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- PDB-4cgu: Full length Tah1 bound to yeast PIH1 and HSP90 peptide SRMEEVD -

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Basic information

Entry
Database: PDB / ID: 4cgu
TitleFull length Tah1 bound to yeast PIH1 and HSP90 peptide SRMEEVD
Components
  • HEAT SHOCK PROTEIN HSP 90-ALPHA
  • PROTEIN INTERACTING WITH HSP90 1
  • TPR REPEAT-CONTAINING PROTEIN ASSOCIATED WITH HSP90
KeywordsCHAPERONE/PEPTIDE / CHAPERONE-PEPTIDE COMPLEX / CHAPERONE / R2TP / TAH1 / HSP90 / PIH1
Function / homology
Function and homology information


R2TP complex / box C/D snoRNP assembly / sperm mitochondrial sheath / sulfonylurea receptor binding / dATP binding / CTP binding / positive regulation of protein polymerization / Scavenging by Class F Receptors / vRNP Assembly / UTP binding ...R2TP complex / box C/D snoRNP assembly / sperm mitochondrial sheath / sulfonylurea receptor binding / dATP binding / CTP binding / positive regulation of protein polymerization / Scavenging by Class F Receptors / vRNP Assembly / UTP binding / sperm plasma membrane / chaperone-mediated autophagy / Rho GDP-dissociation inhibitor binding / regulation of cell size / Respiratory syncytial virus genome replication / telomerase holoenzyme complex assembly / mitochondrial transport / Uptake and function of diphtheria toxin / Drug-mediated inhibition of ERBB2 signaling / Resistance of ERBB2 KD mutants to trastuzumab / Resistance of ERBB2 KD mutants to sapitinib / Resistance of ERBB2 KD mutants to tesevatinib / Resistance of ERBB2 KD mutants to neratinib / Resistance of ERBB2 KD mutants to osimertinib / Resistance of ERBB2 KD mutants to afatinib / Resistance of ERBB2 KD mutants to AEE788 / Resistance of ERBB2 KD mutants to lapatinib / Drug resistance in ERBB2 TMD/JMD mutants / protein import into mitochondrial matrix / dendritic growth cone / TPR domain binding / PIWI-interacting RNA (piRNA) biogenesis / Assembly and release of respiratory syncytial virus (RSV) virions / non-chaperonin molecular chaperone ATPase / protein unfolding / Sema3A PAK dependent Axon repulsion / regulation of protein ubiquitination / positive regulation of cell size / HSF1-dependent transactivation / response to unfolded protein / enzyme-substrate adaptor activity / skeletal muscle contraction / regulation of protein-containing complex assembly / HSF1 activation / telomere maintenance via telomerase / Attenuation phase / chaperone-mediated protein complex assembly / axonal growth cone / neurofibrillary tangle assembly / regulation of postsynaptic membrane neurotransmitter receptor levels / RHOBTB2 GTPase cycle / positive regulation of lamellipodium assembly / nitric oxide metabolic process / eNOS activation / positive regulation of defense response to virus by host / DNA polymerase binding / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / response to salt stress / positive regulation of telomere maintenance via telomerase / Signaling by ERBB2 / cardiac muscle cell apoptotic process / endocytic vesicle lumen / positive regulation of cardiac muscle contraction / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / activation of innate immune response / lysosomal lumen / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / positive regulation of interferon-beta production / RNA splicing / ESR-mediated signaling / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / protein tyrosine kinase binding / response to cold / Constitutive Signaling by Overexpressed ERBB2 / AURKA Activation by TPX2 / nitric-oxide synthase regulator activity / VEGFR2 mediated vascular permeability / response to cocaine / ATP-dependent protein folding chaperone / brush border membrane / Signaling by ERBB2 TMD/JMD mutants / Constitutive Signaling by EGFRvIII / Signaling by ERBB2 ECD mutants / DDX58/IFIH1-mediated induction of interferon-alpha/beta / Signaling by ERBB2 KD Mutants / cellular response to virus / Regulation of actin dynamics for phagocytic cup formation / Regulation of necroptotic cell death / positive regulation of protein import into nucleus / VEGFA-VEGFR2 Pathway / response to estrogen / tau protein binding / Downregulation of ERBB2 signaling / histone deacetylase binding / mRNA processing / Chaperone Mediated Autophagy / neuron migration
Similarity search - Function
Immunoglobulin-like - #4160 / Pih1, Ascomycota, CS domain / Fungal Pih1 CS domain / PIH1, N-terminal / : / PIH1 N-terminal domain / : / Tetratricopeptide repeat / Heat shock protein Hsp90, conserved site / Heat shock hsp90 proteins family signature. ...Immunoglobulin-like - #4160 / Pih1, Ascomycota, CS domain / Fungal Pih1 CS domain / PIH1, N-terminal / : / PIH1 N-terminal domain / : / Tetratricopeptide repeat / Heat shock protein Hsp90, conserved site / Heat shock hsp90 proteins family signature. / HSP90, C-terminal domain / Heat shock protein Hsp90, N-terminal / Heat shock protein Hsp90 family / Hsp90 protein / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / TPR repeat region circular profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase superfamily / Tetratricopeptide-like helical domain superfamily / Ribosomal protein S5 domain 2-type fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Heat shock protein HSP 90-alpha / TPR repeat-containing protein associated with Hsp90 / Protein interacting with Hsp90 1
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
HOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SAD / Resolution: 2.11 Å
AuthorsRoe, S.M. / Pal, M.
CitationJournal: Structure / Year: 2014
Title: Structural Basis for Phosphorylation-Dependent Recruitment of Tel2 to Hsp90 by Pih1.
Authors: Pal, M. / Morgan, M. / Phelps, S.E. / Roe, S.M. / Parry-Morris, S. / Downs, J.A. / Polier, S. / Pearl, L.H. / Prodromou, C.
History
DepositionNov 26, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 14, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 25, 2014Group: Database references
Revision 1.2Jun 28, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.3Oct 9, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TPR REPEAT-CONTAINING PROTEIN ASSOCIATED WITH HSP90
B: PROTEIN INTERACTING WITH HSP90 1
C: HEAT SHOCK PROTEIN HSP 90-ALPHA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8414
Polymers31,7493
Non-polymers921
Water1,60389
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3260 Å2
ΔGint-8.2 kcal/mol
Surface area11300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.010, 78.380, 98.790
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein TPR REPEAT-CONTAINING PROTEIN ASSOCIATED WITH HSP90 / TAH1


