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- PDB-6bmk: Crystal structure of MHC-I like protein -

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Basic information

Entry
Database: PDB / ID: 6bmk
TitleCrystal structure of MHC-I like protein
Components
  • Antigen-presenting glycoprotein CD1d2
  • Beta-2-microglobulin
KeywordsIMMUNE SYSTEM / Major Histocompatibility complex / MHC-I / CD1d / antigen
Function / homology
Function and homology information


positive regulation of NK T cell activation / endogenous lipid antigen binding / exogenous lipid antigen binding / antigen processing and presentation, endogenous lipid antigen via MHC class Ib / antigen processing and presentation, exogenous lipid antigen via MHC class Ib / lipopeptide binding / Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway ...positive regulation of NK T cell activation / endogenous lipid antigen binding / exogenous lipid antigen binding / antigen processing and presentation, endogenous lipid antigen via MHC class Ib / antigen processing and presentation, exogenous lipid antigen via MHC class Ib / lipopeptide binding / 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 / positive regulation of interleukin-4 production / cellular defense response / positive regulation of interleukin-2 production / Neutrophil degranulation / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / negative regulation of forebrain neuron differentiation / regulation of erythrocyte differentiation / peptide antigen assembly with MHC class I protein complex / 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 / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / MHC class I protein complex / negative regulation of neurogenesis / positive regulation of receptor-mediated endocytosis / peptide antigen assembly with MHC class II protein complex / multicellular organismal-level iron ion homeostasis / MHC class II protein complex / cellular response to nicotine / positive regulation of cellular senescence / positive regulation of T cell mediated cytotoxicity / phagocytic vesicle membrane / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / negative regulation of epithelial cell proliferation / positive regulation of immune response / positive regulation of T cell activation / sensory perception of smell / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / iron ion transport / T cell differentiation in thymus / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / endosome membrane / immune response / lysosomal membrane / external side of plasma membrane / innate immune response / structural molecule activity / Golgi apparatus / protein homodimerization activity / extracellular space / cytosol
Similarity search - Function
MHC-I family domain / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / 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 ...MHC-I family domain / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / 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
Chem-F57 / Beta-2-microglobulin / Antigen-presenting glycoprotein CD1d2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.43 Å
AuthorsKhandokar, Y.B. / Le Nours, J. / Rossjohn, J.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Differing roles of CD1d2 and CD1d1 proteins in type I natural killer T cell development and function.
Authors: Sundararaj, S. / Zhang, J. / Krovi, S.H. / Bedel, R. / Tuttle, K.D. / Veerapen, N. / Besra, G.S. / Khandokar, Y. / Praveena, T. / Le Nours, J. / Matsuda, J.L. / Rossjohn, J. / Gapin, L.
History
DepositionNov 15, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 31, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 21, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.0Mar 7, 2018Group: Advisory / Atomic model ...Advisory / Atomic model / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / entity ...atom_site / entity / pdbx_entity_nonpoly / pdbx_unobs_or_zero_occ_atoms / struct_site
Item: _atom_site.auth_comp_id / _atom_site.label_comp_id ..._atom_site.auth_comp_id / _atom_site.label_comp_id / _chem_comp.formula / _chem_comp.id / _chem_comp.name / _chem_comp.pdbx_synonyms / _entity.formula_weight / _entity.pdbx_description / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _struct_site.details / _struct_site.pdbx_auth_comp_id
Revision 3.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 3.1Oct 4, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _chem_comp.pdbx_synonyms / _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: Antigen-presenting glycoprotein CD1d2
B: Beta-2-microglobulin
C: Antigen-presenting glycoprotein CD1d2
D: Beta-2-microglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,76610
Polymers86,2904
Non-polymers2,4776
Water1,15364
1
A: Antigen-presenting glycoprotein CD1d2
B: Beta-2-microglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,3835
Polymers43,1452
Non-polymers1,2383
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3400 Å2
ΔGint-4 kcal/mol
Surface area17980 Å2
MethodPISA
2
C: Antigen-presenting glycoprotein CD1d2
D: Beta-2-microglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,3835
Polymers43,1452
Non-polymers1,2383
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3360 Å2
ΔGint-3 kcal/mol
Surface area17520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.566, 71.549, 104.747
Angle α, β, γ (deg.)90.00, 101.78, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 4 molecules ACBD

#1: Protein Antigen-presenting glycoprotein CD1d2


Mass: 31484.426 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cd1d2, Cd1.2 / Production host: Baculovirus expression vector pFastBac1-HM / References: UniProt: P11610
#2: Protein Beta-2-microglobulin


Mass: 11660.350 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: B2m / Production host: Baculovirus expression vector pFastBac1-HM / References: UniProt: P01887

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Sugars , 2 types, 4 molecules

#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#4: 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.: 2
Source method: isolated from a genetically manipulated source
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

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Non-polymers , 2 types, 66 molecules

#5: Chemical ChemComp-F57 / (2R)-1-(decanoyloxy)-3-(phosphonooxy)propan-2-yl octadecanoate


Mass: 592.785 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C31H61O8P
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / 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: 2.49 Å3/Da / Density % sol: 50.6 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.3
Details: 100 mM BisTris (pH 6-6.5), 200 mM CaCl2 and 21-26% PEG 3350
PH range: 6.0-6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: May 22, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.43→45.77 Å / Num. obs: 32070 / % possible obs: 100 % / Redundancy: 7 % / Biso Wilson estimate: 50.2 Å2 / Rpim(I) all: 0.312 / Net I/σ(I): 17.88
Reflection shellResolution: 2.43→2.52 Å

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1CD1

1cd1


Resolution: 2.43→44.74 Å / Cor.coef. Fo:Fc: 0.9079 / Cor.coef. Fo:Fc free: 0.8809 / SU R Cruickshank DPI: 0.464 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.429 / SU Rfree Blow DPI: 0.254 / SU Rfree Cruickshank DPI: 0.262
RfactorNum. reflection% reflectionSelection details
Rfree0.2487 1627 5.07 %RANDOM
Rwork0.2171 ---
obs0.2187 32070 99.79 %-
Displacement parametersBiso mean: 40.22 Å2
Baniso -1Baniso -2Baniso -3
1-11.9889 Å20 Å22.6306 Å2
2---6.4741 Å20 Å2
3----5.5148 Å2
Refine analyzeLuzzati coordinate error obs: 0.355 Å
Refinement stepCycle: 1 / Resolution: 2.43→44.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5836 0 164 64 6064
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.016187HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.118433HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2775SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes137HARMONIC2
X-RAY DIFFRACTIONt_gen_planes894HARMONIC5
X-RAY DIFFRACTIONt_it6187HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.52
X-RAY DIFFRACTIONt_other_torsion3.07
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion807SEMIHARMONIC5
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_contact6744SEMIHARMONIC4
LS refinement shellResolution: 2.43→2.51 Å / Total num. of bins used: 16
RfactorNum. reflection% reflection
Rfree0.2916 152 5.29 %
Rwork0.2588 2721 -
all0.2606 2873 -
obs--98.2 %

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