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- PDB-9d96: KIR3DL1 - HLA-B38-YHL complex -

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Basic information

Entry
Database: PDB / ID: 9d96
TitleKIR3DL1 - HLA-B38-YHL complex
Components
  • Beta-2-microglobulin
  • Epstein-Barr nuclear antigen 2
  • Killer cell immunoglobulin-like receptor 3DL1
  • MHC class I antigen
KeywordsIMMUNE SYSTEM / Killer Immunoglobulin-like receptor Human Leucocyte Antigen Epstein Barr virus NK cell Immune complex
Function / homology
Function and homology information


HLA-B specific inhibitory MHC class I receptor activity / host cell nuclear matrix / protein serine/threonine phosphatase inhibitor activity / DNA-templated viral transcription / symbiont-mediated perturbation of host transcription / symbiont-mediated perturbation of host cell cycle progression / immune response-regulating signaling pathway / symbiont-mediated suppression of host translation initiation / natural killer cell mediated cytotoxicity / antigen processing and presentation of peptide antigen via MHC class I ...HLA-B specific inhibitory MHC class I receptor activity / host cell nuclear matrix / protein serine/threonine phosphatase inhibitor activity / DNA-templated viral transcription / symbiont-mediated perturbation of host transcription / symbiont-mediated perturbation of host cell cycle progression / immune response-regulating signaling pathway / symbiont-mediated suppression of host translation initiation / natural killer cell mediated cytotoxicity / 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 / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway / 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 / molecular adaptor activity / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / immune response / symbiont-mediated suppression of host innate immune response / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / endoplasmic reticulum lumen / Amyloid fiber formation / Golgi membrane / lysosomal membrane / external side of plasma membrane / focal adhesion / Neutrophil degranulation / positive regulation of DNA-templated transcription / host cell nucleus / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / cell surface / endoplasmic reticulum / Golgi apparatus / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane / cytosol
Similarity search - Function
: / Immunoglobulin / Immunoglobulin domain / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / 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 ...: / Immunoglobulin / Immunoglobulin domain / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / 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 subtype / Immunoglobulin / 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
MHC class I antigen / Epstein-Barr nuclear antigen 2 / Killer cell immunoglobulin-like receptor 3DL1 / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
human gammaherpesvirus 4 (Epstein-Barr virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsZhu, S. / Vivian, J. / Petersen, J. / Rossjohn, J.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia) Australia
CitationJournal: To Be Published
Title: The ancient MHC class I molecule HLA-B*38:01 calibrates the immune system to protect against multiple sclerosis
Authors: Ladell, K. / Zhu, S. / Kaufmann, M. / Vivian, J. / Petersen, J. / Fugger, L. / Rossjohn, J. / Price, D.
History
DepositionAug 21, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 3, 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: Epstein-Barr nuclear antigen 2
G: Killer cell immunoglobulin-like receptor 3DL1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,9697
Polymers78,3064
Non-polymers6643
Water1,63991
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7490 Å2
ΔGint-16 kcal/mol
Surface area32340 Å2
MethodPISA
2
G: Killer cell immunoglobulin-like receptor 3DL1
hetero molecules

A: MHC class I antigen
B: Beta-2-microglobulin
C: Epstein-Barr nuclear antigen 2


Theoretical massNumber of molelcules
Total (without water)78,9697
Polymers78,3064
Non-polymers6643
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_665x+1,y+1,z1
Buried area7690 Å2
ΔGint-8 kcal/mol
Surface area32140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.346, 60.588, 63.288
Angle α, β, γ (deg.)95.060, 95.610, 106.370
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

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Protein , 3 types, 3 molecules ABG

#1: Protein MHC class I antigen / MHC class II antigen


Mass: 32029.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-B, HLA-DRB1 / Production host: Escherichia coli (E. coli) / References: UniProt: E5FQ58
#2: Protein Beta-2-microglobulin


