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

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Basic information

Entry
Database: PDB / ID: 6fdt
TitleNMR structure of the second TPR domain of the human RPAP3 protein in complex with HSP70 peptide SGPTIEEVD
Components
  • Heat shock 70 kDa protein 1B
  • RNA polymerase II-associated protein 3
KeywordsCHAPERONE / TPR HSP RUVBL Polymerase
Function / homology
Function and homology information


cellular heat acclimation / negative regulation of inclusion body assembly / C3HC4-type RING finger domain binding / positive regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway / R2TP complex / positive regulation of microtubule nucleation / ATP-dependent protein disaggregase activity / RPAP3/R2TP/prefoldin-like complex / positive regulation of tumor necrosis factor-mediated signaling pathway / regulation of mitotic spindle assembly ...cellular heat acclimation / negative regulation of inclusion body assembly / C3HC4-type RING finger domain binding / positive regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway / R2TP complex / positive regulation of microtubule nucleation / ATP-dependent protein disaggregase activity / RPAP3/R2TP/prefoldin-like complex / positive regulation of tumor necrosis factor-mediated signaling pathway / regulation of mitotic spindle assembly / protein folding chaperone complex / aggresome / cellular response to steroid hormone stimulus / mRNA catabolic process / chaperone cofactor-dependent protein refolding / regulation of protein ubiquitination / HSF1-dependent transactivation / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / Regulation of HSF1-mediated heat shock response / Attenuation phase / ATP metabolic process / inclusion body / heat shock protein binding / negative regulation of protein ubiquitination / protein folding chaperone / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / centriole / positive regulation of erythrocyte differentiation / positive regulation of interleukin-8 production / G protein-coupled receptor binding / ATP-dependent protein folding chaperone / negative regulation of cell growth / PKR-mediated signaling / histone deacetylase binding / unfolded protein binding / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / positive regulation of NF-kappaB transcription factor activity / virus receptor activity / cellular response to heat / cellular response to oxidative stress / protein refolding / vesicle / blood microparticle / ficolin-1-rich granule lumen / protein stabilization / nuclear speck / ribonucleoprotein complex / negative regulation of cell population proliferation / signaling receptor binding / focal adhesion / centrosome / ubiquitin protein ligase binding / Neutrophil degranulation / positive regulation of gene expression / negative regulation of apoptotic process / perinuclear region of cytoplasm / enzyme binding / endoplasmic reticulum / ATP hydrolysis activity / protein-containing complex / mitochondrion / RNA binding / extracellular exosome / extracellular region / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
: / RNA-polymerase II-associated protein 3-like, C-terminal domain / Potential Monad-binding region of RPAP3 / Tetratricopeptide repeat / Tetratricopeptide repeat / 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 ...: / RNA-polymerase II-associated protein 3-like, C-terminal domain / Potential Monad-binding region of RPAP3 / Tetratricopeptide repeat / Tetratricopeptide repeat / 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 / Tetratricopeptide repeat / Heat shock protein 70 family / Hsp70 protein / Heat shock protein 70kD, C-terminal domain superfamily / Tetratricopeptide repeat domain / Tetratricopeptide repeat / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / ATPase, nucleotide binding domain / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Mainly Alpha
Similarity search - Domain/homology
Heat shock 70 kDa protein 1B / 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 70 kDa protein 1B


Theoretical massNumber of molelcules
Total (without water)14,3142
Polymers14,3142
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area1020 Å2
ΔGint-4 kcal/mol
Surface area7140 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest restraint 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 70 kDa protein 1B / Heat shock 70 kDa protein 2 / HSP70.2


Mass: 945.967 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HSPA1B, HSP72 / Production host: synthetic construct (others) / References: UniProt: P0DMV9

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic13D HNCA
121isotropic13D HN(CA)CB
131isotropic13D CBCA(CO)NH
141isotropic13D HNCO
151isotropic13D HNHA
1131isotropic13D (H)CCH-TOCSY
1151isotropic13D (H)CCH-COSY
1141isotropic12D 1H-15N HSQC
1121isotropic12D 1H-13C HSQC
1111isotropic13D 1H-15N NOESY
1101isotropic13D 1H-15N NOESY
191isotropic13D X-half filtered 1H-15N NOESY
181isotropic13D X-half filtered 1H-13C NOESY
172isotropic13D X-half filtered 1H-13C NOESY
162isotropic12D double X-half filtered 1H-1H NOESY
1162isotropic13D 1H-13C NOESY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent systemDetails
solution11 mM [U-13C; U-15N] RPAP3-TPR2, 1 mM HSP70-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 HSP70-pep, 150 mM sodium chloride, 10 mM sodium phosphate, 0.5 mM TCEP, 100% D2Osample_13C15N_D2O100% D2Osample_13C15N_H2O was lyophilized and resuspended in 100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMRPAP3-TPR2[U-13C; U-15N]1
1 mMHSP70-pepnatural abundance1
150 mMsodium chloridenatural abundance1
10 mMsodium phosphatenatural abundance1
0.5 mMTCEPnatural abundance1
1 mMRPAP3-TPR2[U-13C; U-15N]2
1 mMHSP70-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 web portal
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest restraint energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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