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- PDB-6nsv: Crystal structure of the human CHIP TPR domain in complex with a ... -

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Basic information

Entry
Database: PDB / ID: 6nsv
TitleCrystal structure of the human CHIP TPR domain in complex with a 5mer acetylated optimized peptide
Components
  • ACE-LEU-TRP-TRP-PRO-ASP
  • E3 ubiquitin-protein ligase CHIP
KeywordsLIGASE / CHIP
Function / homology
Function and homology information


positive regulation of chaperone-mediated protein complex assembly / regulation of glucocorticoid metabolic process / ubiquitin conjugating enzyme complex / positive regulation of ERAD pathway / positive regulation of mitophagy / ERBB2 signaling pathway / positive regulation of smooth muscle cell apoptotic process / nuclear inclusion body / misfolded protein binding / protein folding chaperone complex ...positive regulation of chaperone-mediated protein complex assembly / regulation of glucocorticoid metabolic process / ubiquitin conjugating enzyme complex / positive regulation of ERAD pathway / positive regulation of mitophagy / ERBB2 signaling pathway / positive regulation of smooth muscle cell apoptotic process / nuclear inclusion body / misfolded protein binding / protein folding chaperone complex / cellular response to misfolded protein / ubiquitin-ubiquitin ligase activity / RIPK1-mediated regulated necrosis / chaperone-mediated autophagy / protein quality control for misfolded or incompletely synthesized proteins / TPR domain binding / ERAD pathway / SMAD binding / protein monoubiquitination / protein K63-linked ubiquitination / positive regulation of proteolysis / negative regulation of smooth muscle cell apoptotic process / R-SMAD binding / protein maturation / protein autoubiquitination / endoplasmic reticulum unfolded protein response / ubiquitin ligase complex / Hsp70 protein binding / heat shock protein binding / Downregulation of TGF-beta receptor signaling / positive regulation of protein ubiquitination / G protein-coupled receptor binding / response to ischemia / Regulation of TNFR1 signaling / negative regulation of transforming growth factor beta receptor signaling pathway / Hsp90 protein binding / RING-type E3 ubiquitin transferase / regulation of protein stability / tau protein binding / Regulation of necroptotic cell death / Downregulation of ERBB2 signaling / kinase binding / Z disc / Regulation of PTEN stability and activity / protein polyubiquitination / ubiquitin-protein transferase activity / Regulation of RUNX2 expression and activity / ubiquitin protein ligase activity / MAPK cascade / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Antigen processing: Ubiquitination & Proteasome degradation / protein-macromolecule adaptor activity / cellular response to heat / protein-folding chaperone binding / cellular response to hypoxia / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / protein stabilization / protein ubiquitination / DNA repair / ubiquitin protein ligase binding / enzyme binding / endoplasmic reticulum / protein homodimerization activity / mitochondrion / nucleoplasm / nucleus / cytosol / cytoplasm
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 / TPR repeat region circular profile. ...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 / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Zinc finger, RING/FYVE/PHD-type / Mainly Alpha
Similarity search - Domain/homology
E3 ubiquitin-protein ligase CHIP
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.305 Å
AuthorsBasu, K. / Ravalin, M. / Bohn, M.-F. / Craik, C.S. / Gestwicki, J.E.
CitationJournal: Nat.Chem.Biol. / Year: 2019
Title: Specificity for latent C termini links the E3 ubiquitin ligase CHIP to caspases.
Authors: Ravalin, M. / Theofilas, P. / Basu, K. / Opoku-Nsiah, K.A. / Assimon, V.A. / Medina-Cleghorn, D. / Chen, Y.F. / Bohn, M.F. / Arkin, M. / Grinberg, L.T. / Craik, C.S. / Gestwicki, J.E.
History
DepositionJan 25, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 31, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: E3 ubiquitin-protein ligase CHIP
B: E3 ubiquitin-protein ligase CHIP
C: ACE-LEU-TRP-TRP-PRO-ASP
D: ACE-LEU-TRP-TRP-PRO-ASP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8579
Polymers31,3004
Non-polymers5585
Water4,216234
1
A: E3 ubiquitin-protein ligase CHIP
C: ACE-LEU-TRP-TRP-PRO-ASP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,9465
Polymers15,6502
Non-polymers2973
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1960 Å2
ΔGint-28 kcal/mol
Surface area7340 Å2
MethodPISA
2
B: E3 ubiquitin-protein ligase CHIP
D: ACE-LEU-TRP-TRP-PRO-ASP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,9114
Polymers15,6502
Non-polymers2612
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1790 Å2
ΔGint-15 kcal/mol
Surface area7520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.219, 71.920, 77.790
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