Mass: 11879.356 Da / Num. of mol.: 1 / Fragment: UNP residues 21-119
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
#4: Protein Killer cell immunoglobulin-like receptor 3DL1 / CD158 antigen-like family member E / HLA-BW4-specific inhibitory NK cell receptor / Natural killer- ...CD158 antigen-like family member E / HLA-BW4-specific inhibitory NK cell receptor / Natural killer-associated transcript 3 / NKAT-3 / p70 natural killer cell receptor clones CL-2/CL-11 / p70 NK receptor CL-2/CL-11


Mass: 33220.594 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KIR3DL1, CD158E, NKAT3, NKB1 / Production host: Homo sapiens (human) / References: UniProt: P43629

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Protein/peptide / Sugars / Non-polymers , 3 types, 95 molecules C

#3: Protein/peptide Epstein-Barr nuclear antigen 2 / EBNA-2 / EBV nuclear antigen 2


Mass: 1176.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) human gammaherpesvirus 4 (Epstein-Barr virus)
Gene: EBNA2, BYRF1 / Production host: synthetic construct (others) / References: UniProt: P12978
#5: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 2.2 Å3/Da / Density % sol: 44.03 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: 15% PEG 3350, 2% Tacsimate, pH 5.0, and 0.1 M trisodium citrate, pH 5.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95364 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 22, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95364 Å / Relative weight: 1
ReflectionResolution: 2.4→41.97 Å / Num. obs: 25635 / % possible obs: 97.75 % / Redundancy: 2 % / CC1/2: 0.978 / CC star: 0.995 / Net I/σ(I): 8.13
Reflection shellResolution: 2.4→2.486 Å / Mean I/σ(I) obs: 1.69 / Num. unique obs: 2545 / CC1/2: 0.597 / CC star: 0.865

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→41.97 Å / SU ML: 0.3374 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 26.0655
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2385 1193 4.68 %
Rwork0.2008 24304 -
obs0.2026 25497 97.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 50.93 Å2
Refinement stepCycle: LAST / Resolution: 2.4→41.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5367 0 42 91 5500
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00235570
X-RAY DIFFRACTIONf_angle_d0.51527582
X-RAY DIFFRACTIONf_chiral_restr0.042802
X-RAY DIFFRACTIONf_plane_restr0.0039990
X-RAY DIFFRACTIONf_dihedral_angle_d15.20682026
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.50.34181250.28612722X-RAY DIFFRACTION97.2
2.5-2.610.2781360.27252650X-RAY DIFFRACTION96.84
2.61-2.750.29081380.25032691X-RAY DIFFRACTION97.42
2.75-2.920.2611370.24042671X-RAY DIFFRACTION97.64
2.92-3.140.27871350.22292740X-RAY DIFFRACTION98.43
3.14-3.460.26231180.20382711X-RAY DIFFRACTION98.33
3.46-3.960.22951350.19152718X-RAY DIFFRACTION97.61
3.96-4.990.20831390.15792674X-RAY DIFFRACTION98.12
4.99-41.970.19641300.18322727X-RAY DIFFRACTION98.42
Refinement TLS params.Method: refined / Origin x: -29.9248318227 Å / Origin y: -56.2224245479 Å / Origin z: -29.9663711644 Å
111213212223313233
T0.218551447014 Å2-0.000702498215292 Å20.0143458991286 Å2-0.241688790448 Å2-0.00627475893115 Å2--0.234703201888 Å2
L0.0906722423482 °2-0.125678783363 °20.0917403212959 °2-0.426064483064 °2-0.247686204401 °2--0.425845120404 °2
S-0.0142170437244 Å °-0.0167906985921 Å °-0.00653787695685 Å °0.0445993268411 Å °0.024705913902 Å °-0.00739860657712 Å °-0.00791251647031 Å °-0.00250313915787 Å °4.15126237541E-7 Å °
Refinement TLS groupSelection details: all

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