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- PDB-5j6h: Recognition of the MHC class Ib molecule H2-Q10 by the natural ki... -

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Basic information

Entry
Database: PDB / ID: 5j6h
TitleRecognition of the MHC class Ib molecule H2-Q10 by the natural killer cell receptor Ly49C
Components
  • Beta-2-microglobulinBeta-2 microglobulin
  • H-2 class I histocompatibility antigen, Q10 alpha chain
  • VAL-GLY-ILE-THR-ASN-VAL-ASP-LEU
KeywordsIMMUNE SYSTEM
Function / homology
Function and homology information


oligosaccharyltransferase complex / : / TAP1 binding / TAP2 binding / protein N-linked glycosylation / MHC class Ib protein complex / natural killer cell lectin-like receptor binding / cis-Golgi network membrane / Endosomal/Vacuolar pathway / DAP12 interactions ...oligosaccharyltransferase complex / : / TAP1 binding / TAP2 binding / protein N-linked glycosylation / MHC class Ib protein complex / natural killer cell lectin-like receptor binding / cis-Golgi network membrane / Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / DAP12 signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / regulation of membrane depolarization / autophagosome membrane / TAP complex binding / Golgi medial cisterna / CD8 receptor binding / rough endoplasmic reticulum / MHC class I protein binding / cellular defense response / endoplasmic reticulum exit site / beta-2-microglobulin binding / TAP binding / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / Neutrophil degranulation / T cell receptor binding / 14-3-3 protein binding / lumenal side of endoplasmic reticulum membrane / peptide binding / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / cellular response to iron(III) ion / negative regulation of forebrain neuron differentiation / peptide antigen assembly with MHC class I protein complex / response to molecule of bacterial origin / regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / cellular response to iron ion / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / MHC class I protein complex / multicellular organismal-level iron ion homeostasis / positive regulation of T cell mediated cytotoxicity / peptide antigen assembly with MHC class II protein complex / negative regulation of neurogenesis / MHC class II protein complex / positive regulation of receptor-mediated endocytosis / cellular response to nicotine / phagocytic vesicle membrane / peptide antigen binding / positive regulation of cellular senescence / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / negative regulation of epithelial cell proliferation / positive regulation of T cell activation / antimicrobial humoral immune response mediated by antimicrobial peptide / sensory perception of smell / ribosome binding / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / T cell differentiation in thymus / antibacterial humoral response / iron ion transport / protein-folding chaperone binding / protein refolding / early endosome membrane / protein homotetramerization / cellular response to lipopolysaccharide / intracellular iron ion homeostasis / defense response to Gram-negative bacterium / amyloid fibril formation / learning or memory / nuclear body / early endosome / defense response to Gram-positive bacterium / immune response / response to xenobiotic stimulus / lysosomal membrane / external side of plasma membrane / Golgi membrane / signaling receptor binding / innate immune response / protein-containing complex binding / endoplasmic reticulum membrane / structural molecule activity / Golgi apparatus / cell surface / endoplasmic reticulum / protein homodimerization activity / extracellular space / identical protein binding / plasma membrane / cytosol
Similarity search - Function
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit Swp1 / Oligosaccharyltransferase subunit Ribophorin II / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / 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 ...Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit Swp1 / Oligosaccharyltransferase subunit Ribophorin II / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / 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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE / Beta-2-microglobulin / H-2 class I histocompatibility antigen, Q10 alpha chain / Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsBerry, R. / Rossjohn, J.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)GNT1109901 Australia
CitationJournal: J.Biol.Chem. / Year: 2016
Title: Recognition of the Major Histocompatibility Complex (MHC) Class Ib Molecule H2-Q10 by the Natural Killer Cell Receptor Ly49C.
Authors: Sullivan, L.C. / Berry, R. / Sosnin, N. / Widjaja, J.M. / Deuss, F.A. / Balaji, G.R. / LaGruta, N.L. / Mirams, M. / Trapani, J.A. / Rossjohn, J. / Brooks, A.G. / Andrews, D.M.
History
DepositionApr 5, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 13, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 20, 2016Group: Database references
Revision 1.2Sep 14, 2016Group: Database references
Revision 1.3Aug 9, 2017Group: Data collection / Database references / Derived calculations
Category: citation / diffrn_source / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: H-2 class I histocompatibility antigen, Q10 alpha chain
B: Beta-2-microglobulin
F: VAL-GLY-ILE-THR-ASN-VAL-ASP-LEU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,8046
Polymers47,6363
Non-polymers1683
Water2,648147
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4500 Å2
ΔGint-42 kcal/mol
Surface area17980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.420, 81.660, 97.920
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein H-2 class I histocompatibility antigen, Q10 alpha chain


