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- PDB-6ez4: NMR structure of the C-terminal domain of the human RPAP3 protein -

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Basic information

Entry
Database: PDB / ID: 6ez4
TitleNMR structure of the C-terminal domain of the human RPAP3 protein
ComponentsRNA polymerase II-associated protein 3
KeywordsCHAPERONE / Rvb1 / Rvb2 / RUVBL1 / RUVBL2 / RNA polymerase / R2TP / snoRNP / PIH
Function / homology
Function and homology information


R2TP complex / RPAP3/R2TP/prefoldin-like complex / protein folding chaperone complex / protein stabilization / cytosol
Similarity search - Function
RNA-polymerase II-associated protein 3-like, C-terminal domain / Potential Monad-binding region of RPAP3 / Tetratricopeptide repeat / Tetratricopeptide repeat 1 / Tetratricopeptide repeat / Tetratricopeptide repeat / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily
Similarity search - Domain/homology
RNA polymerase II-associated protein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / molecular dynamics
AuthorsFabre, P. / Chagot, M.E. / Bragantini, B. / Manival, X. / Quinternet, M.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research Agency France
CitationJournal: Nat Commun / Year: 2018
Title: The RPAP3-Cterminal domain identifies R2TP-like quaternary chaperones.
Authors: Maurizy, C. / Quinternet, M. / Abel, Y. / Verheggen, C. / Santo, P.E. / Bourguet, M. / C F Paiva, A. / Bragantini, B. / Chagot, M.E. / Robert, M.C. / Abeza, C. / Fabre, P. / Fort, P. / ...Authors: Maurizy, C. / Quinternet, M. / Abel, Y. / Verheggen, C. / Santo, P.E. / Bourguet, M. / C F Paiva, A. / Bragantini, B. / Chagot, M.E. / Robert, M.C. / Abeza, C. / Fabre, P. / Fort, P. / Vandermoere, F. / M F Sousa, P. / Rain, J.C. / Charpentier, B. / Cianferani, S. / Bandeiras, T.M. / Pradet-Balade, B. / Manival, X. / Bertrand, E.
History
DepositionNov 14, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 18, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 13, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2May 8, 2019Group: Data collection / Category: pdbx_nmr_software / Item: _pdbx_nmr_software.name
Revision 1.3Jan 17, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model

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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)15,8041
Polymers15,8041
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8300 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest restraint energies
RepresentativeModel #1lowest energy

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Components

#1: Protein RNA polymerase II-associated protein 3


Mass: 15804.365 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-Gold(DE3)pLysS AG' (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-15N HSQC
121isotropic12D 1H-13C HSQC aliphatic
131isotropic12D 1H-13C HSQC aromatic
141isotropic13D HNCA
151isotropic13D HN(CA)CB
1161isotropic13D CBCA(CO)NH
1151isotropic13D HNCO
1141isotropic13D HN(CA)CO
1131isotropic13D HNCO E.COSY
1121isotropic13D HNHA
1111isotropic13D H(CCO)NH
1101isotropic13D (H)CC(CO)NH
191isotropic13D (H)CCH-TOCSY
181isotropic13D (H)CCH-COSY
171isotropic13D HBHA(CO)NH
161isotropic12D 1H-1H NOESY
1181isotropic13D 1H-15N NOESY
1171isotropic13D 1H-13C NOESY

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Sample preparation

DetailsType: solution
Contents: 1 mM [U-13C; U-15N] RPAP3 C-terminal domain, 150 mM sodium chloride, 10 mM sodium phosphate, 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 C-terminal domain[U-13C; U-15N]1
150 mMsodium chloridenatural abundance1
10 mMsodium phosphatenatural abundance1
0.5 mMTCEPnatural abundance1
Sample conditionsIonic strength: 150 mM / Label: condition_1 / pH: 6.4 / Pressure: 1 atm / Temperature: 298 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: refinement performed via the AMPS-NMR web portal
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest restraint energies
Conformers calculated total number: 100 / Conformers submitted total number: 20

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