+Open data
-Basic information
Entry | Database: PDB / ID: 2c2l | ||||||
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Title | Crystal structure of the CHIP U-box E3 ubiquitin ligase | ||||||
Components |
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Keywords | CHAPERONE / E3 LIGASE / UBIQUITINYLATION / TPR / HEAT-SHOCK PROTEIN COMPLEX | ||||||
Function / homology | Function and homology information : / positive regulation of chaperone-mediated protein complex assembly / Downregulation of TGF-beta receptor signaling / regulation of glucocorticoid metabolic process / Downregulation of ERBB2 signaling / positive regulation of ERAD pathway / Regulation of TNFR1 signaling / Regulation of necroptotic cell death / Regulation of PTEN stability and activity / Regulation of RUNX2 expression and activity ...: / positive regulation of chaperone-mediated protein complex assembly / Downregulation of TGF-beta receptor signaling / regulation of glucocorticoid metabolic process / Downregulation of ERBB2 signaling / positive regulation of ERAD pathway / Regulation of TNFR1 signaling / Regulation of necroptotic cell death / Regulation of PTEN stability and activity / Regulation of RUNX2 expression and activity / ubiquitin conjugating enzyme complex / cellular response to misfolded protein / nuclear inclusion body / Antigen processing: Ubiquitination & Proteasome degradation / misfolded protein binding / protein folding chaperone complex / positive regulation of ubiquitin-protein transferase activity / ubiquitin-ubiquitin ligase activity / sperm mitochondrial sheath / dATP binding / Scavenging by Class F Receptors / sulfonylurea receptor binding / CTP binding / positive regulation of protein polymerization / vRNP Assembly / UTP binding / sperm plasma membrane / positive regulation of tau-protein kinase activity / protein insertion into mitochondrial outer membrane / telomerase holoenzyme complex assembly / chaperone-mediated autophagy / Rho GDP-dissociation inhibitor binding / protein quality control for misfolded or incompletely synthesized proteins / Uptake and function of diphtheria toxin / mitochondrial transport / protein monoubiquitination / Drug-mediated inhibition of ERBB2 signaling / Resistance of ERBB2 KD mutants to trastuzumab / Resistance of ERBB2 KD mutants to sapitinib / Resistance of ERBB2 KD mutants to tesevatinib / Resistance of ERBB2 KD mutants to neratinib / Resistance of ERBB2 KD mutants to osimertinib / Resistance of ERBB2 KD mutants to afatinib / Resistance of ERBB2 KD mutants to AEE788 / Resistance of ERBB2 KD mutants to lapatinib / Drug resistance in ERBB2 TMD/JMD mutants / PIWI-interacting RNA (piRNA) biogenesis / TPR domain binding / non-chaperonin molecular chaperone ATPase / SMAD binding / regulation of postsynaptic membrane neurotransmitter receptor levels / protein K63-linked ubiquitination / dendritic growth cone / positive regulation of proteolysis / R-SMAD binding / protein maturation / Sema3A PAK dependent Axon repulsion / regulation of protein ubiquitination / positive regulation of cell size / skeletal muscle contraction / protein unfolding / regulation of protein-containing complex assembly / HSF1-dependent transactivation / telomere maintenance via telomerase / response to unfolded protein / chaperone-mediated protein complex assembly / HSF1 activation / Attenuation phase / RHOBTB2 GTPase cycle / protein autoubiquitination / DNA polymerase binding / ubiquitin ligase complex / positive regulation of lamellipodium assembly / axonal growth cone / eNOS activation / endoplasmic reticulum unfolded protein response / : / endocytic vesicle lumen / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / positive regulation of defense response to virus by host / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / positive regulation of cardiac muscle contraction / cardiac muscle cell apoptotic process / Recruitment of mitotic centrosome proteins and complexes / Signaling by ERBB2 / response to salt stress / positive regulation of telomerase activity / Recruitment of NuMA to mitotic centrosomes / heat shock protein binding / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / protein tyrosine kinase binding / Anchoring of the basal body to the plasma membrane / activation of innate immune response / positive regulation of interferon-beta production / response to cold / nitric-oxide synthase regulator activity / lysosomal lumen / Constitutive Signaling by Overexpressed ERBB2 / AURKA Activation by TPX2 Similarity search - Function | ||||||
Biological species | MUS MUSCULUS (house mouse) HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å | ||||||
Authors | Zhang, M. / Roe, S.M. / Pearl, L.H. | ||||||
Citation | Journal: Mol.Cell / Year: 2005 Title: Chaperoned Ubiquitylation-Crystal Structures of the Chip U Box E3 Ubiquitin Ligase and a Chip-Ubc13-Uev1A Complex Authors: Zhang, M. / Windheim, M. / Roe, S.M. / Peggie, M. / Cohen, P. / Prodromou, C. / Pearl, L.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2c2l.cif.gz | 235.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2c2l.ent.gz | 198.5 KB | Display | PDB format |
PDBx/mmJSON format | 2c2l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c2/2c2l ftp://data.pdbj.org/pub/pdb/validation_reports/c2/2c2l | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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4 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 32728.904 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) MUS MUSCULUS (house mouse) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q9DCJ0, UniProt: Q9WUD1*PLUS #2: Protein/peptide | Mass: 1082.120 Da / Num. of mol.: 4 / Fragment: C-TERMINAL PEPTIDE, UNP RESIDUES 414-422 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: Q96HX7, UniProt: P07900*PLUS #3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-NI / #5: 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: 4.4 Å3/Da / Density % sol: 71.5 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 7.5 Details: MCHIP WAS MIXED WITH HUMAN HSP90 C-TERMINAL PEPTIDE AT A 1:3 MOLAR RATIO, RESPECTIVELY, INCUBATED FOR 30 MIN AT 4C AND CONCENTRATED TO 10 MG/ML. INITIAL MULTIPLE CRYSTALS WERE GROWN BY ...Details: MCHIP WAS MIXED WITH HUMAN HSP90 C-TERMINAL PEPTIDE AT A 1:3 MOLAR RATIO, RESPECTIVELY, INCUBATED FOR 30 MIN AT 4C AND CONCENTRATED TO 10 MG/ML. INITIAL MULTIPLE CRYSTALS WERE GROWN BY VAPOUR DIFFUSION AT 20C AGAINST 30% W/V PEG4000, 100 MM TRIS [PH 7.5] AND 200 MM LITHIUM SULPHATE. SUBSEQUENT STREAK-SEEDING INTO SOLUTIONS OF 16% W/V PEG4000, 100 MM TRIS [PH 7.5] AND 400 MM LITHIUM SULPHATE PRODUCED SINGLE PLATES. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9801 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Mar 17, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9801 Å / Relative weight: 1 |
Reflection | Resolution: 3.3→40 Å / Num. obs: 68272 / % possible obs: 98.1 % / Observed criterion σ(I): 0 / Redundancy: 2.1 % / Biso Wilson estimate: 84.6 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 10 |
Reflection shell | Resolution: 3.3→3.47 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 2.7 / % possible all: 98.1 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: IN-HOUSE MODEL Resolution: 3.3→40 Å / Data cutoff high absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Solvent model: FLAT / Bsol: 14.9172 Å2 / ksol: 0.307367 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 80.1 Å2
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Refinement step | Cycle: LAST / Resolution: 3.3→40 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.3→3.49 Å / Total num. of bins used: 7
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Xplor file |
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