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- PDB-2c2l: Crystal structure of the CHIP U-box E3 ubiquitin ligase -

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Basic information

Entry
Database: PDB / ID: 2c2l
TitleCrystal structure of the CHIP U-box E3 ubiquitin ligase
Components
  • CARBOXY TERMINUS OF HSP70-INTERACTING PROTEIN
  • HSP90
KeywordsCHAPERONE / 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 / negative regulation of vascular associated smooth muscle contraction / Downregulation of ERBB2 signaling / Regulation of TNFR1 signaling / negative regulation of peroxisome proliferator activated receptor signaling pathway / Regulation of PTEN stability and activity / Regulation of RUNX2 expression and activity / Regulation of necroptotic cell death ...positive regulation of chaperone-mediated protein complex assembly / Downregulation of TGF-beta receptor signaling / regulation of glucocorticoid metabolic process / negative regulation of vascular associated smooth muscle contraction / Downregulation of ERBB2 signaling / Regulation of TNFR1 signaling / negative regulation of peroxisome proliferator activated receptor signaling pathway / Regulation of PTEN stability and activity / Regulation of RUNX2 expression and activity / Regulation of necroptotic cell death / ubiquitin conjugating enzyme complex / positive regulation of ERAD pathway / positive regulation of smooth muscle cell apoptotic process / positive regulation of mitophagy / negative regulation of cardiac muscle hypertrophy / nuclear inclusion body / misfolded protein binding / Antigen processing: Ubiquitination & Proteasome degradation / cellular response to misfolded protein / protein folding chaperone complex / positive regulation of ubiquitin-protein transferase activity / ubiquitin-ubiquitin ligase activity / sperm mitochondrial sheath / sulfonylurea receptor binding / dATP binding / CTP binding / positive regulation of protein polymerization / Scavenging by Class F Receptors / vRNP Assembly / UTP binding / sperm plasma membrane / chaperone-mediated autophagy / Rho GDP-dissociation inhibitor binding / Respiratory syncytial virus genome replication / telomerase holoenzyme complex assembly / mitochondrial transport / Uptake and function of diphtheria toxin / 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 / protein import into mitochondrial matrix / dendritic growth cone / TPR domain binding / PIWI-interacting RNA (piRNA) biogenesis / negative regulation of smooth muscle cell apoptotic process / Assembly and release of respiratory syncytial virus (RSV) virions / non-chaperonin molecular chaperone ATPase / protein quality control for misfolded or incompletely synthesized proteins / R-SMAD binding / positive regulation of proteolysis / protein unfolding / Sema3A PAK dependent Axon repulsion / regulation of protein ubiquitination / protein K63-linked ubiquitination / positive regulation of cell size / protein monoubiquitination / HSF1-dependent transactivation / ubiquitin ligase complex / response to unfolded protein / enzyme-substrate adaptor activity / skeletal muscle contraction / regulation of protein-containing complex assembly / HSF1 activation / telomere maintenance via telomerase / Attenuation phase / chaperone-mediated protein complex assembly / axonal growth cone / neurofibrillary tangle assembly / regulation of postsynaptic membrane neurotransmitter receptor levels / RHOBTB2 GTPase cycle / endoplasmic reticulum unfolded protein response / negative regulation of protein binding / protein autoubiquitination / positive regulation of lamellipodium assembly / nitric oxide metabolic process / eNOS activation / positive regulation of defense response to virus by host / DNA polymerase binding / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / heat shock protein binding / ERAD pathway / response to salt stress / positive regulation of telomere maintenance via telomerase / Signaling by ERBB2 / cardiac muscle cell apoptotic process / Hsp70 protein binding / endocytic vesicle lumen / positive regulation of cardiac muscle contraction / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / activation of innate immune response / lysosomal lumen
Similarity search - Function
