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- PDB-1zt4: The crystal structure of human CD1d with and without alpha-Galact... -

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Basic information

Entry
Database: PDB / ID: 1zt4
TitleThe crystal structure of human CD1d with and without alpha-Galactosylceramide
Components
  • Beta-2-microglobulinBeta-2 microglobulin
  • T-cell surface glycoprotein CD1d
KeywordsIMMUNE SYSTEM / human CD1d / CD1 / MHC class I / empty binding groove / glycolipid / alpha-galactosylceramide / alpha-GalCer / Structural Proteomics in Europe / SPINE / Structural Genomics
Function / homology
Function and homology information


lipid antigen binding / T cell selection / 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 regulation of innate immune response / heterotypic cell-cell adhesion / beta-2-microglobulin binding ...lipid antigen binding / T cell selection / 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 regulation of innate immune response / heterotypic cell-cell adhesion / beta-2-microglobulin binding / positive regulation of T cell proliferation / detection of bacterium / cell adhesion molecule binding / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / early endosome lumen / positive regulation of receptor binding / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / 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 / ER to Golgi transport vesicle membrane / 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 / recycling endosome membrane / phagocytic vesicle membrane / specific granule lumen / peptide antigen binding / positive regulation of cellular senescence / antigen processing and presentation of exogenous peptide antigen via MHC class II / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / positive regulation of immune response / negative regulation of epithelial cell proliferation / Modulation by Mtb of host immune system / positive regulation of T cell activation / sensory perception of smell / negative regulation of neuron projection development / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / late endosome membrane / T cell differentiation in thymus / positive regulation of protein binding / ER-Phagosome pathway / iron ion transport / histone binding / protein refolding / early endosome membrane / protein homotetramerization / basolateral plasma membrane / intracellular iron ion homeostasis / amyloid fibril formation / lysosome / learning or memory / endosome membrane / immune response / Amyloid fiber formation / lysosomal membrane / endoplasmic reticulum lumen / external side of plasma membrane / Golgi membrane / focal adhesion / innate immune response / Neutrophil degranulation / endoplasmic reticulum membrane / SARS-CoV-2 activates/modulates innate and adaptive immune responses / Golgi apparatus / cell surface / endoplasmic reticulum / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / membrane / 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
Chem-AGH / Antigen-presenting glycoprotein CD1d / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsKoch, M. / Stronge, V.S. / Shepherd, D. / Gadola, S.D. / Mathew, B. / Ritter, G. / Fersht, A.R. / Besra, G.S. / Schmidt, R.R. / Jones, E.Y. ...Koch, M. / Stronge, V.S. / Shepherd, D. / Gadola, S.D. / Mathew, B. / Ritter, G. / Fersht, A.R. / Besra, G.S. / Schmidt, R.R. / Jones, E.Y. / Cerundolo, V. / Structural Proteomics in Europe (SPINE)
CitationJournal: Nat.Immunol. / Year: 2005
Title: The crystal structure of human CD1d with and without alpha-galactosylceramide
Authors: Koch, M. / Stronge, V.S. / Shepherd, D. / Gadola, S.D. / Mathew, B. / Ritter, G. / Fersht, A.R. / Besra, G.S. / Schmidt, R.R. / Jones, E.Y. / Cerundolo, V.
History
DepositionMay 26, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 19, 2005Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Refinement description / Category: software
Item: _software.contact_author / _software.contact_author_email ..._software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 2.0Jun 17, 2020Group: Data collection / Database references / Polymer sequence
Category: entity_poly / pdbx_database_related ...entity_poly / pdbx_database_related / struct_biol / struct_ref_seq_dif
Item: _entity_poly.pdbx_target_identifier / _struct_ref_seq_dif.details
Revision 2.1Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: T-cell surface glycoprotein CD1d
B: Beta-2-microglobulin
C: T-cell surface glycoprotein CD1d
D: Beta-2-microglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,2555
Polymers87,3964
Non-polymers8581
Water32418
1
A: T-cell surface glycoprotein CD1d
B: Beta-2-microglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,5563
Polymers43,6982
Non-polymers8581
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4780 Å2
ΔGint-33 kcal/mol
Surface area18690 Å2
MethodPISA
2
C: T-cell surface glycoprotein CD1d
D: Beta-2-microglobulin


Theoretical massNumber of molelcules
Total (without water)43,6982
Polymers43,6982
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2500 Å2
ΔGint-10 kcal/mol
Surface area20090 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10170 Å2
ΔGint-55 kcal/mol
Surface area35880 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)50.470, 94.300, 176.070
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Detailsthe biological assembly is heavy chain from CD1d plus beta-microglobulin, chains A and B (ligand bound molecule) or chains C and D (non-ligand or empty molecule).

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Components

#1: Protein T-cell surface glycoprotein CD1d / CD1d antigen / R3G1


Mass: 31818.814 Da / Num. of mol.: 2 / Fragment: CD1d heavy chain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD1D / Plasmid: pET23d / Production host: Escherichia coli (E. coli) / Strain (production host): HMS174 / References: UniProt: P15813
#2: Protein Beta-2-microglobulin / Beta-2 microglobulin / HDCMA22P


Mass: 11879.356 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M / Plasmid: pET23d / Production host: Escherichia coli (E. coli) / Strain (production host): HMS174 / References: UniProt: P61769
#3: Sugar ChemComp-AGH / N-{(1S,2R,3S)-1-[(ALPHA-D-GALACTOPYRANOSYLOXY)METHYL]-2,3-DIHYDROXYHEPTADECYL}HEXACOSANAMIDE / Alpha-Galactosylceramide


Type: D-saccharide / Mass: 858.322 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C50H99NO9
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 18 / 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: 2.6 Å3/Da / Density % sol: 53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: PEG3350, potassium fluoride, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 11, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 3→30 Å / Num. obs: 17523 / % possible obs: 99.8 % / Observed criterion σ(F): 0.5 / Observed criterion σ(I): 0.5 / Redundancy: 11.2 % / Rmerge(I) obs: 0.184 / Rsym value: 0.184 / Net I/σ(I): 15.2
Reflection shellResolution: 3→3.19 Å / Redundancy: 11.2 % / Rmerge(I) obs: 0.94 / Mean I/σ(I) obs: 3.2 / Num. unique all: 2864 / Rsym value: 0.94 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
CNS1.1refinement
PDB_EXTRACT1.601data extraction
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1CD1

1cd1


Resolution: 3→30 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.326 867 4.9 %RANDOM
Rwork0.234 ---
all0.234 17523 --
obs0.234 17432 99.5 %-
Solvent computationBsol: 80 Å2
Displacement parametersBiso mean: 32.247 Å2
Baniso -1Baniso -2Baniso -3
1--0.606 Å20 Å20 Å2
2---0.145 Å20 Å2
3---0.75 Å2
Refinement stepCycle: LAST / Resolution: 3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6015 0 60 18 6093
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.65
X-RAY DIFFRACTIONc_bond_d0.01
LS refinement shellResolution: 3→3.14 Å
RfactorNum. reflection% reflection
Rfree0.401 96 -
Rwork0.325 --
obs-2134 100 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION3AGL_new_cns.par

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