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

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Basic information

Entry
Database: PDB / ID: 6efk
TitleCrystal structure of the human CHIP TPR domain in complex with a 5mer acetylated HSP70 peptide
Components
  • ACE-ILE-GLU-GLU-VAL-ASP
  • E3 ubiquitin-protein ligase CHIP
KeywordsLIGASE / C-terminus of Hsc70-interacting protein / Heat Shock Protein 70 / CHIP / HSP70
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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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
DepositionAug 16, 2018Deposition 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 / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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-ILE-GLU-GLU-VAL-ASP
D: ACE-ILE-GLU-GLU-VAL-ASP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,7275
Polymers31,7044
Non-polymers231
Water5,134285
1
A: E3 ubiquitin-protein ligase CHIP
D: ACE-ILE-GLU-GLU-VAL-ASP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8753
Polymers15,8522
Non-polymers231
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1300 Å2
ΔGint-12 kcal/mol
Surface area7710 Å2
MethodPISA
2
B: E3 ubiquitin-protein ligase CHIP
C: ACE-ILE-GLU-GLU-VAL-ASP


Theoretical massNumber of molelcules
Total (without water)15,8522
Polymers15,8522
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1160 Å2
ΔGint-4 kcal/mol
Surface area7700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.709, 70.342, 77.072
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#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: 15222.310 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-ILE-GLU-GLU-VAL-ASP


Mass: 629.657 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 285 / 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 Å3/Da / Density % sol: 38.4 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 0.4 M CaCl2, 0.1 M HEPES (pH 7.5), 25% PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.116 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 8, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.116 Å / Relative weight: 1
ReflectionResolution: 1.5→39.95 Å / Num. obs: 40943 / % possible obs: 96.64 % / Redundancy: 11.5 % / Net I/σ(I): 9.42
Reflection shellResolution: 1.5→1.554 Å / Redundancy: 7.1 % / Mean I/σ(I) obs: 1.55 / Num. unique obs: 3686 / % possible all: 86.34

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
xia2data reduction
xia2data scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3Q49

3q49


Resolution: 1.5→39.946 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.2
RfactorNum. reflection% reflection
Rfree0.244 1921 4.8 %
Rwork0.2108 --
obs0.2124 39998 96.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.5→39.946 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2191 0 1 285 2477
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072252
X-RAY DIFFRACTIONf_angle_d0.8443035
X-RAY DIFFRACTIONf_dihedral_angle_d23.474877
X-RAY DIFFRACTIONf_chiral_restr0.288323
X-RAY DIFFRACTIONf_plane_restr0.005407
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5001-1.53760.30431220.34632431X-RAY DIFFRACTION88
1.5376-1.57910.4417900.40582114X-RAY DIFFRACTION76
1.5791-1.62560.36211340.29672697X-RAY DIFFRACTION97
1.6256-1.67810.26511270.29582741X-RAY DIFFRACTION98
1.6781-1.73810.33011430.29992636X-RAY DIFFRACTION95
1.7381-1.80770.27111590.24222764X-RAY DIFFRACTION100
1.8077-1.88990.26181310.21552784X-RAY DIFFRACTION100
1.8899-1.98960.23281500.20772765X-RAY DIFFRACTION100
1.9896-2.11420.23991500.19952813X-RAY DIFFRACTION100
2.1142-2.27740.2151390.17662800X-RAY DIFFRACTION100
2.2774-2.50660.19751400.18462824X-RAY DIFFRACTION100
2.5066-2.86920.23441350.19692832X-RAY DIFFRACTION100
2.8692-3.61450.21471530.17782868X-RAY DIFFRACTION100
3.6145-39.95990.23081480.17693008X-RAY DIFFRACTION100

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