+Open data
-Basic information
Entry | Database: PDB / ID: 7mx4 | ||||||
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Title | CD1c with antigen analogue 1 | ||||||
Components |
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Keywords | LIPID BINDING PROTEIN / IMMUNE SYSTEM / lipid / CD1c / antigen-presenting / tuberculosis | ||||||
Function / homology | Function and homology information glycolipid binding / T cell activation involved in immune response / 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 ferrous iron binding / positive regulation of transferrin receptor binding / negative regulation of receptor binding ...glycolipid binding / T cell activation involved in immune response / 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 ferrous iron binding / positive regulation of transferrin receptor binding / negative regulation of receptor binding / DAP12 interactions / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / 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 / peptide antigen assembly with MHC class I protein complex / ER to Golgi transport vesicle membrane / 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 / sensory perception of smell / MHC class I protein complex / negative regulation of neurogenesis / multicellular organismal-level iron ion homeostasis / positive regulation of receptor-mediated endocytosis / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / specific granule lumen / phagocytic vesicle membrane / recycling endosome 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 / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / positive regulation of immune response / positive regulation of T cell activation / Modulation by Mtb of host immune system / negative regulation of neuron projection development / positive regulation of protein binding / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / late endosome membrane / iron ion transport / ER-Phagosome pathway / early endosome membrane / T cell differentiation in thymus / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / adaptive immune response / amyloid fibril formation / learning or memory / lysosome / endosome membrane / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / lysosomal membrane / external side of plasma membrane / Golgi membrane / intracellular membrane-bounded organelle / 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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.73 Å | ||||||
Authors | Cao, T.P. / Shahine, A. / Rossjohn, J. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2021 Title: Rational design of a hydrolysis-resistant mycobacterial phosphoglycolipid antigen presented by CD1c to T cells. Authors: Reijneveld, J.F. / Marino, L. / Cao, T.P. / Cheng, T.Y. / Dam, D. / Shahine, A. / Witte, M.D. / Filippov, D.V. / Suliman, S. / van der Marel, G.A. / Moody, D.B. / Minnaard, A.J. / Rossjohn, ...Authors: Reijneveld, J.F. / Marino, L. / Cao, T.P. / Cheng, T.Y. / Dam, D. / Shahine, A. / Witte, M.D. / Filippov, D.V. / Suliman, S. / van der Marel, G.A. / Moody, D.B. / Minnaard, A.J. / Rossjohn, J. / Codee, J.D.C. / Van Rhijn, I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7mx4.cif.gz | 187.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7mx4.ent.gz | 143.5 KB | Display | PDB format |
PDBx/mmJSON format | 7mx4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7mx4_validation.pdf.gz | 811.8 KB | Display | wwPDB validaton report |
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Full document | 7mx4_full_validation.pdf.gz | 817.8 KB | Display | |
Data in XML | 7mx4_validation.xml.gz | 20.3 KB | Display | |
Data in CIF | 7mx4_validation.cif.gz | 28.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mx/7mx4 ftp://data.pdbj.org/pub/pdb/validation_reports/mx/7mx4 | HTTPS FTP |
-Related structure data
Related structure data | 7mxfC 7mxhC 3ov6S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 31645.354 Da / Num. of mol.: 1 / Mutation: N52Q, N57Q, K108G, N128Q, W241G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CD1C, CD1B / Cell line (production host): HEK293S / Production host: Homo sapiens (human) / References: UniProt: P29017, UniProt: P29016 |
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#2: Protein | Mass: 12616.132 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Cell line (production host): HEK293S / Production host: Homo sapiens (human) / References: UniProt: P61769 |
-Sugars , 1 types, 1 molecules
#3: Sugar | ChemComp-NAG / |
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-Non-polymers , 6 types, 228 molecules
#4: Chemical | ChemComp-ZPD / ( | ||
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#5: Chemical | ChemComp-D12 / | ||
#6: Chemical | ChemComp-ZP7 / ( | ||
#7: Chemical | ChemComp-NHE / | ||
#8: Chemical | #9: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.63 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9.4 Details: 100 mM CHES, 1.05 M sodium citrate, 25 mM triglycine |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9322 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 9, 2020 |
Radiation | Monochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9322 Å / Relative weight: 1 |
Reflection | Resolution: 1.73→48.56 Å / Num. obs: 42680 / % possible obs: 99.82 % / Redundancy: 2 % / Biso Wilson estimate: 27.33 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.01974 / Rpim(I) all: 0.01974 / Rrim(I) all: 0.02792 / Net I/σ(I): 11.61 |
Reflection shell | Resolution: 1.73→1.792 Å / Redundancy: 2 % / Rmerge(I) obs: 0.3305 / Mean I/σ(I) obs: 1.71 / Num. unique obs: 4208 / CC1/2: 0.796 / CC star: 0.941 / Rpim(I) all: 0.3305 / Rrim(I) all: 0.4674 / % possible all: 99.33 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3OV6 Resolution: 1.73→48.56 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.52 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.46 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.73→48.56 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -13.7175 Å / Origin y: -17.782 Å / Origin z: 16.7926 Å
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Refinement TLS group | Selection details: all |