Mass: 12777.980 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P25638
#2: Protein PROTEIN INTERACTING WITH HSP90 1 / PIH1 / NUCLEOLAR PROTEIN 17


Mass: 18105.193 Da / Num. of mol.: 1 / Fragment: C-TERMINAL DOMAIN, RESIDUES 187-344
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P38768
#3: Protein/peptide HEAT SHOCK PROTEIN HSP 90-ALPHA / HSP90 / HEAT SHOCK 86 KDA / HSP 86 / HSP86 / RENAL CARCINOMA ANTIGEN NY-REN-38


Mass: 865.929 Da / Num. of mol.: 1 / Fragment: C-TERMINAL PEPTIDE, RESIDUES 726-732 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: P07900
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 89 / 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: 2.25 Å3/Da / Density % sol: 44.97 % / Description: NONE
Crystal growpH: 7 / Details: pH 7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5419
DetectorType: RIGAKU CCD / Detector: CCD / Date: Mar 15, 2013 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5419 Å / Relative weight: 1
ReflectionResolution: 2.11→39.19 Å / Num. obs: 12533 / % possible obs: 97.4 % / Observed criterion σ(I): 0 / Redundancy: 56.6 % / Biso Wilson estimate: 23.48 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 83.7
Reflection shellResolution: 2.11→2.16 Å / Redundancy: 3 % / Rmerge(I) obs: 0.21 / Mean I/σ(I) obs: 5.7 / % possible all: 67.3

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
xia2data reduction
xia2data scaling
SHELXphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.11→39.19 Å / SU ML: 0.18 / σ(F): 1.13 / Phase error: 20.42 / Stereochemistry target values: ML
Details: RESIDUES 187-263 MISSING, PRESUMABLY DISORDERED OR CLEAVED, IN PIH1
RfactorNum. reflection% reflection
Rfree0.2101 1122 4.8 %
Rwork0.1688 --
obs0.1708 12510 96.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.11→39.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1601 0 6 89 1696
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051661
X-RAY DIFFRACTIONf_angle_d0.9132243
X-RAY DIFFRACTIONf_dihedral_angle_d14.29643
X-RAY DIFFRACTIONf_chiral_restr0.057243
X-RAY DIFFRACTIONf_plane_restr0.004294
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.11-2.2060.26521020.20742026X-RAY DIFFRACTION71
2.206-2.32230.26131360.19672873X-RAY DIFFRACTION100
2.3223-2.46780.26451730.19292852X-RAY DIFFRACTION100
2.4678-2.65830.24971300.18712906X-RAY DIFFRACTION100
2.6583-2.92570.26151440.18512858X-RAY DIFFRACTION100
2.9257-3.34890.18511560.1722859X-RAY DIFFRACTION100
3.3489-4.21850.17621430.14742895X-RAY DIFFRACTION100
4.2185-39.19670.17421380.14812879X-RAY DIFFRACTION100

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