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- PDB-6gxz: Crystal structure of the human RPAP3(TPR2)-PIH1D1(CS) complex -

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Basic information

Entry
Database: PDB / ID: 6gxz
TitleCrystal structure of the human RPAP3(TPR2)-PIH1D1(CS) complex
Components
  • PIH1 domain-containing protein 1
  • RNA polymerase II-associated protein 3
KeywordsCHAPERONE / Cochaperone / Complex / TPR domain
Function / homology
Function and homology information


TORC1 complex assembly / snoRNA localization / positive regulation of glucose mediated signaling pathway / pre-snoRNP complex / positive regulation of transcription of nucleolar large rRNA by RNA polymerase I / negative regulation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway / R2TP complex / RPAP3/R2TP/prefoldin-like complex / protein folding chaperone complex / box C/D snoRNP assembly ...TORC1 complex assembly / snoRNA localization / positive regulation of glucose mediated signaling pathway / pre-snoRNP complex / positive regulation of transcription of nucleolar large rRNA by RNA polymerase I / negative regulation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway / R2TP complex / RPAP3/R2TP/prefoldin-like complex / protein folding chaperone complex / box C/D snoRNP assembly / epithelial cell differentiation / positive regulation of TORC1 signaling / histone reader activity / phosphoprotein binding / positive regulation of protein serine/threonine kinase activity / rRNA processing / histone binding / ATPase binding / protein stabilization / ribonucleoprotein complex / chromatin remodeling / nucleolus / protein kinase binding / nucleus / cytosol / cytoplasm
Similarity search - Function
: / PIH1D1/2/3, CS-like domain / PIH1 CS-like domain / : / PIH1, N-terminal / PIH1 N-terminal domain / RNA-polymerase II-associated protein 3-like, C-terminal domain / Potential Monad-binding region of RPAP3 / Tetratricopeptide repeat / Tetratricopeptide repeat ...: / PIH1D1/2/3, CS-like domain / PIH1 CS-like domain / : / PIH1, N-terminal / PIH1 N-terminal domain / RNA-polymerase II-associated protein 3-like, C-terminal domain / Potential Monad-binding region of RPAP3 / Tetratricopeptide repeat / Tetratricopeptide repeat / 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 / PIH1 domain-containing protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.965 Å
AuthorsHenri, J. / Quinternet, M. / Manival, X. / Chagot, M.-E. / Charpentier, B. / Meyer, P.
Funding support France, 2items
OrganizationGrant numberCountry
French National Research AgencyANR-AA-BSV8-01503 France
French National Research AgencyANR-16-CE11-0032-02 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
DepositionJun 27, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 8, 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 1.2Oct 3, 2018Group: Data collection / Category: diffrn_source
Item: _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.type
Revision 1.3Jan 17, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA polymerase II-associated protein 3
C: RNA polymerase II-associated protein 3
D: PIH1 domain-containing protein 1
E: PIH1 domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,1855
Polymers58,1454
Non-polymers401
Water30617
1
A: RNA polymerase II-associated protein 3
E: PIH1 domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1123
Polymers29,0722
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3170 Å2
ΔGint-21 kcal/mol
Surface area12790 Å2
MethodPISA
2
C: RNA polymerase II-associated protein 3
D: PIH1 domain-containing protein 1


Theoretical massNumber of molelcules
Total (without water)29,0722
Polymers29,0722
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3460 Å2
ΔGint-24 kcal/mol
Surface area13050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.980, 42.440, 112.710
Angle α, β, γ (deg.)90.00, 98.25, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein RNA polymerase II-associated protein 3


Mass: 18481.020 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RPAP3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9H6T3
#2: Protein PIH1 domain-containing protein 1 / Nucleolar protein 17 homolog


Mass: 10591.316 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PIH1D1, NOP17 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NWS0
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.77 Å3/Da / Density % sol: 55.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG-3350 25%, CaCl2 50mM, Tris-HCL 100mM pH 7.7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.9677 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 18, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 2.965→67.287 Å / Num. obs: 13488 / % possible obs: 98.99 % / Redundancy: 7 % / Biso Wilson estimate: 70.4 Å2 / Net I/σ(I): 11.6
Reflection shellResolution: 2.965→3.016 Å / Redundancy: 7.4 % / Num. unique obs: 1345 / % possible all: 99.26

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6FDP

6fdp


Resolution: 2.965→67.287 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 29.48
RfactorNum. reflection% reflection
Rfree0.2837 647 4.8 %
Rwork0.2234 --
obs0.2261 13467 98.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.965→67.287 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3775 0 1 17 3793
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043926
X-RAY DIFFRACTIONf_angle_d0.585305
X-RAY DIFFRACTIONf_dihedral_angle_d11.3662466
X-RAY DIFFRACTIONf_chiral_restr0.04584
X-RAY DIFFRACTIONf_plane_restr0.005693
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9653-3.19430.38111240.3222537X-RAY DIFFRACTION99
3.1943-3.51570.35911260.2912550X-RAY DIFFRACTION100
3.5157-4.02440.34191240.23472559X-RAY DIFFRACTION100
4.0244-5.070.22241340.18012532X-RAY DIFFRACTION98
5.07-67.3040.25091390.20422642X-RAY DIFFRACTION98

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