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- PDB-6fd7: NMR structure of the first TPR domain of the human RPAP3 protein -

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Basic information

Entry
Database: PDB / ID: 6fd7
TitleNMR structure of the first TPR domain of the human RPAP3 protein
ComponentsRNA polymerase II-associated protein 3
KeywordsCHAPERONE / TPR HSP chaperone
Function / homology
Function and homology information


R2TP complex / RPAP3/R2TP/prefoldin-like complex / protein folding chaperone complex / protein stabilization / cilium / ciliary basal body / cytosol
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 / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats ...: / 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 / 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 / Mainly Alpha
Similarity search - Domain/homology
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
Citation
Journal: 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.
#1: Journal: Biomol NMR Assign / Year: 2015
Title: (1)H, (15)N and (13)C resonance assignments of the two TPR domains from the human RPAP3 protein.
Authors: Chagot, M.E. / Jacquemin, C. / Branlant, C. / Charpentier, B. / Manival, X. / Quinternet, M.
History
DepositionDec 22, 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


Theoretical massNumber of molelcules
Total (without water)14,4901
Polymers14,4901
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7440 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest restraint energies
RepresentativeModel #1lowest energy

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Components

#1: Protein RNA polymerase II-associated protein 3


Mass: 14490.407 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

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-1H NOESY
121isotropic13D 1H-15N NOESY
131isotropic13D 1H-13C NOESY
191isotropic13D HNCA
181isotropic13D HNCO
171isotropic13D HN(CA)CB
161isotropic13D (H)CCH-TOCSY
151isotropic13D HNHA
141isotropic13D (H)CCH-COSY
1111isotropic12D 1H-15N HSQC
1101isotropic12D 1H-13C HSQC

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Sample preparation

DetailsType: solution
Contents: 1 mM [U-13C; U-15N] RPAP3-TPR1, 10 mM sodium phosphate, 150 mM sodium chloride, 0.5 mM TCEP, 95% H2O/5% D2O
Label: sample_1 / Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMRPAP3-TPR1[U-13C; U-15N]1
10 mMsodium phosphatenatural abundance1
150 mMsodium chloridenatural abundance1
0.5 mMTCEPnatural abundance1
Sample conditionsIonic strength: 150 mM / Label: cond_1 / pH: 6.4 / Pressure: 1 atm / Temperature: 303 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
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest restraint energies
Conformers calculated total number: 200 / Conformers submitted total number: 20

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