+
Open data
-
Basic information
Entry | Database: PDB / ID: 2ak5 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | beta PIX-SH3 complexed with a Cbl-b peptide | |||||||||
![]() |
| |||||||||
![]() | ENDOCYTOSIS/EXOCYTOSIS / adaptor proteins / Cin85 / PIX/COOL / Cbl / protein-protein interaction / endocytosis / ENDOCYTOSIS-EXOCYTOSIS COMPLEX | |||||||||
Function / homology | ![]() negative regulation of microtubule nucleation / presynaptic actin cytoskeleton organization / Ephrin signaling / NRAGE signals death through JNK / EGFR downregulation / RHOU GTPase cycle / RHOV GTPase cycle / G alpha (12/13) signalling events / RHOQ GTPase cycle / RAC1 GTPase cycle ...negative regulation of microtubule nucleation / presynaptic actin cytoskeleton organization / Ephrin signaling / NRAGE signals death through JNK / EGFR downregulation / RHOU GTPase cycle / RHOV GTPase cycle / G alpha (12/13) signalling events / RHOQ GTPase cycle / RAC1 GTPase cycle / postsynaptic actin cytoskeleton organization / RHOA GTPase cycle / regulation of platelet-derived growth factor receptor-alpha signaling pathway / positive regulation of growth hormone secretion / storage vacuole / astrocyte cell migration / T cell anergy / positive regulation of T cell anergy / CD4-positive, alpha-beta T cell proliferation / regulation protein catabolic process at postsynapse / negative regulation of CD4-positive, alpha-beta T cell proliferation / NLS-bearing protein import into nucleus / gamma-tubulin binding / lamellipodium assembly / negative regulation of T cell receptor signaling pathway / small GTPase-mediated signal transduction / mitotic spindle pole / regulation of postsynaptic neurotransmitter receptor internalization / Golgi organization / negative regulation of epidermal growth factor receptor signaling pathway / Rho protein signal transduction / hematopoietic progenitor cell differentiation / ruffle / phosphotyrosine residue binding / guanyl-nucleotide exchange factor activity / positive regulation of protein ubiquitination / GABA-ergic synapse / protein catabolic process / RING-type E3 ubiquitin transferase / receptor tyrosine kinase binding / positive regulation of protein catabolic process / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / lamellipodium / T cell receptor signaling pathway / growth cone / cell cortex / postsynapse / neuron projection / intracellular signal transduction / protein ubiquitination / immune response / positive regulation of apoptotic process / membrane raft / focal adhesion / neuronal cell body / centrosome / calcium ion binding / protein kinase binding / glutamatergic synapse / signal transduction / protein-containing complex / zinc ion binding / nucleoplasm / plasma membrane / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Jozic, D. / Cardenes, N. / Deribe, Y.L. / Moncalian, G. / Hoeller, D. / Groemping, Y. / Dikic, I. / Rittinger, K. / Bravo, J. | |||||||||
![]() | ![]() 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 |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 41.8 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 29 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 2bz8C ![]() 1semS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
Unit cell |
|
-
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.) ![]() ![]() ![]() ![]() #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 / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.59 Å3/Da / Density % sol: 52.43 % |
---|---|
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 |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
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 |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() 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
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.85→26.17 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|