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Protein / Protein/peptide , 2 types, 4 molecules ABCD

#1: Protein E3 ubiquitin-protein ligase CHIP / Antigen NY-CO-7 / CLL-associated antigen KW-8 / Carboxy terminus of Hsp70-interacting protein / ...Antigen NY-CO-7 / CLL-associated antigen KW-8 / Carboxy terminus of Hsp70-interacting protein / RING-type E3 ubiquitin transferase CHIP / STIP1 homology and U box-containing protein 1


Mass: 14907.922 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: STUB1, CHIP, PP1131 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q9UNE7, RING-type E3 ubiquitin transferase
#2: Protein/peptide ACE-LEU-TRP-TRP-PRO-ASP


Mass: 741.833 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 4 types, 239 molecules

#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 / Polyethylene glycol


Mass: 238.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 234 / 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: 2.08 Å3/Da / Density % sol: 40.94 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.05 M CaCl2, 0.1 M HEPES pH 7, 28% PEG 4K, 0.01 M CoCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1158 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 29, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1158 Å / Relative weight: 1
ReflectionResolution: 1.305→39.73 Å / Num. obs: 60500 / % possible obs: 94.66 % / Redundancy: 2 % / Net I/σ(I): 11.09
Reflection shellResolution: 1.305→1.352 Å

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
MOSFLMdata reduction
Aimlessdata scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3Q49

3q49


Resolution: 1.305→39.735 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2427 2970 4.92 %
Rwork0.2141 --
obs0.2155 60399 94.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.305→39.735 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2166 0 35 234 2435
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092254
X-RAY DIFFRACTIONf_angle_d1.123031
X-RAY DIFFRACTIONf_dihedral_angle_d18.218861
X-RAY DIFFRACTIONf_chiral_restr0.065310
X-RAY DIFFRACTIONf_plane_restr0.006397
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.305-1.32640.47461340.46262549X-RAY DIFFRACTION89
1.3264-1.34930.47131380.45492553X-RAY DIFFRACTION90
1.3493-1.37380.45351350.42942535X-RAY DIFFRACTION89
1.3738-1.40020.39791330.42212541X-RAY DIFFRACTION89
1.4002-1.42880.45221290.39032575X-RAY DIFFRACTION90
1.4288-1.45990.35971510.35582551X-RAY DIFFRACTION90
1.4599-1.49380.38051510.33492608X-RAY DIFFRACTION91
1.4938-1.53120.32381560.29742633X-RAY DIFFRACTION92
1.5312-1.57260.28141300.27192636X-RAY DIFFRACTION93
1.5726-1.61890.26811370.25532633X-RAY DIFFRACTION92
1.6189-1.67110.3031210.24322716X-RAY DIFFRACTION94
1.6711-1.73080.28051440.22922761X-RAY DIFFRACTION96
1.7308-1.80010.28361200.22242822X-RAY DIFFRACTION97
1.8001-1.88210.24121410.20662820X-RAY DIFFRACTION98
1.8821-1.98130.24071580.20282840X-RAY DIFFRACTION99
1.9813-2.10540.2051540.1872899X-RAY DIFFRACTION100
2.1054-2.2680.23111310.17462908X-RAY DIFFRACTION100
2.268-2.49620.22191460.17692898X-RAY DIFFRACTION100
2.4962-2.85730.18291380.18272927X-RAY DIFFRACTION99
2.8573-3.59950.20251470.17252959X-RAY DIFFRACTION99
3.5995-39.7530.19411760.17723065X-RAY DIFFRACTION99

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