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- PDB-8gck: Crystal structure of the human CHIP-TPR domain in complex with a ... -

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Basic information

Entry
Database: PDB / ID: 8gck
TitleCrystal structure of the human CHIP-TPR domain in complex with a 6mer acetylated tau peptide
Components
  • ACE-SER-ILE-ASP-MET-VAL-ASP
  • E3 ubiquitin-protein ligase CHIP
KeywordsLIGASE / E3 ligase / ligand / TPR domain
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 / TPR domain binding / protein quality control for misfolded or incompletely synthesized proteins / SMAD binding / protein monoubiquitination / negative regulation of smooth muscle cell apoptotic process / R-SMAD binding / protein K63-linked ubiquitination / positive regulation of proteolysis / protein maturation / protein autoubiquitination / ERAD pathway / ubiquitin ligase complex / endoplasmic reticulum unfolded protein response / heat shock protein binding / Hsp70 protein binding / Downregulation of TGF-beta receptor signaling / positive regulation of protein ubiquitination / response to ischemia / G protein-coupled receptor binding / 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 / MAPK cascade / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / 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 / cytoplasm / cytosol
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 / TPR repeat region circular profile. / TPR repeat 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 / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
E3 ubiquitin-protein ligase CHIP
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.36823537069 Å
AuthorsWucherer, K. / Bohn, M.F. / Basu, K. / Nadel, C.M. / Gestwicki, J.E. / Craik, C.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Aging (NIH/NIA)RF1AG068125 United States
CitationJournal: To Be Published
Title: Intersecting PTMs regulate clearance of pathogenic tau by the ubiquitin ligase CHIP.
Authors: Nadel, C.M. / Wucherer, K.N. / Thwin, A. / Southworth, D. / Gestwicki, J.E.
History
DepositionMar 2, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 6, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: E3 ubiquitin-protein ligase CHIP
A: E3 ubiquitin-protein ligase CHIP
E: ACE-SER-ILE-ASP-MET-VAL-ASP
C: ACE-SER-ILE-ASP-MET-VAL-ASP


Theoretical massNumber of molelcules
Total (without water)30,7414
Polymers30,7414
Non-polymers00
Water4,089227
1
B: E3 ubiquitin-protein ligase CHIP
E: ACE-SER-ILE-ASP-MET-VAL-ASP


Theoretical massNumber of molelcules
Total (without water)15,3712
Polymers15,3712
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1180 Å2
ΔGint-5 kcal/mol
Surface area7470 Å2
MethodPISA
2
A: E3 ubiquitin-protein ligase CHIP
C: ACE-SER-ILE-ASP-MET-VAL-ASP


Theoretical massNumber of molelcules
Total (without water)15,3712
Polymers15,3712
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1070 Å2
ΔGint-7 kcal/mol
Surface area7440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.745, 65.717, 77.237
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11B-223-

HOH

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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: 14665.716 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 (E. coli)
References: UniProt: Q9UNE7, RING-type E3 ubiquitin transferase
#2: Protein/peptide ACE-SER-ILE-ASP-MET-VAL-ASP


Mass: 704.791 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 227 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 34.46 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 0.1 M CaCl2, 0.1 M HEPES pH 7.4, 25% PEG 3350

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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: Apr 16, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.116 Å / Relative weight: 1
ReflectionResolution: 1.368→45.75 Å / Num. obs: 49457 / % possible obs: 99.15 % / Redundancy: 11.8 % / Biso Wilson estimate: 14.6039888245 Å2 / CC1/2: 0.996 / CC star: 0.999 / Net I/σ(I): 7.61
Reflection shellResolution: 1.368→1.417 Å / Num. unique obs: 4695 / CC1/2: 0.406 / CC star: 0.76 / % possible all: 94.96

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
xia2data reduction
xia2data scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.36823537069→45.7453 Å / SU ML: 0.158961093042 / Cross valid method: FREE R-VALUE / σ(F): 1.33601201102 / Phase error: 22.9206234848
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.209939305154 2428 4.90941442899 %
Rwork0.192428531184 47028 -
obs0.193268926362 49456 99.1539356029 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.5993112746 Å2
Refinement stepCycle: LAST / Resolution: 1.36823537069→45.7453 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2133 0 0 227 2360
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006333216646272209
X-RAY DIFFRACTIONf_angle_d0.8420011238782980
X-RAY DIFFRACTIONf_chiral_restr0.0662691597612315
X-RAY DIFFRACTIONf_plane_restr0.00499777544871396
X-RAY DIFFRACTIONf_dihedral_angle_d21.7945516929861
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.36823537069-1.39620.3600718449281300.3241554837332527X-RAY DIFFRACTION91.937716263
1.3962-1.42650.3028936050821470.2903316417222756X-RAY DIFFRACTION99.3837726806
1.4265-1.45970.2531304932661340.2718138300052707X-RAY DIFFRACTION99.3356643357
1.4597-1.49620.2931223595011530.2515793342932711X-RAY DIFFRACTION99.1689750693
1.4962-1.53670.2648634416291500.2410345404092739X-RAY DIFFRACTION99.4834710744
1.5367-1.58190.278072299961430.2295788436072742X-RAY DIFFRACTION99.7234704459
1.5819-1.6330.2251981908681530.2179366907482753X-RAY DIFFRACTION99.4864772338
1.633-1.69130.2357365295571570.2032680343872737X-RAY DIFFRACTION99.6556473829
1.6913-1.7590.2171883597911280.2053972741582779X-RAY DIFFRACTION99.7940267765
1.759-1.83910.2196656033741400.196961237292761X-RAY DIFFRACTION99.588053553
1.8391-1.93610.2067663693021510.1923057447352755X-RAY DIFFRACTION99.6912521441
1.9361-2.05740.190238088281400.1821346045342781X-RAY DIFFRACTION99.7950119576
2.0574-2.21620.1887555265141450.1736950848782787X-RAY DIFFRACTION99.7618237496
2.2162-2.43920.1886578514411320.1752654155442822X-RAY DIFFRACTION99.7972972973
2.4392-2.79210.1786205508451350.1831207801962817X-RAY DIFFRACTION99.5951417004
2.7921-3.51760.2091330487011560.177082601492845X-RAY DIFFRACTION99.5686794957
3.5176-45.74530.1920960952481340.1776846737773009X-RAY DIFFRACTION99.7461123453

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