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- PDB-9l49: Crystal structure of HLA-C*12:03-RV9 -

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Basic information

Entry
Database: PDB / ID: 9l49
TitleCrystal structure of HLA-C*12:03-RV9
Components
  • Beta-2-microglobulin
  • MHC class I antigen
  • Toll-like receptor 9
KeywordsIMMUNE SYSTEM / HLA-C*12:03 / 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 / TRAF6 mediated induction of NFkB and MAP kinases upon TLR7/8 or 9 activation / positive regulation of interleukin-18 production / unmethylated CpG binding / toll-like receptor 9 signaling pathway / siRNA binding / early phagosome / endolysosome membrane / interleukin-1 receptor binding / 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 / antigen processing and presentation of peptide antigen via MHC class I / positive regulation of interferon-alpha production / positive regulation of interleukin-10 production / PI3K Cascade / canonical NF-kappaB signal transduction / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / 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 / 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 / lumenal side of endoplasmic reticulum membrane / positive regulation of interleukin-8 production / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / positive regulation of JNK cascade / peptide antigen assembly with MHC class II protein complex / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / cellular response to iron(III) ion / microglial cell activation / MHC class II protein complex / negative regulation of forebrain neuron differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of erythrocyte differentiation / regulation of iron ion transport / response to molecule of bacterial origin / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / MHC class I protein complex / negative regulation of ERK1 and ERK2 cascade / positive regulation of T cell activation / peptide antigen binding / positive regulation of receptor-mediated endocytosis / negative regulation of neurogenesis / positive regulation of T cell mediated cytotoxicity / positive regulation of interleukin-6 production / cellular response to nicotine / multicellular organismal-level iron ion homeostasis / Modulation by Mtb of host immune system / specific granule lumen / male gonad development / positive regulation of type II interferon production / phagocytic vesicle membrane / recycling endosome membrane / positive regulation of inflammatory response / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / negative regulation of epithelial cell proliferation / positive regulation of tumor necrosis factor production / MHC class II protein complex binding / late endosome membrane / sensory perception of smell / positive regulation of cellular senescence / tertiary granule lumen / DAP12 signaling / T cell differentiation in thymus / ER-Phagosome pathway / negative regulation of neuron projection development / cellular response to lipopolysaccharide / 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. / Leucine-rich repeat, SDS22-like subfamily / Toll/interleukin-1 receptor homology (TIR) domain / Toll/interleukin-1 receptor homology (TIR) domain superfamily ...Leucine-rich repeat unit / Leucine-rich repeat / TIR domain / Leucine Rich repeat / Toll - interleukin 1 - resistance / Leucine-rich repeats, bacterial type / TIR domain profile. / Leucine-rich repeat, SDS22-like subfamily / Toll/interleukin-1 receptor homology (TIR) domain / Toll/interleukin-1 receptor homology (TIR) domain superfamily / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat profile. / Leucine-rich repeat / 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 / 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 / MHC class I antigen / Toll-like receptor 9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 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)44,4603
Polymers44,4603
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4470 Å2
ΔGint-16 kcal/mol
Surface area18710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.309, 95.270, 119.190
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Space group name HallI22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1/2
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein MHC class I antigen


Mass: 31703.779 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: Q2UV93
#2: Protein Beta-2-microglobulin


Mass: 11676.032 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
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: 2.74 Å3/Da / Density % sol: 55.19 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop
Details: 1.5 M Ammonium sulfate 0.1 M Sodium HEPES pH7.5 2% v/v PEG400

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL18U / 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: 3→47.63 Å / Num. obs: 10021 / % possible obs: 99.8 % / Redundancy: 11.6 % / CC1/2: 0.993 / Rmerge(I) obs: 0.182 / Rpim(I) all: 0.078 / Rrim(I) all: 0.198 / Net I/σ(I): 12.9
Reflection shellResolution: 3→3.18 Å / Redundancy: 12.5 % / Rmerge(I) obs: 0.466 / Num. unique obs: 1593 / CC1/2: 0.963 / Rpim(I) all: 0.195 / Rrim(I) all: 0.506 / % possible all: 100

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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: 3→42.65 Å / SU ML: 0.3088 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.4545
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2349 1001 9.99 %
Rwork0.2035 9015 -
obs0.2067 10016 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.36 Å2
Refinement stepCycle: LAST / Resolution: 3→42.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3115 0 0 0 3115
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023204
X-RAY DIFFRACTIONf_angle_d0.52884351
X-RAY DIFFRACTIONf_chiral_restr0.0386437
X-RAY DIFFRACTIONf_plane_restr0.0064573
X-RAY DIFFRACTIONf_dihedral_angle_d4.5364429
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.160.24621400.23781265X-RAY DIFFRACTION100
3.16-3.360.25321410.23661268X-RAY DIFFRACTION99.93
3.36-3.610.24241410.21521270X-RAY DIFFRACTION99.93
3.62-3.980.27321420.19471277X-RAY DIFFRACTION99.51
3.98-4.550.19531420.18411282X-RAY DIFFRACTION99.72
4.55-5.730.22211460.17611299X-RAY DIFFRACTION100
5.74-42.650.22921490.21211354X-RAY DIFFRACTION98.88
Refinement TLS params.Method: refined / Origin x: -23.4314560631 Å / Origin y: -17.0880756079 Å / Origin z: -32.8952905787 Å
111213212223313233
T0.0812980611305 Å20.0446565592858 Å20.012837617123 Å2-0.096402169812 Å2-0.00798512387984 Å2--0.112601108374 Å2
L0.247318625951 °20.0847104952023 °2-0.144305183774 °2-0.320460756369 °2-0.0700235778843 °2--0.466726950865 °2
S0.0297358066985 Å °0.0169598177496 Å °0.0158773826988 Å °0.00774408285532 Å °-0.00770599766057 Å °0.0254569487628 Å °-0.105473151834 Å °-0.00561018450014 Å °0.00942779509372 Å °
Refinement TLS groupSelection details: all

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