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- PDB-6fdp: NMR structure of the second TPR domain of the human RPAP3 protein... -

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Basic information

Entry
Database: PDB / ID: 6fdp
TitleNMR structure of the second TPR domain of the human RPAP3 protein in complex with HSP90 peptide DTSRMEEVD
Components
  • Heat shock protein HSP 90-alpha
  • RNA polymerase II-associated protein 3
KeywordsCHAPERONE / TPR HSP RUVBL Polymerase
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 / Scavenging by Class F Receptors / vRNP Assembly ...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 / Scavenging by Class F Receptors / vRNP Assembly / 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 / 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 / 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 / Chaperone Mediated Autophagy / neuron migration / Aggrephagy / positive regulation of nitric oxide biosynthetic process
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 / Tetratricopeptide repeat domain / Tetratricopeptide repeat / Heat shock protein Hsp90, conserved site / Heat shock hsp90 proteins family signature. ...: / RNA-polymerase II-associated protein 3-like, C-terminal domain / Potential Monad-binding region of RPAP3 / Tetratricopeptide repeat / 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 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)
MethodSOLUTION NMR / molecular dynamics
AuthorsQuinternet, M. / Chagot, M.E. / Manival, X.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research AgencyANR-11-BSV8-01503 France
CitationJournal: Structure / Year: 2018
Title: Deep Structural Analysis of RPAP3 and PIH1D1, Two Components of the HSP90 Co-chaperone R2TP Complex.
Authors: Henri, J. / Chagot, M.E. / Bourguet, M. / Abel, Y. / Terral, G. / Maurizy, C. / Aigueperse, C. / Georgescauld, F. / Vandermoere, F. / Saint-Fort, R. / Behm-Ansmant, I. / Charpentier, B. / ...Authors: Henri, J. / Chagot, M.E. / Bourguet, M. / Abel, Y. / Terral, G. / Maurizy, C. / Aigueperse, C. / Georgescauld, F. / Vandermoere, F. / Saint-Fort, R. / Behm-Ansmant, I. / Charpentier, B. / Pradet-Balade, B. / Verheggen, C. / Bertrand, E. / Meyer, P. / Cianferani, S. / Manival, X. / Quinternet, M.
History
DepositionDec 26, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 1, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 12, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2May 8, 2019Group: Data collection / Category: pdbx_nmr_software / Item: _pdbx_nmr_software.name
Revision 1.3Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_spectrometer.model
Revision 1.4Jun 19, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA polymerase II-associated protein 3
B: Heat shock protein HSP 90-alpha


Theoretical massNumber of molelcules
Total (without water)14,4502
Polymers14,4502
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area1350 Å2
ΔGint-4 kcal/mol
Surface area7100 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the restraint lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein RNA polymerase II-associated protein 3


Mass: 13368.283 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RPAP3 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9H6T3
#2: Protein/peptide Heat shock protein HSP 90-alpha / Heat shock 86 kDa / HSP86 / Lipopolysaccharide-associated protein 2 / LPS-associated protein 2 / ...Heat shock 86 kDa / HSP86 / Lipopolysaccharide-associated protein 2 / LPS-associated protein 2 / Renal carcinoma antigen NY-REN-38


Mass: 1082.120 Da / Num. of mol.: 1 / Fragment: UNP residues 724-732
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HSP90AA1, HSP90A, HSPC1, HSPCA / Production host: synthetic construct (others) / References: UniProt: P07900

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic13D CBCA(CO)NH
121isotropic13D HNCA
131isotropic13D HNCO
141isotropic13D HN(CA)CB
151isotropic13D HNHA
181isotropic13D (H)CCH-TOCSY
171isotropic13D (H)CCH-COSY
1131isotropic13D 1H-13C NOESY aliphatic
1121isotropic13D 1H-15N NOESY
1111isotropic12D 1H-15N HSQC
1101isotropic12D 1H-13C HSQC
191isotropic13D X-half filtered 1H-15N NOESY
162isotropic13D X-halffiltered 1H-13C NOESY
1171isotropic12D double X-half filtered 1H-1H NOESY
1162isotropic12D double X-half filtered 1H-1H NOESY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent systemDetails
solution11 mM [U-13C; U-15N] RPAP3-TPR2, 1 mM HSP90-pep, 150 mM sodium chloride, 10 mM sodium phosphate, 0.5 mM TCEP, 95% H2O/5% D2Osample_13C15N_H2O95% H2O/5% D2O
solution21 mM [U-13C; U-15N] RPAP3-TPR2, 1 mM HSP90-pep, 150 mM sodium chloride, 10 mM sodium phosphate, 0.5 mM TCEP, 100% D2Osample_13C15N_D2O100% D2O1mM of RPAP3-TPR2 and HSP90-pep in ratio 1:1 in NaPi 10 mM, NaCl 150 mM, TCEP 0.5 mM were lyophilized and resuspended in 100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMRPAP3-TPR2[U-13C; U-15N]1
1 mMHSP90-pepnatural abundance1
150 mMsodium chloridenatural abundance1
10 mMsodium phosphatenatural abundance1
0.5 mMTCEPnatural abundance1
1 mMRPAP3-TPR2[U-13C; U-15N]2
1 mMHSP90-pepnatural abundance2
150 mMsodium chloridenatural abundance2
10 mMsodium phosphatenatural abundance2
0.5 mMTCEPnatural abundance2
Sample conditionsIonic strength: 150 mM / Label: cond_1 / pH: 6.4 / Pressure: 1 atm / Temperature: 293 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
CARAKeller and Wuthrichchemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
TALOSCornilescu, Delaglio and Baxstructure calculation
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
RefinementMethod: molecular dynamics / Software ordinal: 5 / Details: use of the AMPS-NMR webportal
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the restraint lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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