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- PDB-9dya: CHIP-TPR in complex with the Hsp70 tail -

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Basic information

Entry
Database: PDB / ID: 9dya
TitleCHIP-TPR in complex with the Hsp70 tail
Components
  • E3 ubiquitin-protein ligase CHIP
  • Heat shock 70 kDa protein 1A
KeywordsLIGASE / ubiquitin ligase / chaperone
Function / homology
Function and homology information


positive regulation of chaperone-mediated protein complex assembly / regulation of glucocorticoid metabolic process / negative regulation of vascular associated smooth muscle contraction / negative regulation of peroxisome proliferator activated receptor signaling pathway / : / denatured protein binding / ubiquitin conjugating enzyme complex / positive regulation of ERAD pathway / cellular heat acclimation / positive regulation of mitophagy ...positive regulation of chaperone-mediated protein complex assembly / regulation of glucocorticoid metabolic process / negative regulation of vascular associated smooth muscle contraction / negative regulation of peroxisome proliferator activated receptor signaling pathway / : / denatured protein binding / ubiquitin conjugating enzyme complex / positive regulation of ERAD pathway / cellular heat acclimation / positive regulation of mitophagy / positive regulation of smooth muscle cell apoptotic process / negative regulation of inclusion body assembly / ERBB2 signaling pathway / Viral RNP Complexes in the Host Cell Nucleus / negative regulation of cardiac muscle hypertrophy / death receptor agonist activity / C3HC4-type RING finger domain binding / positive regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway / nuclear inclusion body / positive regulation of microtubule nucleation / ATP-dependent protein disaggregase activity / misfolded protein binding / positive regulation of tumor necrosis factor-mediated signaling pathway / negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / regulation of mitotic spindle assembly / cellular response to misfolded protein / protein folding chaperone complex / aggresome / lysosomal transport / RIPK1-mediated regulated necrosis / ubiquitin-ubiquitin ligase activity / cellular response to steroid hormone stimulus / chaperone-mediated autophagy / SMAD binding / TPR domain binding / mRNA catabolic process / negative regulation of smooth muscle cell apoptotic process / : / R-SMAD binding / protein quality control for misfolded or incompletely synthesized proteins / positive regulation of proteolysis / regulation of protein ubiquitination / protein K63-linked ubiquitination / cellular response to unfolded protein / HSF1-dependent transactivation / Regulation of HSF1-mediated heat shock response / protein monoubiquitination / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / response to unfolded protein / ubiquitin ligase complex / Mitochondrial unfolded protein response (UPRmt) / Attenuation phase / chaperone-mediated protein complex assembly / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / ATP metabolic process / endoplasmic reticulum unfolded protein response / transcription regulator inhibitor activity / protein autoubiquitination / heat shock protein binding / ERAD pathway / inclusion body / protein folding chaperone / centriole / negative regulation of protein ubiquitination / Hsp70 protein binding / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / positive regulation of erythrocyte differentiation / positive regulation of RNA splicing / positive regulation of protein ubiquitination / Downregulation of TGF-beta receptor signaling / response to ischemia / positive regulation of interleukin-8 production / AUF1 (hnRNP D0) binds and destabilizes mRNA / ATP-dependent protein folding chaperone / negative regulation of transforming growth factor beta receptor signaling pathway / Regulation of TNFR1 signaling / Hsp90 protein binding / : / negative regulation of cell growth / G protein-coupled receptor binding / PKR-mediated signaling / RING-type E3 ubiquitin transferase / regulation of protein stability / Regulation of necroptotic cell death / histone deacetylase binding / tau protein binding / kinase binding / Downregulation of ERBB2 signaling / Z disc / Regulation of PTEN stability and activity / protein polyubiquitination / disordered domain specific binding / ubiquitin-protein transferase activity / Regulation of RUNX2 expression and activity / ubiquitin protein ligase activity / transcription corepressor activity / unfolded protein binding / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Antigen processing: Ubiquitination & Proteasome degradation / MAPK cascade
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 / Heat shock hsp70 proteins family signature 2. / Heat shock hsp70 proteins family signature 1. ...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 / Heat shock hsp70 proteins family signature 2. / Heat shock hsp70 proteins family signature 1. / Heat shock hsp70 proteins family signature 3. / Heat shock protein 70, conserved site / Heat shock protein 70kD, peptide-binding domain superfamily / Heat shock protein 70kD, C-terminal domain superfamily / Heat shock protein 70 family / Hsp70 protein / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / ATPase, nucleotide binding domain / Tetratricopeptide-like helical domain superfamily / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
Heat shock 70 kDa protein 1A / E3 ubiquitin-protein ligase CHIP
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å
AuthorsZhang, H. / Nix, J.C. / Page, R.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM128595 United States
Citation
Journal: Biorxiv / Year: 2025
Title: Phosphorylation-State Modulated Binding of HSP70: Structural Insights and Compensatory Protein Engineering.
Authors: Stewart, M. / Paththamperuma, C. / McCann, C. / Cottingim, K. / Zhang, H. / DelVecchio, R. / Peng, I. / Fennimore, E. / Nix, J.C. / Saeed, M.N. / George, K. / Makaroff, K. / Colie, M. / ...Authors: Stewart, M. / Paththamperuma, C. / McCann, C. / Cottingim, K. / Zhang, H. / DelVecchio, R. / Peng, I. / Fennimore, E. / Nix, J.C. / Saeed, M.N. / George, K. / Makaroff, K. / Colie, M. / Paulakonis, E. / Almeida, M.F. / Afolayan, A.J. / Brown, N.G. / Page, R.C. / Schisler, J.C.
#1: Journal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
History
DepositionOct 13, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 26, 2025Provider: repository / Type: Initial release

