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Yorodumi- PDB-6ez4: NMR structure of the C-terminal domain of the human RPAP3 protein -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ez4 | ||||||
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Title | NMR structure of the C-terminal domain of the human RPAP3 protein | ||||||
Components | RNA polymerase II-associated protein 3 | ||||||
Keywords | CHAPERONE / 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 | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / molecular dynamics | ||||||
Authors | Fabre, P. / Chagot, M.E. / Bragantini, B. / Manival, X. / Quinternet, M. | ||||||
Funding support | France, 1items
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ez4.cif.gz | 859.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ez4.ent.gz | 736.2 KB | Display | PDB format |
PDBx/mmJSON format | 6ez4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ez4_validation.pdf.gz | 402.6 KB | Display | wwPDB validaton report |
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Full document | 6ez4_full_validation.pdf.gz | 482.4 KB | Display | |
Data in XML | 6ez4_validation.xml.gz | 36.7 KB | Display | |
Data in CIF | 6ez4_validation.cif.gz | 66.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ez/6ez4 ftp://data.pdbj.org/pub/pdb/validation_reports/ez/6ez4 | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
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-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | 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
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Type: 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 | ||||||||||||||||||||
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Sample |
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Sample conditions | Ionic strength: 150 mM / Label: condition_1 / pH: 6.4 / Pressure: 1 atm / Temperature: 298 K |
-NMR measurement
NMR spectrometer | Type: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 600 MHz |
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-Processing
NMR software |
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Refinement | Method: molecular dynamics / Software ordinal: 5 / Details: refinement performed via the AMPS-NMR web portal | ||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest restraint energies Conformers calculated total number: 100 / Conformers submitted total number: 20 |