ(I): 17
Reflection shellResolution: 1.9→1.94 Å / Redundancy: 10.9 % / Rmerge(I) obs: 0.502 / Num. unique obs: 4455 / CC1/2: 0.915 / Rpim(I) all: 0.232 / Rrim(I) all: 0.554 / % possible all: 98.7

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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: 1.9→41.22 Å / SU ML: 0.197 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.8156
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2073 2000 2.72 %
Rwork0.1643 71572 -
obs0.1655 73572 99.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.13 Å2
Refinement stepCycle: LAST / Resolution: 1.9→41.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6264 0 0 1009 7273
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01956459
X-RAY DIFFRACTIONf_angle_d1.48728771
X-RAY DIFFRACTIONf_chiral_restr0.1042877
X-RAY DIFFRACTIONf_plane_restr0.01571165
X-RAY DIFFRACTIONf_dihedral_angle_d14.83382391
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.950.28691400.20385020X-RAY DIFFRACTION98.68
1.95-20.25671400.17545008X-RAY DIFFRACTION98.73
2-2.060.2211390.16845001X-RAY DIFFRACTION98.92
2.06-2.130.20321410.1725041X-RAY DIFFRACTION99.04
2.13-2.20.25161420.16855059X-RAY DIFFRACTION99.1
2.2-2.290.21641420.1665074X-RAY DIFFRACTION99.77
2.29-2.390.25611420.16945086X-RAY DIFFRACTION99.94
2.39-2.520.21361430.17055113X-RAY DIFFRACTION99.94
2.52-2.680.23431430.17275133X-RAY DIFFRACTION99.74
2.68-2.880.17731430.17225079X-RAY DIFFRACTION99.62
2.88-3.170.21961440.16645169X-RAY DIFFRACTION99.98
3.17-3.630.18381440.15765176X-RAY DIFFRACTION99.98
3.63-4.580.17081450.13975201X-RAY DIFFRACTION99.53
4.58-41.220.19181520.16495412X-RAY DIFFRACTION99.55

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