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- PDB-3q4a: Crystal structure of the TPR domain of CHIP complexed with phosph... -

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Basic information

Entry
Database: PDB / ID: 3q4a
TitleCrystal structure of the TPR domain of CHIP complexed with phosphorylated Smad1 peptide
Components
  • STIP1 homology and U box-containing protein 1
  • Smad1 peptide
KeywordsLIGASE/TRANSCRIPTION / E3 ubiquitin ligase / LIGASE-TRANSCRIPTION complex
Function / homology
Function and homology information


mesodermal cell fate commitment / homomeric SMAD protein complex / positive regulation of chaperone-mediated protein complex assembly / osteoblast fate commitment / Downregulation of TGF-beta receptor signaling / SMAD protein complex / regulation of glucocorticoid metabolic process / negative regulation of vascular associated smooth muscle contraction / Downregulation of ERBB2 signaling / RUNX2 regulates bone development ...mesodermal cell fate commitment / homomeric SMAD protein complex / positive regulation of chaperone-mediated protein complex assembly / osteoblast fate commitment / Downregulation of TGF-beta receptor signaling / SMAD protein complex / regulation of glucocorticoid metabolic process / negative regulation of vascular associated smooth muscle contraction / Downregulation of ERBB2 signaling / RUNX2 regulates bone development / Regulation of TNFR1 signaling / heteromeric SMAD protein complex / negative regulation of peroxisome proliferator activated receptor signaling pathway / Regulation of PTEN stability and activity / co-SMAD binding / Regulation of RUNX2 expression and activity / Regulation of necroptotic cell death / negative regulation of muscle cell differentiation / positive regulation of cartilage development / ubiquitin conjugating enzyme complex / DEAD/H-box RNA helicase binding / positive regulation of ERAD pathway / primary miRNA binding / positive regulation of smooth muscle cell apoptotic process / positive regulation of mitophagy / negative regulation of cardiac muscle hypertrophy / gamete generation / hindbrain development / cardiac conduction system development / primary miRNA processing / nuclear inclusion body / SMAD protein signal transduction / Signaling by BMP / embryonic pattern specification / misfolded protein binding / I-SMAD binding / Antigen processing: Ubiquitination & Proteasome degradation / cartilage development / nuclear inner membrane / cellular response to misfolded protein / Cardiogenesis / protein folding chaperone complex / positive regulation of dendrite development / positive regulation of ubiquitin-protein transferase activity / ureteric bud development / ubiquitin-ubiquitin ligase activity / chaperone-mediated autophagy / positive regulation of sprouting angiogenesis / midbrain development / TPR domain binding / negative regulation of smooth muscle cell apoptotic process / protein quality control for misfolded or incompletely synthesized proteins / R-SMAD binding / positive regulation of proteolysis / anatomical structure morphogenesis / protein K63-linked ubiquitination / protein monoubiquitination / ubiquitin ligase complex / cardiac muscle cell proliferation / positive regulation of osteoblast differentiation / BMP signaling pathway / endoplasmic reticulum unfolded protein response / negative regulation of protein binding / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / protein autoubiquitination / heat shock protein binding / ERAD pathway / Hsp70 protein binding / transforming growth factor beta receptor signaling pathway / ossification / response to ischemia / positive regulation of protein ubiquitination / male germ cell nucleus / stem cell differentiation / Hsp90 protein binding / negative regulation of transforming growth factor beta receptor signaling pathway / G protein-coupled receptor binding / bone development / RING-type E3 ubiquitin transferase / positive regulation of miRNA transcription / kinase binding / Z disc / protein polyubiquitination / ubiquitin-protein transferase activity / osteoblast differentiation / ubiquitin protein ligase activity / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / protein folding / MAPK cascade / cellular response to heat / DNA-binding transcription activator activity, RNA polymerase II-specific / ubiquitin-dependent protein catabolic process / protein-macromolecule adaptor activity / cellular response to hypoxia / proteasome-mediated ubiquitin-dependent protein catabolic process / intracellular iron ion homeostasis / transcription by RNA polymerase II / DNA-binding transcription factor activity, RNA polymerase II-specific / cell differentiation / Ub-specific processing proteases
Similarity search - Function
CHIP, N-terminal tetratricopeptide repeat domain / CHIP/LubX , U box domain / CHIP N-terminal tetratricopeptide repeat domain / MAD homology, MH1 / Dwarfin / SMAD MH1 domain superfamily / MAD homology domain 1 (MH1) profile. / SMAD domain, Dwarfin-type / MH2 domain / MAD homology domain 2 (MH2) profile. ...CHIP, N-terminal tetratricopeptide repeat domain / CHIP/LubX , U box domain / CHIP N-terminal tetratricopeptide repeat domain / MAD homology, MH1 / Dwarfin / SMAD MH1 domain superfamily / MAD homology domain 1 (MH1) profile. / SMAD domain, Dwarfin-type / MH2 domain / MAD homology domain 2 (MH2) profile. / Domain B in dwarfin family proteins / MAD homology 1, Dwarfin-type / MH1 domain / Domain A in dwarfin family proteins / SMAD-like domain superfamily / Anaphase-promoting complex, cyclosome, subunit 3 / U-box domain / U-box domain profile. / Modified RING finger domain / U-box domain / Tetratricopeptide repeat domain / SMAD/FHA domain superfamily / 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
Mothers against decapentaplegic homolog 1 / E3 ubiquitin-protein ligase CHIP
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.542 Å
AuthorsWang, L. / Chen, L. / Wu, J.W.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Molecular Mechanism of the Negative Regulation of Smad1/5 Protein by Carboxyl Terminus of Hsc70-interacting Protein (CHIP).
Authors: Wang, L. / Liu, Y.T. / Hao, R. / Chen, L. / Chang, Z. / Wang, H.R. / Wang, Z.X. / Wu, J.W.
History
DepositionDec 23, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 16, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: STIP1 homology and U box-containing protein 1
C: Smad1 peptide


