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- PDB-1cd1: CD1(MOUSE) ANTIGEN PRESENTING MOLECULE -

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Basic information

Entry
Database: PDB / ID: 1cd1
TitleCD1(MOUSE) ANTIGEN PRESENTING MOLECULE
Components(CD1) x 2
KeywordsCD1 / IMMUNOLOGY / MHC / TCR / GLYCOPROTEIN / IMMUNOGLOBULIN FOLD / T-CELL
Function / homology
Function and homology information


regulation of immature T cell proliferation in thymus / positive regulation of NK T cell differentiation / lipid antigen binding / positive regulation of NK T cell activation / NK T cell differentiation / 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 ...regulation of immature T cell proliferation in thymus / positive regulation of NK T cell differentiation / lipid antigen binding / positive regulation of NK T cell activation / NK T cell differentiation / 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 / positive thymic T cell selection / positive regulation of macrophage activation / 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 / antigen processing and presentation / positive regulation of interleukin-4 production / regulation of immune response / cellular defense response / positive regulation of T cell proliferation / positive regulation of interleukin-2 production / Neutrophil degranulation / cell adhesion molecule binding / T cell receptor 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 / positive regulation of type II interferon production / sensory perception of smell / negative regulation of neuron projection development / late endosome / MHC class II protein complex binding / late endosome membrane / T cell differentiation in thymus / antibacterial humoral response / iron ion transport / histone binding / protein refolding / protein homotetramerization / cellular response to lipopolysaccharide / intracellular iron ion homeostasis / defense response to Gram-negative bacterium / amyloid fibril formation / lysosome / learning or memory / early endosome / endosome membrane / defense response to Gram-positive bacterium / immune response / lysosomal membrane / external side of plasma membrane / innate immune response / structural molecule activity / Golgi apparatus / cell surface / endoplasmic reticulum / protein homodimerization activity / extracellular space / identical protein binding / plasma membrane / cytosol / cytoplasm
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
Beta-2-microglobulin / Antigen-presenting glycoprotein CD1d1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.67 Å
AuthorsZeng, Z.H. / Segelke, B.W. / Wilson, I.A.
CitationJournal: Science / Year: 1997
Title: Crystal structure of mouse CD1: An MHC-like fold with a large hydrophobic binding groove.
Authors: Zeng, Z. / Castano, A.R. / Segelke, B.W. / Stura, E.A. / Peterson, P.A. / Wilson, I.A.
History
DepositionApr 2, 1997Processing site: BNL
Revision 1.0Oct 15, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 3, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CD1
B: CD1
C: CD1
D: CD1


Theoretical massNumber of molelcules
Total (without water)95,4574
Polymers95,4574
Non-polymers00
Water0
1
A: CD1
B: CD1


Theoretical massNumber of molelcules
Total (without water)47,7282
Polymers47,7282
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2480 Å2
ΔGint-16 kcal/mol
Surface area19080 Å2
MethodPISA
2
C: CD1
D: CD1


Theoretical massNumber of molelcules
Total (without water)47,7282
Polymers47,7282
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2480 Å2
ΔGint-16 kcal/mol
Surface area19320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.340, 76.200, 103.400
Angle α, β, γ (deg.)90.00, 102.29, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.999868, -0.015556, -0.004795), (-0.015976, 0.994259, 0.105805), (0.003121, 0.105868, -0.994375)5.85139, -5.49172, 105.15204
2given(-0.999964, -0.007846, 0.003296), (-0.007356, 0.991654, 0.128721), (-0.004279, 0.128692, -0.991675)5.34525, -7.239, 105.30692

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Components

#1: Protein CD1 / MCD1D.1


Mass: 36023.934 Da / Num. of mol.: 2 / Fragment: ALPHA1, ALPHA2, ALPHA3, BETA2-MICROGLOBULIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Strain: C57BL/6 / Cell: CORTICAL THYMOCYTES, DENDRITIC CELLS / Cell line: SC2 / Cellular location: EXTRACELLULARGlossary of biology / Gene: CD1.1 / Plasmid: PRMHA-3 / Gene (production host): CD1.1 / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: P11609
#2: Protein CD1 / MCD1D.1


Mass: 11704.359 Da / Num. of mol.: 2 / Fragment: ALPHA1, ALPHA2, ALPHA3, BETA2-MICROGLOBULIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Strain: C57BL/6 / Cell: CORTICAL THYMOCYTES, DENDRITIC CELLS / Cell line: SC2 / Cellular location: EXTRACELLULARGlossary of biology / Gene: CD1.1 / Plasmid: PRMHA-3 / Gene (production host): CD1.1 / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: P01887

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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: 2.19 Å3/Da / Density % sol: 44 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 6.5
Details: 6 MG/ML PROTEIN 2.0M (NH4)2SO4 100 MM SODIUM CACODYLATE, 20MM EDTA, PH 6.5 5 UL PROTEIN + 2.5 UL RESERVOIR SITTING DROP, vapor diffusion - sitting drop
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
16 mg/mlmCD1d111
22.0 Mammonium sulfate12
30.15 Msodium citrate12
42 mM12ZnSO4

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: ELLIOTT GX-18 / Wavelength: 1.5418
DetectorType: ELLIOT / Detector: AREA DETECTOR / Date: Sep 2, 1994 / Details: MIRRORS
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.557→46.142 Å / Num. obs: 22974 / % possible obs: 75.01 % / Observed criterion σ(I): -3 / Redundancy: 1.93 % / Biso Wilson estimate: 27.7 Å2 / Rsym value: 0.15 / Net I/σ(I): 7.795
Reflection shellResolution: 2.557→2.661 Å / Redundancy: 1.3 % / Mean I/σ(I) obs: 1.3 / Rsym value: 0.46 / % possible all: 21
Reflection
*PLUS
Num. measured all: 57464 / Rmerge(I) obs: 0.095

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Processing

Software
NameVersionClassification
XENGENdata collection
XENGENdata reduction
X-PLOR3.1model building
X-PLOR3.1refinement
XENGENdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: FCRN, HLA-B27

Resolution: 2.67→10 Å / Rfactor Rfree error: 0.0072 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / Cross valid method: POST REFINEMENT / σ(F): 1.5
RfactorNum. reflection% reflectionSelection details
Rfree0.33 2177 10 %RANDOM
Rwork0.192 ---
obs0.192 19916 83.7 %-
Displacement parametersBiso mean: 24.8 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.55 Å0.27 Å
Luzzati d res low-10 Å
Refinement stepCycle: LAST / Resolution: 2.67→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6026 0 0 0 6026
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.95
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d27
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.7
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refine LS restraints NCSNCS model details: RESTRAINTS
LS refinement shellResolution: 2.67→2.79 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.38 216 10.4 %
Rwork0.26 1850 -
obs--42.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.33
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg27
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.7

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