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- PDB-9l48: Crystal structure of HLA-C*12:02-RV9 -

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Basic information

Entry
Database: PDB / ID: 9l48
TitleCrystal structure of HLA-C*12:02-RV9
Components
  • Beta-2-microglobulin
  • MHC class I antigen
  • Toll-like receptor 9
KeywordsIMMUNE SYSTEM / protein complex
Function / homology
Function and homology information


cellular response to chloroquine / positive regulation of intestinal epithelial cell development / negative regulation of ATPase-coupled calcium transmembrane transporter activity / detection of molecule of bacterial origin / cellular response to metal ion / regulation of B cell differentiation / Toll Like Receptor 9 (TLR9) Cascade / endolysosome / positive regulation of toll-like receptor 9 signaling pathway / regulation of dendritic cell cytokine production ...cellular response to chloroquine / positive regulation of intestinal epithelial cell development / negative regulation of ATPase-coupled calcium transmembrane transporter activity / detection of molecule of bacterial origin / cellular response to metal ion / regulation of B cell differentiation / Toll Like Receptor 9 (TLR9) Cascade / endolysosome / positive regulation of toll-like receptor 9 signaling pathway / regulation of dendritic cell cytokine production / maintenance of gastrointestinal epithelium / positive regulation of B cell activation / MyD88 dependent cascade initiated on endosome / positive regulation of interleukin-18 production / TRAF6 mediated induction of NFkB and MAP kinases upon TLR7/8 or 9 activation / unmethylated CpG binding / toll-like receptor 9 signaling pathway / siRNA binding / early phagosome / interleukin-1 receptor binding / endolysosome membrane / Trafficking and processing of endosomal TLR / positive regulation of granulocyte macrophage colony-stimulating factor production / MyD88-dependent toll-like receptor signaling pathway / positive regulation of immunoglobulin production / toll-like receptor signaling pathway / pattern recognition receptor activity / positive regulation of interferon-alpha production / positive regulation of interleukin-10 production / PI3K Cascade / antigen processing and presentation of peptide antigen via MHC class I / canonical NF-kappaB signal transduction / positive regulation of chemokine production / positive regulation of B cell proliferation / positive regulation of interleukin-12 production / positive regulation of autophagy / positive regulation of interferon-beta production / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / 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 / positive regulation of interleukin-8 production / Endosomal/Vacuolar pathway / positive regulation of JNK cascade / 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 / microglial cell activation / 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 / negative regulation of ERK1 and ERK2 cascade / positive regulation of receptor-mediated endocytosis / negative regulation of neurogenesis / positive regulation of interleukin-6 production / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / multicellular organismal-level iron ion homeostasis / male gonad development / 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 / positive regulation of inflammatory response / positive regulation of tumor necrosis factor production / 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 / cellular response to lipopolysaccharide / ER-Phagosome pathway / protein refolding / early endosome membrane
Similarity search - Function
Leucine-rich repeat unit / Leucine-rich repeat / TIR domain / Leucine Rich repeat / Toll - interleukin 1 - resistance / Leucine-rich repeats, bacterial type / TIR domain profile. / Toll/interleukin-1 receptor homology (TIR) domain / Toll/interleukin-1 receptor homology (TIR) domain superfamily / Leucine-rich repeat, SDS22-like subfamily ...Leucine-rich repeat unit / Leucine-rich repeat / TIR domain / Leucine Rich repeat / Toll - interleukin 1 - resistance / Leucine-rich repeats, bacterial type / TIR domain profile. / Toll/interleukin-1 receptor homology (TIR) domain / Toll/interleukin-1 receptor homology (TIR) domain superfamily / Leucine-rich repeat, SDS22-like subfamily / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat profile. / MHC class I alpha chain, alpha1 alpha2 domains / Leucine-rich repeat / 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 / Leucine-rich repeat domain 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 / Toll-like receptor 9 / 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

