+Open data
-Basic information
Entry | Database: PDB / ID: 2bz8 | ||||||
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Title | N-terminal Sh3 domain of CIN85 bound to Cbl-b peptide | ||||||
Components |
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Keywords | SH3 DOMAIN / CIN85 ADAPTOR PROTEIN / CBL UBIQUITIN LIGASE / ENDOCYTOSIS | ||||||
Function / homology | Function and homology information regulation of platelet-derived growth factor receptor-alpha signaling pathway / Reelin signalling pathway / T cell anergy / positive regulation of T cell anergy / positive regulation of B cell activation / CD4-positive, alpha-beta T cell proliferation / negative regulation of CD4-positive, alpha-beta T cell proliferation / negative regulation of T cell receptor signaling pathway / NLS-bearing protein import into nucleus / endocytic vesicle ...regulation of platelet-derived growth factor receptor-alpha signaling pathway / Reelin signalling pathway / T cell anergy / positive regulation of T cell anergy / positive regulation of B cell activation / CD4-positive, alpha-beta T cell proliferation / negative regulation of CD4-positive, alpha-beta T cell proliferation / negative regulation of T cell receptor signaling pathway / NLS-bearing protein import into nucleus / endocytic vesicle / cytoskeleton organization / phosphotyrosine residue binding / EGFR downregulation / InlB-mediated entry of Listeria monocytogenes into host cell / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / positive regulation of protein ubiquitination / actin filament organization / RING-type E3 ubiquitin transferase / cytoplasmic vesicle membrane / protein catabolic process / Negative regulation of MET activity / receptor tyrosine kinase binding / SH3 domain binding / positive regulation of protein catabolic process / endocytosis / Cargo recognition for clathrin-mediated endocytosis / ubiquitin protein ligase activity / cell-cell junction / Clathrin-mediated endocytosis / Antigen processing: Ubiquitination & Proteasome degradation / cell migration / cell-cell signaling / T cell receptor signaling pathway / regulation of cell shape / Potential therapeutics for SARS / cytoskeleton / intracellular signal transduction / protein ubiquitination / neuron projection / membrane raft / immune response / focal adhesion / ubiquitin protein ligase binding / synapse / calcium ion binding / apoptotic process / signal transduction / zinc ion binding / nucleoplasm / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Cardenes, N. / Moncalian, G. / Bravo, J. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2005 Title: Cbl Promotes Clustering of Endocytic Adaptor Proteins Authors: Jozic, D. / Cardenes, N. / Lissanu-Deribe, Y. / 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 | 2bz8.cif.gz | 38.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2bz8.ent.gz | 27.4 KB | Display | PDB format |
PDBx/mmJSON format | 2bz8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2bz8_validation.pdf.gz | 442.7 KB | Display | wwPDB validaton report |
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Full document | 2bz8_full_validation.pdf.gz | 448.3 KB | Display | |
Data in XML | 2bz8_validation.xml.gz | 9 KB | Display | |
Data in CIF | 2bz8_validation.cif.gz | 11.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bz/2bz8 ftp://data.pdbj.org/pub/pdb/validation_reports/bz/2bz8 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.423197, 0.905071, 0.041843), Vector: |
-Components
#1: Protein | Mass: 6772.526 Da / Num. of mol.: 2 / Fragment: N-TERMINAL SH3 DOMAIN RESIDUES 1-58 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) Organ: BRAIN, KIDNEY, HEART, PLACENTA, LUNG, LIVER, SKELETAL MUSCLE, PANCREAS Plasmid: PET29B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ROSETTA(DE3)PLYS / References: UniProt: Q96B97 #2: Protein/peptide | | Mass: 1332.622 Da / Num. of mol.: 1 / Fragment: POLYPROLINE RICH REGION RESIDUES 902-912 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: Q13191 #3: Chemical | #4: Water | ChemComp-HOH / | |
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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: 2.4 Å3/Da / Density % sol: 47.3 % Description: STARTING MODEL FOR MOLECULAR REPLACEMENT WAS THE ISOLATED CIN85 N-TERMINAL SH3, UNPUBLISHED. |
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Crystal grow | pH: 7.5 Details: 0.8 M NA CITRATE, 0.1 M BIS-TRIS PH 7.5, 0.2 M NACL |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Site: SRS / Beamline: 14.2 / Type: BRUKER / Wavelength: 1.5418 |
Detector | Type: BRUKER / Detector: CCD / Date: Nov 3, 2004 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→2 Å / Num. obs: 9738 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 11.8 % / Biso Wilson estimate: 19.1 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 29 |
Reflection shell | Resolution: 2→2.07 Å / Mean I/σ(I) obs: 2.87 / % possible all: 98.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→20 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 1029899.76 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: A TWINING FRACTION OF 0.305 WAS CONSIDERED DURING REFINEMENT.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 82.5224 Å2 / ksol: 0.386287 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.4 Å2
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Refinement step | Cycle: LAST / Resolution: 2→20 Å
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Refine LS restraints |
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Xplor file |
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