Theoretical massNumber of molelcules
Total (without water)16,9192
Polymers16,9192
Non-polymers00
Water3,333185
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area980 Å2
ΔGint-9 kcal/mol
Surface area7840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.132, 77.444, 36.456
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein STIP1 homology and U box-containing protein 1


Mass: 15733.964 Da / Num. of mol.: 1 / Fragment: TPR domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Stub1, Chip / Plasmid: pET-Duet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9WUD1, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Protein/peptide Smad1 peptide


Mass: 1185.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: The peptide was chemically synthesized. / Source: (synth.) Homo sapiens (human) / References: UniProt: Q15797*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 185 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.92 Å3/Da / Density % sol: 36.09 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 100mM Bis-tris propane pH 7.0, 40% PEG MME 2000, 1% PEG MME 550, 50mM magnesium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97924 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 12, 2009
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97924 Å / Relative weight: 1
ReflectionResolution: 1.54→33 Å / Num. all: 19828 / Num. obs: 19797 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.7 % / Rmerge(I) obs: 0.053 / Net I/σ(I): 57.7
Reflection shellResolution: 1.54→1.57 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.171 / Mean I/σ(I) obs: 11.8 / % possible all: 97.9

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2C2L

2c2l


Resolution: 1.542→32.984 Å / SU ML: 0.16 / σ(F): 1.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.208 1011 5.11 %RANDOM
Rwork0.1684 ---
obs0.1703 19797 99.41 %-
all-19828 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 82.234 Å2 / ksol: 0.379 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-3.5559 Å20 Å2-0 Å2
2--0.8051 Å20 Å2
3----3.3033 Å2
Refinement stepCycle: LAST / Resolution: 1.542→32.984 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1114 0 0 185 1299
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011132
X-RAY DIFFRACTIONf_angle_d1.0281525
X-RAY DIFFRACTIONf_dihedral_angle_d16.94435
X-RAY DIFFRACTIONf_chiral_restr0.068159
X-RAY DIFFRACTIONf_plane_restr0.004201
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.5417-1.6230.19691430.1532257699
1.623-1.72470.20181460.16342666100
1.7247-1.85780.21241580.16282627100
1.8578-2.04480.21281450.16782689100
2.0448-2.34060.19721500.15662671100
2.3406-2.94860.2121410.1752741100
2.9486-32.99170.19681280.1639281698

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