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Assembly

Deposited unit
A: MHC class I antigen
B: Beta-2-microglobulin
C: Toll-like receptor 9


Theoretical massNumber of molelcules
Total (without water)44,5023
Polymers44,5023
Non-polymers00
Water8,251458
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4300 Å2
ΔGint-17 kcal/mol
Surface area18790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.170, 71.860, 124.850
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.: 1
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: 11747.110 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 (E. coli) / References: UniProt: P61769
#3: Protein/peptide Toll-like receptor 9


Mass: 1080.283 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TLR9, UNQ5798/PRO19605 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NR96
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 458 / 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: 2.63 Å3/Da / Density % sol: 53.3 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop
Details: 0.2 M sodium citrate tribasic dihydrate, 20% w/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97849 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: 0.97849 Å / Relative weight: 1
ReflectionResolution: 1.9→48.14 Å / Num. obs: 37484 / % possible obs: 99.2 % / Redundancy: 11 % / CC1/2: 0.999 / Rmerge(I) obs: 0.106 / Rpim(I) all: 0.046 / Rrim(I) all: 0.116 / Net I/σ(I): 14.8
Reflection shellResolution: 1.9→1.94 Å / Redundancy: 10.7 % / Rmerge(I) obs: 0.477 / Num. unique obs: 2355 / CC1/2: 0.925 / Rpim(I) all: 0.209 / Rrim(I) all: 0.522 / % possible all: 98.3

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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→48.14 Å / SU ML: 0.2005 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.204
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2043 2000 5.35 %
Rwork0.1746 35417 -
obs0.1762 37417 99.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.33 Å2
Refinement stepCycle: LAST / Resolution: 1.9→48.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3141 0 0 458 3599
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00623263
X-RAY DIFFRACTIONf_angle_d0.8154433
X-RAY DIFFRACTIONf_chiral_restr0.0543442
X-RAY DIFFRACTIONf_plane_restr0.0079591
X-RAY DIFFRACTIONf_dihedral_angle_d5.6686445
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.950.27731390.21742472X-RAY DIFFRACTION98.27
1.95-20.25141400.19322462X-RAY DIFFRACTION97.93
2-2.060.25571380.18112459X-RAY DIFFRACTION97.96
2.06-2.130.22731400.18312485X-RAY DIFFRACTION98.65
2.13-2.20.231410.18542485X-RAY DIFFRACTION99.21
2.2-2.290.2391420.18392512X-RAY DIFFRACTION98.88
2.29-2.390.25611430.192535X-RAY DIFFRACTION99.15
2.39-2.520.24291410.18762496X-RAY DIFFRACTION99.7
2.52-2.680.23541430.18272536X-RAY DIFFRACTION99.74
2.68-2.880.20821450.1892573X-RAY DIFFRACTION99.89
2.88-3.170.21131430.18192532X-RAY DIFFRACTION99.33
3.17-3.630.15651440.1642548X-RAY DIFFRACTION99.08
3.63-4.580.15781470.14012608X-RAY DIFFRACTION99.89
4.58-48.140.16391540.16682714X-RAY DIFFRACTION98.66
Refinement TLS params.Method: refined / Origin x: -6.34702066101 Å / Origin y: 6.01208838523 Å / Origin z: -20.9052150983 Å
111213212223313233
T0.0565660696207 Å2-0.022979094735 Å2-0.00316703074933 Å2-0.0428113217272 Å2-0.0174479215195 Å2--0.0646172769374 Å2
L0.506319311929 °2-0.268021781011 °2-0.189774418385 °2-0.255592281826 °20.0902374704505 °2--0.389818915224 °2
S0.0059704710665 Å °0.0570826751904 Å °-0.0650460292386 Å °0.0218069063278 Å °-0.0144080411555 Å °0.0065536895508 Å °-0.000785228361524 Å °-0.0463555104557 Å °0.0198727545647 Å °
Refinement TLS groupSelection details: all

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