+Open data
-Basic information
Entry | Database: PDB / ID: 8ek5 | |||||||||
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Title | Engineered scFv 10LH bound to PHOX2B/HLA-A24:02 | |||||||||
Components |
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Keywords | ANTITUMOR PROTEIN / Neuroblastoma / PHOX2B | |||||||||
Function / homology | Function and homology information medullary reticular formation development / autonomic nervous system development / parasympathetic nervous system development / efferent axon development in a lateral line nerve / retrotrapezoid nucleus neuron differentiation / negative regulation of type B pancreatic cell proliferation / noradrenergic neuron development / cell differentiation in hindbrain / respiratory system development / hindbrain tangential cell migration ...medullary reticular formation development / autonomic nervous system development / parasympathetic nervous system development / efferent axon development in a lateral line nerve / retrotrapezoid nucleus neuron differentiation / negative regulation of type B pancreatic cell proliferation / noradrenergic neuron development / cell differentiation in hindbrain / respiratory system development / hindbrain tangential cell migration / cellular response to carbon dioxide / noradrenergic neuron differentiation / brainstem development / regulation of respiratory gaseous exchange by nervous system process / motor neuron migration / sympathetic ganglion development / enteric nervous system development / neural crest cell migration involved in autonomic nervous system development / glial cell differentiation / type B pancreatic cell proliferation / sympathetic nervous system development / cellular response to BMP stimulus / dopaminergic neuron differentiation / skeletal muscle cell differentiation / inner ear development / membrane depolarization / negative regulation of neuron differentiation / positive regulation of G2/M transition of mitotic cell cycle / positive regulation of neuron differentiation / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / response to activity / 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 / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / RNA polymerase II transcription regulatory region sequence-specific DNA binding / neuron migration / 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 / 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 / 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 / positive regulation of immune response / negative regulation of epithelial cell proliferation / Interferon gamma signaling / positive regulation of T cell activation / Modulation by Mtb of host immune system / sensory perception of smell / sequence-specific double-stranded DNA binding / negative regulation of neuron projection development / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / T cell differentiation in thymus / late endosome membrane / positive regulation of cold-induced thermogenesis / positive regulation of protein binding / ER-Phagosome pathway / iron ion transport / protein refolding / early endosome membrane / regulation of gene expression / DNA-binding transcription activator activity, RNA polymerase II-specific / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / Amyloid fiber formation / lysosomal membrane / external side of plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.11 Å | |||||||||
Authors | Garfinkle, S.E. / Florio, T.J. / Sgourakis, N.G. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Sci Immunol / Year: 2023 Title: Structural principles of peptide-centric chimeric antigen receptor recognition guide therapeutic expansion. Authors: Sun, Y. / Florio, T.J. / Gupta, S. / Young, M.C. / Marshall, Q.F. / Garfinkle, S.E. / Papadaki, G.F. / Truong, H.V. / Mycek, E. / Li, P. / Farrel, A. / Church, N.L. / Jabar, S. / Beasley, M. ...Authors: Sun, Y. / Florio, T.J. / Gupta, S. / Young, M.C. / Marshall, Q.F. / Garfinkle, S.E. / Papadaki, G.F. / Truong, H.V. / Mycek, E. / Li, P. / Farrel, A. / Church, N.L. / Jabar, S. / Beasley, M.D. / Kiefel, B.R. / Yarmarkovich, M. / Mallik, L. / Maris, J.M. / Sgourakis, N.G. #1: Journal: Sci Immunol / Year: 2023 Title: The chilling origin of germinal centers. Authors: Boehm, T. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8ek5.cif.gz | 267 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ek5.ent.gz | 210.4 KB | Display | PDB format |
PDBx/mmJSON format | 8ek5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ek/8ek5 ftp://data.pdbj.org/pub/pdb/validation_reports/ek/8ek5 | HTTPS FTP |
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-Related structure data
Related structure data | 8sbkC 8sblC 7mjaS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-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: 31909.312 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-A Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: F6IR24 |
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#2: Protein | Mass: 11879.356 Da / Num. of mol.: 1 / Fragment: UNP residues 21-119 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: P61769 |
-Protein/peptide / Antibody , 2 types, 2 molecules CE
#3: Protein/peptide | Mass: 1140.268 Da / Num. of mol.: 1 / Fragment: Residues 43-51 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q99453 |
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#4: Antibody | Mass: 49898.523 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) |
-Non-polymers , 3 types, 310 molecules
#5: Chemical | #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / Details: 20% PEG 3350, 0.2M Sodium Nitrate |
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-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 27, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97946 Å / Relative weight: 1 |
Reflection | Resolution: 2.108→43.68 Å / Num. obs: 37369 / % possible obs: 97.4 % / Redundancy: 3.8 % / CC1/2: 0.995 / Rmerge(I) obs: 0.095 / Rpim(I) all: 0.057 / Rrim(I) all: 0.111 / Net I/σ(I): 4.5 |
Reflection shell | Resolution: 2.108→2.115 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.644 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 377 / CC1/2: 0.817 / Rpim(I) all: 0.389 / Rrim(I) all: 0.776 / % possible all: 98.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7MJA Resolution: 2.11→43.68 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.941 / SU B: 13.01 / SU ML: 0.168 / Cross valid method: THROUGHOUT / ESU R: 0.236 / ESU R Free: 0.177 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
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Solvent computation | Ion probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.173 Å2
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Refinement step | Cycle: LAST / Resolution: 2.11→43.68 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.11→2.163 Å
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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