CHIP, N-terminal tetratricopeptide repeat domain / CHIP/LubX , U box domain / CHIP N-terminal tetratricopeptide repeat domain / Anaphase-promoting complex, cyclosome, subunit 3 / U-box domain / U-box domain profile. / Modified RING finger domain / U-box domain / Tetratricopeptide repeat domain / Zinc/RING finger domain, C3HC4 (zinc finger) ...CHIP, N-terminal tetratricopeptide repeat domain / CHIP/LubX , U box domain / CHIP N-terminal tetratricopeptide repeat domain / Anaphase-promoting complex, cyclosome, subunit 3 / U-box domain / U-box domain profile. / Modified RING finger domain / U-box domain / Tetratricopeptide repeat domain / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / Heat shock protein Hsp90, conserved site / Heat shock hsp90 proteins family signature. / HSP90, C-terminal domain / Heat shock protein Hsp90, N-terminal / Heat shock protein Hsp90 family / Hsp90 protein / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase superfamily / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Zinc finger, RING/FYVE/PHD-type / Ribosomal protein S5 domain 2-type fold / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
NICKEL (II) ION / Heat shock protein HSP 90-alpha / HSP90AA1 protein / E3 ubiquitin-protein ligase CHIP / E3 ubiquitin-protein ligase CHIP
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
HOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsZhang, M. / Roe, S.M. / Pearl, L.H.
CitationJournal: 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
DepositionSep 29, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 23, 2005Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2016Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Refinement description / Source and taxonomy / Structure summary / Version format compliance
Revision 1.2Mar 6, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.3May 15, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / struct_biol / Item: _exptl_crystal_grow.temp
Revision 1.4May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CARBOXY TERMINUS OF HSP70-INTERACTING PROTEIN
B: CARBOXY TERMINUS OF HSP70-INTERACTING PROTEIN
C: CARBOXY TERMINUS OF HSP70-INTERACTING PROTEIN
D: CARBOXY TERMINUS OF HSP70-INTERACTING PROTEIN
E: HSP90
F: HSP90
G: HSP90
H: HSP90
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,15119
Polymers135,2448
Non-polymers90711
Water18010
1
A: CARBOXY TERMINUS OF HSP70-INTERACTING PROTEIN
E: HSP90
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0995
Polymers33,8112
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: CARBOXY TERMINUS OF HSP70-INTERACTING PROTEIN
F: HSP90
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,2388
Polymers33,8112
Non-polymers4276
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
C: CARBOXY TERMINUS OF HSP70-INTERACTING PROTEIN
G: HSP90
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,9073
Polymers33,8112
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
D: CARBOXY TERMINUS OF HSP70-INTERACTING PROTEIN
H: HSP90
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,9073
Polymers33,8112
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)76.042, 204.406, 144.709
Angle α, β, γ (deg.)90.00, 90.75, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.99993, 0.00628, 0.00955), (0.00628, -0.99998, -0.00019), (0.00955, 0.00025, -0.99995)-38.17154, -49.60815, 71.90923
2given(0.99994, 0.00225, 0.01112), (0.00227, -1, -0.00196), (0.01112, 0.00198, -0.99994)-38.27748, -49.44993, 71.97064

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Components

#1: Protein
CARBOXY TERMINUS OF HSP70-INTERACTING PROTEIN / CHIP


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
HSP90


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 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ni
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 4.4 Å3/Da / Density % sol: 71.5 %
Crystal growTemperature: 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.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9801
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 17, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 3.3→3.47 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 2.7 / % possible all: 98.1

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod 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
RfactorNum. reflection% reflectionSelection details
Rfree0.2859 1606 5 %RANDOM
Rwork0.2475 ---
obs0.2475 31916 21.5 %-
Solvent computationSolvent model: FLAT / Bsol: 14.9172 Å2 / ksol: 0.307367 e/Å3
Displacement parametersBiso mean: 80.1 Å2
Baniso -1Baniso -2Baniso -3
1-23.988 Å20 Å20.474 Å2
2--18.4 Å20 Å2
3----42.388 Å2
Refinement stepCycle: LAST / Resolution: 3.3→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9472 0 39 10 9521
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.010001
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.22611
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 3.3→3.49 Å / Total num. of bins used: 7
RfactorNum. reflection% reflection
Rfree0.4412 221 5.22 %
Rwork0.3901 4232 -
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP

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