Mass: 35014.133 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-Q10 / Production host: Escherichia coli (E. coli) / References: UniProt: P01898
#2: Protein Beta-2-microglobulin / Beta-2 microglobulin


Mass: 11791.545 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: B2m / Production host: Escherichia coli (E. coli) / References: UniProt: P01887

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Protein/peptide , 1 types, 1 molecules F

#3: Protein/peptide VAL-GLY-ILE-THR-ASN-VAL-ASP-LEU


Mass: 829.939 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse) / References: UniProt: Q9DBG6*PLUS

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Non-polymers , 3 types, 150 molecules

#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-NCA / NICOTINAMIDE / Nicotinamide


Mass: 122.125 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H6N2O / Comment: medication*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 147 / Source method: isolated from a natural source / Formula: H2O

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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: 2.33 Å3/Da / Density % sol: 47.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 8% Peg3350, 0.1M sodium malonate ph 5.0, 0.01M b-nicotinamide adenine dinucleotide hydrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9436 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 30, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9436 Å / Relative weight: 1
ReflectionResolution: 2.3→42 Å / Num. obs: 20349 / % possible obs: 99.8 % / Redundancy: 6.7 % / Biso Wilson estimate: 38.8 Å2 / Rmerge(I) obs: 0.241 / Net I/σ(I): 6.6

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Processing

Software
NameVersionClassification
BUSTER2.10.0refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YN6

1yn6


Resolution: 2.3→33.47 Å / Cor.coef. Fo:Fc: 0.9378 / Cor.coef. Fo:Fc free: 0.8906 / SU R Cruickshank DPI: 0.264 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.278 / SU Rfree Blow DPI: 0.223 / SU Rfree Cruickshank DPI: 0.222
RfactorNum. reflection% reflectionSelection details
Rfree0.2434 1039 5.12 %RANDOM
Rwork0.1768 ---
obs0.1802 20310 99.74 %-
Displacement parametersBiso mean: 34.17 Å2
Baniso -1Baniso -2Baniso -3
1-4.8669 Å20 Å20 Å2
2---6.9226 Å20 Å2
3---2.0557 Å2
Refine analyzeLuzzati coordinate error obs: 0.282 Å
Refinement stepCycle: LAST / Resolution: 2.3→33.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3035 0 11 147 3193
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013138HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.084282HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1372SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes71HARMONIC2
X-RAY DIFFRACTIONt_gen_planes459HARMONIC5
X-RAY DIFFRACTIONt_it3138HARMONIC20
X-RAY DIFFRACTIONt_nbd3SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.45
X-RAY DIFFRACTIONt_other_torsion3.04
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion399SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3539SEMIHARMONIC4
LS refinement shellResolution: 2.3→2.42 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.2668 141 4.88 %
Rwork0.204 2746 -
all0.207 2887 -
obs--99.74 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.52020.0248-0.45380.5279-0.11040.95130.02840.0749-0.1553-0.01350.0465-0.0490.0433-0.015-0.0749-0.0897-0.0532-0.0316-0.00440.0267-0.032676.751882.4146104.089
21.86391.6526-1.63943.2504-2.0652.65810.08160.17760.2158-0.00610.06840.14440.0135-0.0348-0.1499-0.1443-0.04040.0010.07930.0486-0.131880.0082100.65698.4779
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|1 - A|276 }A1 - 276
2X-RAY DIFFRACTION2{ B|1 - B|99 }B1 - 99

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