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Open data
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Basic information
Entry | Database: PDB / ID: 1gzp | ||||||
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Title | CD1b in complex with GM2 ganglioside | ||||||
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![]() | GLYCOPROTEIN / LIPID / GANGLIOSIDE / MHC / ANTIGEN PRESENTATION | ||||||
Function / homology | ![]() : / : / regulation of membrane depolarization / 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 / retina homeostasis / positive regulation of ferrous iron binding ...: / : / regulation of membrane depolarization / 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 / retina homeostasis / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / 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 / ER to Golgi transport vesicle membrane / 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 / specific granule lumen / recycling endosome membrane / phagocytic vesicle membrane / antimicrobial humoral immune response mediated by antimicrobial peptide / positive regulation of cellular senescence / peptide antigen binding / negative regulation of epithelial cell proliferation / 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 / Modulation by Mtb of host immune system / sensory perception of smell / positive regulation of T cell activation / positive regulation of protein binding / tertiary granule lumen / DAP12 signaling / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / iron ion transport / ER-Phagosome pathway / early endosome membrane / antibacterial humoral response / T cell differentiation in thymus / protein refolding / cellular response to lipopolysaccharide / protein homotetramerization / defense response to Gram-negative bacterium / intracellular iron ion homeostasis / adaptive immune response / amyloid fibril formation / learning or memory / endosome membrane / defense response to Gram-positive bacterium / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / lysosomal membrane / external side of plasma membrane / Golgi membrane / intracellular membrane-bounded organelle / innate immune response / focal adhesion / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / Golgi apparatus / cell surface / endoplasmic reticulum / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Gadola, S.D. / Zaccai, N.R. / Harlos, K. / Shepherd, D. / Ritter, G. / Schmidt, R.R. / Jones, E.Y. / Cerundolo, V. | ||||||
![]() | ![]() Title: Structure of human CD1b with bound ligands at 2.3 A, a maze for alkyl chains. Authors: Gadola, S.D. / Zaccai, N.R. / Harlos, K. / Shepherd, D. / Castro-Palomino, J.C. / Ritter, G. / Schmidt, R.R. / Jones, E.Y. / Cerundolo, V. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 95.4 KB | Display | ![]() |
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PDB format | ![]() | 70.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 775.9 KB | Display | ![]() |
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Full document | ![]() | 781.9 KB | Display | |
Data in XML | ![]() | 16.8 KB | Display | |
Data in CIF | ![]() | 22.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1gzqC ![]() 1cd1S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 33088.215 Da / Num. of mol.: 1 / Fragment: RESIDUES 18-295 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein | Mass: 11879.356 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
-Non-polymers , 4 types, 43 molecules ![](data/chem/img/GM2.gif)
![](data/chem/img/D12.gif)
![](data/chem/img/TWT.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/D12.gif)
![](data/chem/img/TWT.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-GM2 / |
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#4: Chemical | ChemComp-D12 / |
#5: Chemical | ChemComp-TWT / |
#6: Water | ChemComp-HOH / |
-Details
Sequence details | RESIDUES GLYCINE A278 AND PROLINE A279 ARE THE STARTING RESIDUES OF A BIRA TAG ...RESIDUES GLYCINE A278 AND PROLINE A279 ARE THE STARTING RESIDUES OF A BIRA TAG (GPGSGGGLND |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.24 Å3/Da / Density % sol: 64 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / pH: 7.1 Details: 20 DEGREE C 2UL OF PROTEIN + 1UL OF MOTHER LIQUOR 0.2M LITHIUM NITRATE 20% W/V POLYETHYLENE GLYCOL 3350, PH 7.1 | ||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Oct 15, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.93 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→100 Å / Num. obs: 89500 / % possible obs: 87.4 % / Observed criterion σ(I): -0.5 / Redundancy: 6.8 % / Biso Wilson estimate: 95.2 Å2 / Rmerge(I) obs: 0.103 / Net I/σ(I): 13.7 |
Reflection shell | Resolution: 2.8→2.9 Å / Rmerge(I) obs: 0.325 / Mean I/σ(I) obs: 1.8 / % possible all: 71.1 |
Reflection | *PLUS Lowest resolution: 100 Å / Num. obs: 13203 / % possible obs: 88.8 % / Num. measured all: 89500 |
Reflection shell | *PLUS Highest resolution: 2.8 Å / Lowest resolution: 2.91 Å / % possible obs: 71.1 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1CD1 Resolution: 2.8→34.78 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 355814.88 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 14.0445 Å2 / ksol: 0.282575 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 50.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.8→34.78 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.98 Å / Rfactor Rfree error: 0.051 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Lowest resolution: 100 Å / Rfactor Rfree: 0.274 / Rfactor Rwork: 0.223 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Lowest resolution: 2.91 Å |