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- PDB-4cgv: First TPR of Spaghetti (RPAP3) bound to HSP90 peptide SRMEEVD -

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Basic information

Entry
Database: PDB / ID: 4cgv
TitleFirst TPR of Spaghetti (RPAP3) bound to HSP90 peptide SRMEEVD
Components
  • HEAT SHOCK PROTEIN HSP 90-ALPHA
  • RNA POLYMERASE II-ASSOCIATED PROTEIN 3
KeywordsCHAPERONE / R2TP / TAH1 / PIH1
Function / homology
Function and homology information


R2TP complex / RPAP3/R2TP/prefoldin-like complex / protein folding chaperone complex / sperm mitochondrial sheath / sulfonylurea receptor binding / dATP binding / CTP binding / positive regulation of protein polymerization / vRNP Assembly / Scavenging by Class F Receptors ...R2TP complex / RPAP3/R2TP/prefoldin-like complex / protein folding chaperone complex / sperm mitochondrial sheath / sulfonylurea receptor binding / dATP binding / CTP binding / positive regulation of protein polymerization / vRNP Assembly / Scavenging by Class F Receptors / UTP binding / sperm plasma membrane / chaperone-mediated autophagy / Rho GDP-dissociation inhibitor binding / Respiratory syncytial virus genome replication / telomerase holoenzyme complex assembly / mitochondrial transport / Uptake and function of diphtheria toxin / protein insertion into mitochondrial outer membrane / 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 / TPR domain binding / PIWI-interacting RNA (piRNA) biogenesis / Assembly and release of respiratory syncytial virus (RSV) virions / non-chaperonin molecular chaperone ATPase / dendritic growth cone / Sema3A PAK dependent Axon repulsion / protein unfolding / positive regulation of cell size / regulation of protein ubiquitination / HSF1-dependent transactivation / response to unfolded protein / enzyme-substrate adaptor activity / skeletal muscle contraction / regulation of postsynaptic membrane neurotransmitter receptor levels / regulation of protein-containing complex assembly / HSF1 activation / telomere maintenance via telomerase / Attenuation phase / chaperone-mediated protein complex assembly / neurofibrillary tangle assembly / axonal growth cone / RHOBTB2 GTPase cycle / positive regulation of lamellipodium assembly / eNOS activation / nitric oxide metabolic process / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / DNA polymerase binding / positive regulation of defense response to virus by host / response to salt stress / Signaling by ERBB2 / cardiac muscle cell apoptotic process / positive regulation of telomere maintenance via telomerase / 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 / nitric-oxide synthase regulator activity / Recruitment of mitotic centrosome proteins and complexes / Recruitment of NuMA to mitotic centrosomes / activation of innate immune response / Anchoring of the basal body to the plasma membrane / lysosomal lumen / positive regulation of interferon-beta production / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / response to cold / ESR-mediated signaling / Constitutive Signaling by Overexpressed ERBB2 / protein tyrosine kinase binding / AURKA Activation by TPX2 / VEGFR2 mediated vascular permeability / ATP-dependent protein folding chaperone / response to cocaine / Signaling by ERBB2 TMD/JMD mutants / brush border membrane / Constitutive Signaling by EGFRvIII / Signaling by ERBB2 ECD mutants / Signaling by ERBB2 KD Mutants / DDX58/IFIH1-mediated induction of interferon-alpha/beta / cellular response to virus / Regulation of actin dynamics for phagocytic cup formation / Regulation of necroptotic cell death / tau protein binding / VEGFA-VEGFR2 Pathway / histone deacetylase binding / positive regulation of protein import into nucleus / Downregulation of ERBB2 signaling / response to estrogen / Chaperone Mediated Autophagy / positive regulation of protein catabolic process / neuron migration / Aggrephagy
Similarity search - Function
: / RNA-polymerase II-associated protein 3-like, C-terminal domain / Potential Monad-binding region of RPAP3 / Tetratricopeptide repeat / Tetratricopeptide repeat / Tetratricopeptide repeat domain / Tetratricopeptide repeat / Heat shock protein Hsp90, conserved site / Heat shock hsp90 proteins family signature. / HSP90, C-terminal domain ...: / RNA-polymerase II-associated protein 3-like, C-terminal domain / Potential Monad-binding region of RPAP3 / Tetratricopeptide repeat / Tetratricopeptide repeat / Tetratricopeptide repeat 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. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Ribosomal protein S5 domain 2-type fold / Mainly Alpha
Similarity search - Domain/homology
Heat shock protein HSP 90-alpha / RNA polymerase II-associated protein 3
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.54 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 1.2May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / 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_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