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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: Heat shock 70 kDa protein 1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,8393
Polymers16,7432
Non-polymers961
Water3,081171
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1230 Å2
ΔGint-14 kcal/mol
Surface area7390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.899, 74.363, 77.634
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-312-

HOH

21A-404-

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: 15884.057 Da / Num. of mol.: 1 / Fragment: TPR domain
Source method: isolated from a genetically manipulated source
Details: residues "GAMGS" at N-terminus are part of the fusion protein added during cloning
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 Heat shock 70 kDa protein 1A / Heat shock 70 kDa protein 1 / HSP70-1 / HSP70.1 / Heat shock protein family A member 1A


Mass: 858.890 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P0DMV8
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 171 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 2.02 Å3/Da / Density % sol: 39.15 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M lithium sulfate, 0.1 M Tris-HCl, 30% (w/v) PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 5, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.89→39.67 Å / Num. obs: 20723 / % possible obs: 98.93 % / Redundancy: 3.8 % / Biso Wilson estimate: 14.66 Å2 / CC1/2: 0.988 / CC star: 0.997 / Rmerge(I) obs: 0.17 / Rpim(I) all: 0.1011 / Net I/σ(I): 7.05
Reflection shellResolution: 1.89→1.98 Å / Redundancy: 3.2 % / Rmerge(I) obs: 1.014 / Mean I/σ(I) obs: 0.99 / Num. unique obs: 2406 / CC1/2: 0.442 / CC star: 0.783 / Rpim(I) all: 0.6548 / % possible all: 91.46

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Processing

Software
NameVersionClassification
PHENIX1.21rc1_5127refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.89→39.67 Å / SU ML: 0.247 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.7166
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2337 1095 9.92 %
Rwork0.1895 9945 -
obs0.1938 11040 98.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.18 Å2
Refinement stepCycle: LAST / Resolution: 1.89→39.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1086 0 5 171 1262
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00991108
X-RAY DIFFRACTIONf_angle_d1.15591492
X-RAY DIFFRACTIONf_chiral_restr0.0606158
X-RAY DIFFRACTIONf_plane_restr0.0047197
X-RAY DIFFRACTIONf_dihedral_angle_d15.9068422
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.89-1.980.35921220.3311120X-RAY DIFFRACTION91.46
1.98-2.080.2821390.23111236X-RAY DIFFRACTION99.93
2.08-2.210.21661430.19141243X-RAY DIFFRACTION100
2.21-2.380.25511350.18631224X-RAY DIFFRACTION100
2.38-2.620.24571310.18411256X-RAY DIFFRACTION100
2.62-30.28361440.19341258X-RAY DIFFRACTION100
3-3.780.20951360.16161266X-RAY DIFFRACTION100
3.78-39.670.17081450.16751342X-RAY DIFFRACTION99.87
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.851127101390.00826902529803-0.1459566098312.74694678154-0.203879531125.20656961-0.0946215810109-0.042684805177-0.1759732141970.14628915812-0.0247807334604-0.1160089070290.1339161344170.242968824090.09192947610790.05623373968630.01615065612130.002782865643430.05760398571430.006980834232830.1102686625565.29251504548-29.53489345092.66240104607
22.740243698320.1739413060161.696024293352.350855775751.587172476274.388663353620.05182678107160.126021953429-0.0147338987098-0.03277114097660.07257990480460.0407085395830.004771265740480.0656882039328-0.1157684612740.05817157036640.01203128016160.0205196269810.08620634362680.01355402585540.0656318565149-3.4362670912-19.30095541393.49370900594
33.91418215212.782087399541.436469312537.495902522035.411997186686.096024005350.02975799408780.05404467955270.054925508360.000698615449490.0907176035062-0.240258078395-0.1264115812390.234938826927-0.1326852069370.08702668522990.03147828913510.02002435248740.1205645806920.02549706271060.0791778262482-8.0238189278-15.905410871912.853497725
42.316102952390.151776843930.08495798863921.88801379315-0.381366417642.47233742515-0.0289099025913-0.280835637816-0.1214414445080.3011372269530.05240756634120.2649386943180.252168076073-0.27871560651-0.06817518424020.145510043305-0.01851068640970.02018216977920.1748005234360.0514850993640.102559795299-17.2585424488-21.164419444913.0816458415
55.95097540381.67255579299-1.026757077054.021532949530.6236310703265.086207186190.311650010165-0.5202102642790.3550522091020.604683757693-0.2882199297750.2389218795070.08925072068580.148130245404-0.03708923027250.149515417497-0.01615668444780.029965694640.270442969670.04031392855470.114307274433-13.2650982469-14.324705887324.5028128333
66.9640668912-4.36504810892-3.160589835753.817991546861.445119280161.70017746294-0.553662560024-0.297420164021-0.6299580391990.732419819202-0.01913196867540.3426013220160.665930199595-0.1768789835540.5793332263770.338626693312-0.06477988646060.02108731470470.1758565610980.01544574663640.194846674318-5.99998875575-28.956194241311.7753571507
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 23 through 55 )AA23 - 551 - 33
22chain 'A' and (resid 56 through 93 )AA56 - 9334 - 71
33chain 'A' and (resid 94 through 109 )AA94 - 10972 - 87
44chain 'A' and (resid 110 through 133 )AA110 - 13388 - 111
55chain 'A' and (resid 134 through 151 )AA134 - 151112 - 129
66chain 'B' and (resid 641 through 646 )BB641 - 6462 - 7

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