+Open data
-Basic information
Entry | Database: PDB / ID: 2ak5 | |||||||||
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Title | beta PIX-SH3 complexed with a Cbl-b peptide | |||||||||
Components |
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Keywords | ENDOCYTOSIS/EXOCYTOSIS / adaptor proteins / Cin85 / PIX/COOL / Cbl / protein-protein interaction / endocytosis / ENDOCYTOSIS-EXOCYTOSIS COMPLEX | |||||||||
Function / homology | Function and homology information presynaptic actin cytoskeleton organization / negative regulation of microtubule nucleation / Ephrin signaling / RHOU GTPase cycle / RHOV GTPase cycle / NRAGE signals death through JNK / EGFR downregulation / G alpha (12/13) signalling events / RHOQ GTPase cycle / RAC1 GTPase cycle ...presynaptic actin cytoskeleton organization / negative regulation of microtubule nucleation / Ephrin signaling / RHOU GTPase cycle / RHOV GTPase cycle / NRAGE signals death through JNK / EGFR downregulation / G alpha (12/13) signalling events / RHOQ GTPase cycle / RAC1 GTPase cycle / RHOA GTPase cycle / regulation of platelet-derived growth factor receptor-alpha signaling pathway / T cell anergy / positive regulation of T cell anergy / storage vacuole / astrocyte cell migration / positive regulation of growth hormone secretion / postsynaptic actin cytoskeleton organization / CD4-positive, alpha-beta T cell proliferation / negative regulation of CD4-positive, alpha-beta T cell proliferation / gamma-tubulin binding / lamellipodium assembly / negative regulation of T cell receptor signaling pathway / small GTPase-mediated signal transduction / NLS-bearing protein import into nucleus / mitotic spindle pole / Golgi organization / Rho protein signal transduction / GABA-ergic synapse / hematopoietic progenitor cell differentiation / ruffle / phosphotyrosine residue binding / guanyl-nucleotide exchange factor activity / positive regulation of protein ubiquitination / RING-type E3 ubiquitin transferase / protein catabolic process / receptor tyrosine kinase binding / SH3 domain binding / positive regulation of protein catabolic process / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / lamellipodium / T cell receptor signaling pathway / cell cortex / growth cone / postsynapse / intracellular signal transduction / protein ubiquitination / neuron projection / membrane raft / immune response / positive regulation of apoptotic process / focal adhesion / centrosome / neuronal cell body / calcium ion binding / protein kinase binding / signal transduction / protein-containing complex / zinc ion binding / nucleoplasm / plasma membrane / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Rattus norvegicus (Norway rat) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | |||||||||
Authors | Jozic, D. / Cardenes, N. / Deribe, Y.L. / Moncalian, G. / Hoeller, D. / Groemping, Y. / Dikic, I. / Rittinger, K. / Bravo, J. | |||||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2005 Title: Cbl promotes clustering of endocytic adaptor proteins. Authors: Jozic, D. / Cardenes, N. / Deribe, Y.L. / Moncalian, G. / Hoeller, D. / Groemping, Y. / Dikic, I. / Rittinger, K. / Bravo, J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ak5.cif.gz | 41.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ak5.ent.gz | 29 KB | Display | PDB format |
PDBx/mmJSON format | 2ak5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2ak5_validation.pdf.gz | 440.8 KB | Display | wwPDB validaton report |
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Full document | 2ak5_full_validation.pdf.gz | 442.2 KB | Display | |
Data in XML | 2ak5_validation.xml.gz | 9.5 KB | Display | |
Data in CIF | 2ak5_validation.cif.gz | 13.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ak/2ak5 ftp://data.pdbj.org/pub/pdb/validation_reports/ak/2ak5 | HTTPS FTP |
-Related structure data
Related structure data | 2bz8C 1semS 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
#1: Protein | Mass: 7290.925 Da / Num. of mol.: 2 / Fragment: beta-pix SH3A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 DE3 / References: UniProt: O55043 #2: Protein/peptide | | Mass: 1007.236 Da / Num. of mol.: 1 / Fragment: residues 904-911 / Source method: obtained synthetically Details: The peptide was chemically synthesized. The sequence of the peptide can be naturally found in Homo sapiens (Human)Cbl-b References: UniProt: Q13191 #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.59 Å3/Da / Density % sol: 52.43 % |
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Crystal grow | Temperature: 291 K / pH: 6.5 Details: PEG 3000, SODIUM CITRATE, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K, pH 6.50 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX14.2 / Wavelength: 1.5418 |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Details: MIRRORS |
Radiation | Monochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→26.17 Å / Num. obs: 14106 / % possible obs: 99.5 % / Redundancy: 2.94 % / Rsym value: 0.086 / Net I/σ(I): 31.8 |
Reflection shell | Resolution: 1.85→1.93 Å / % possible all: 98.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 1SEM Resolution: 1.85→26.17 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.9263 / SU B: 9.0032 / SU ML: 0.1122 / Cross valid method: THROUGHOUT / ESU R: 0.3046 / ESU R Free: 0.1528
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.85→26.17 Å
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Refine LS restraints |
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