Downloads & links

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Assembly

Deposited unit
A: RNA POLYMERASE II-ASSOCIATED PROTEIN 3
B: RNA POLYMERASE II-ASSOCIATED PROTEIN 3
C: RNA POLYMERASE II-ASSOCIATED PROTEIN 3
D: RNA POLYMERASE II-ASSOCIATED PROTEIN 3
E: HEAT SHOCK PROTEIN HSP 90-ALPHA
F: HEAT SHOCK PROTEIN HSP 90-ALPHA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,9177
Polymers63,8256
Non-polymers921
Water1,44180
1
B: RNA POLYMERASE II-ASSOCIATED PROTEIN 3
F: HEAT SHOCK PROTEIN HSP 90-ALPHA


Theoretical massNumber of molelcules
Total (without water)16,3892
Polymers16,3892
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area560 Å2
ΔGint-1.7 kcal/mol
Surface area6820 Å2
MethodPISA
2
A: RNA POLYMERASE II-ASSOCIATED PROTEIN 3


Theoretical massNumber of molelcules
Total (without water)15,5231
Polymers15,5231
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: RNA POLYMERASE II-ASSOCIATED PROTEIN 3
E: HEAT SHOCK PROTEIN HSP 90-ALPHA


Theoretical massNumber of molelcules
Total (without water)16,3892
Polymers16,3892
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: RNA POLYMERASE II-ASSOCIATED PROTEIN 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,6152
Polymers15,5231
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.050, 59.120, 65.860
Angle α, β, γ (deg.)63.42, 67.50, 82.43
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND (RESSEQ 128:251 )
211CHAIN D AND (RESSEQ 128:251 )
112CHAIN B AND (RESSEQ 128:251 )
212CHAIN C AND (RESSEQ 128:251 )

NCS ensembles :
ID
1
2

NCS oper:
IDCodeMatrixVector
1given(-0.96454, 0.263937, 0.000842), (0.263937, 0.96454, -0.000358), (-0.000907, -0.000123, -1)8.41701, -1.06655, 2.72084
2given(-0.964958, 0.262404, 0.00071), (0.262405, 0.964954, 0.002638), (7.0E-6, 0.002732, -0.999996)8.41165, -1.10225, 2.7077

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Components

#1: Protein
RNA POLYMERASE II-ASSOCIATED PROTEIN 3 / SPAGHETTI


Mass: 15523.374 Da / Num. of mol.: 4 / Fragment: FIRST TPR, RESIDUES 120-255
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q9H6T3
#2: Protein/peptide HEAT SHOCK PROTEIN HSP 90-ALPHA / HEAT SHOCK 86 KDA / HSP 86 / HSP86 / RENAL CARCINOMA ANTIGEN NY-REN-38 / HSP90


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


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


Mass: 18.015 Da / Num. of mol.: 80 / 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: 2.75 Å3/Da / Density % sol: 55.3 % / Description: NONE
Crystal growpH: 7 / Details: pH 7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 21, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.54→54.83 Å / Num. obs: 20092 / % possible obs: 94 % / Observed criterion σ(I): 0 / Redundancy: 2.7 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 8.1
Reflection shellResolution: 2.54→2.61 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 2 / % possible all: 94.1

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: IN-HOUSE STRUCTURE

Resolution: 2.54→54.832 Å / SU ML: 0.34 / σ(F): 0.12 / Phase error: 32.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2671 1991 5.1 %
Rwork0.2403 --
obs0.2416 19592 91.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.54→54.832 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3923 0 6 80 4009
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053990
X-RAY DIFFRACTIONf_angle_d0.7515391
X-RAY DIFFRACTIONf_dihedral_angle_d13.5091462
X-RAY DIFFRACTIONf_chiral_restr0.042590
X-RAY DIFFRACTIONf_plane_restr0.003717
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A927X-RAY DIFFRACTIONPOSITIONAL
12D927X-RAY DIFFRACTIONPOSITIONAL0.065
21B941X-RAY DIFFRACTIONPOSITIONAL
22C941X-RAY DIFFRACTIONPOSITIONAL0.025
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5401-2.60360.39321130.33182337X-RAY DIFFRACTION81
2.6036-2.6740.3514900.30182402X-RAY DIFFRACTION82
2.674-2.75270.35031500.29712460X-RAY DIFFRACTION85
2.7527-2.84150.34561420.292500X-RAY DIFFRACTION88
2.8415-2.94310.37561240.29272518X-RAY DIFFRACTION86
2.9431-3.06090.32181680.28462726X-RAY DIFFRACTION95
3.0609-3.20020.2851540.26312776X-RAY DIFFRACTION96
3.2002-3.36890.30521700.24342758X-RAY DIFFRACTION97
3.3689-3.57990.26451560.24022782X-RAY DIFFRACTION96
3.5799-3.85630.23821300.22142778X-RAY DIFFRACTION94
3.8563-4.24420.22121540.2092726X-RAY DIFFRACTION94
4.2442-4.8580.1971360.20032734X-RAY DIFFRACTION94
4.858-6.11930.2871560.24172806X-RAY DIFFRACTION97
6.1193-54.84430.19981480.20962740X-RAY DIFFRACTION94

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