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

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Basic information

Entry
Database: PDB / ID: 6bmh
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 / 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 / negative regulation of neurogenesis / peptide antigen assembly with MHC class II protein complex / positive regulation of receptor-mediated endocytosis / MHC class II protein complex / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / phagocytic vesicle membrane / peptide antigen binding / positive regulation of cellular senescence / antigen processing and presentation of exogenous peptide antigen via MHC class II / negative regulation of epithelial cell proliferation / positive regulation of immune response / sensory perception of smell / positive regulation of T cell activation / 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 / 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 / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type ...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-F61 / Beta-2-microglobulin / Antigen-presenting glycoprotein CD1d2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.298 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 14, 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 / pdbx_validate_close_contact / 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 / _entity.formula_weight / _entity.pdbx_description / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_validate_close_contact.auth_comp_id_2 / _struct_site.details / _struct_site.pdbx_auth_comp_id
Revision 3.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / 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 / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _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 / pdbx_unobs_or_zero_occ_residues
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
E: Antigen-presenting glycoprotein CD1d2
F: Beta-2-microglobulin
G: Antigen-presenting glycoprotein CD1d2
H: Beta-2-microglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)177,97421
Polymers172,5798
Non-polymers5,39513
Water5,423301
1
A: Antigen-presenting glycoprotein CD1d2
B: Beta-2-microglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,4385
Polymers43,1452
Non-polymers1,2943
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4640 Å2
ΔGint-16 kcal/mol
Surface area18110 Å2
MethodPISA
2
C: Antigen-presenting glycoprotein CD1d2
D: Beta-2-microglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,4385
Polymers43,1452
Non-polymers1,2943
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4690 Å2
ΔGint-15 kcal/mol
Surface area17790 Å2
MethodPISA
3
E: Antigen-presenting glycoprotein CD1d2
F: Beta-2-microglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,4385
Polymers43,1452
Non-polymers1,2943
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4680 Å2
ΔGint-15 kcal/mol
Surface area18060 Å2
MethodPISA
4
G: Antigen-presenting glycoprotein CD1d2
H: Beta-2-microglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,6606
Polymers43,1452
Non-polymers1,5154
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4970 Å2
ΔGint-14 kcal/mol
Surface area18270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.955, 74.229, 117.594
Angle α, β, γ (deg.)90.00, 102.94, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 8 molecules ACEGBDFH

#1: Protein
Antigen-presenting glycoprotein CD1d2


Mass: 31484.426 Da / Num. of mol.: 4
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.: 4
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, 9 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.: 4
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
#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.: 5
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, 305 molecules

#4: Chemical
ChemComp-F61 / N-[(2S,3S,4R)-1-(alpha-D-galactopyranosyloxy)-3,4-dihydroxyoctadecan-2-yl]undecanamide


Mass: 647.924 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C35H69NO9
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 301 / 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: 2.61 Å3/Da / Density % sol: 52.9 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.3
Details: 100 mM BisTris (pH 6-6.5), 200 mM CaCl2, 21-26% PEG 3350
PH range: 6-6.5

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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 315r / Detector: CCD / Date: May 23, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.3→45.93 Å / Num. obs: 79496 / % possible obs: 99.8 % / Redundancy: 7 % / Rpim(I) all: 0.043 / Net I/σ(I): 11.6
Reflection shellResolution: 2.3→2.38 Å

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1CD1

1cd1


Resolution: 2.298→45.931 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2799 4000 5.04 %
Rwork0.2298 --
obs0.2323 79388 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.298→45.931 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11694 0 363 301 12358
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01112475
X-RAY DIFFRACTIONf_angle_d0.90717006
X-RAY DIFFRACTIONf_dihedral_angle_d21.1914467
X-RAY DIFFRACTIONf_chiral_restr0.0561855
X-RAY DIFFRACTIONf_plane_restr0.0062137
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.298-2.3250.38781390.29662517X-RAY DIFFRACTION96
2.325-2.35340.30911300.28092592X-RAY DIFFRACTION100
2.3534-2.38310.37821460.28032528X-RAY DIFFRACTION100
2.3831-2.41450.35421520.28272586X-RAY DIFFRACTION100
2.4145-2.44760.34291350.2732597X-RAY DIFFRACTION100
2.4476-2.48250.35721310.28082602X-RAY DIFFRACTION100
2.4825-2.51960.34821520.27482565X-RAY DIFFRACTION100
2.5196-2.5590.35611460.27652599X-RAY DIFFRACTION100
2.559-2.60090.2891290.26152566X-RAY DIFFRACTION100
2.6009-2.64580.31531250.2542652X-RAY DIFFRACTION100
2.6458-2.69390.3681330.262545X-RAY DIFFRACTION100
2.6939-2.74570.29461380.27052639X-RAY DIFFRACTION100
2.7457-2.80170.38091250.26892591X-RAY DIFFRACTION100
2.8017-2.86260.351490.27432600X-RAY DIFFRACTION100
2.8626-2.92920.32211280.26652574X-RAY DIFFRACTION100
2.9292-3.00240.31211330.26152598X-RAY DIFFRACTION100
3.0024-3.08360.30851410.26482613X-RAY DIFFRACTION100
3.0836-3.17430.34631350.26512564X-RAY DIFFRACTION100
3.1743-3.27670.31451480.25972611X-RAY DIFFRACTION100
3.2767-3.39380.29851470.23932624X-RAY DIFFRACTION100
3.3938-3.52970.28151290.23152595X-RAY DIFFRACTION100
3.5297-3.69020.26381410.22572594X-RAY DIFFRACTION100
3.6902-3.88470.24821310.2132636X-RAY DIFFRACTION100
3.8847-4.12790.22391520.19572589X-RAY DIFFRACTION100
4.1279-4.44640.23521370.17322614X-RAY DIFFRACTION100
4.4464-4.89340.19311580.15722618X-RAY DIFFRACTION100
4.8934-5.60040.23451340.18742660X-RAY DIFFRACTION100
5.6004-7.05190.23111350.22372635X-RAY DIFFRACTION100
7.0519-45.94050.24221210.21642684X-RAY DIFFRACTION98

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