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- PDB-6qi9: Truncated human R2TP complex, structure 4 (ADP-empty) -

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Basic information

Entry
Database: PDB / ID: 6qi9
TitleTruncated human R2TP complex, structure 4 (ADP-empty)
Components
  • RuvB-like 1
  • RuvB-like 2
KeywordsCHAPERONE / R2TP / HSP90 co-chaperone / PIH1D1 / RPAP3 / RUVBL1 / RUVBL2 / cryo-EM
Function / homology
Function and homology information


negative regulation of estrogen receptor binding / transcriptional activation by promoter-enhancer looping / histone H2A acetylation / positive regulation of telomerase RNA localization to Cajal body / R2TP complex / establishment of protein localization to chromatin / Swr1 complex / Ino80 complex / 5'-3' DNA helicase activity / box C/D snoRNP assembly ...negative regulation of estrogen receptor binding / transcriptional activation by promoter-enhancer looping / histone H2A acetylation / positive regulation of telomerase RNA localization to Cajal body / R2TP complex / establishment of protein localization to chromatin / Swr1 complex / Ino80 complex / 5'-3' DNA helicase activity / box C/D snoRNP assembly / NuA4 histone acetyltransferase complex / regulation of growth / TFIID-class transcription factor complex binding / MLL1 complex / beta-catenin-TCF complex assembly / CENP-A containing nucleosome assembly / nuclear euchromatin / intracellular / histone H4 acetylation / histone acetylation / RNA polymerase II core promoter sequence-specific DNA binding / ADP binding / TBP-class protein binding / positive regulation of histone acetylation / microtubule organizing center / DNA helicase / cellular response to estradiol stimulus / DNA helicase activity / chromatin DNA binding / cellular response to UV / nuclear matrix / transcription corepressor activity / beta-catenin binding / positive regulation of canonical Wnt signaling pathway / negative regulation of canonical Wnt signaling pathway / ribonucleoprotein complex / spermatogenesis / unfolded protein binding / protein folding / ATPase binding / chromatin remodeling / transcription coactivator activity / DNA recombination / cell cycle / ATPase activity / cadherin binding / protein deubiquitination / RNA polymerase II cis-regulatory region sequence-specific DNA binding / cell division / centrosome / regulation of transcription by RNA polymerase II / DNA repair / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / extracellular exosome / membrane / nucleoplasm / ATP binding / identical protein binding / nucleus / cytosol / cytoplasm
TIP49 AAA-lid domain / RuvB-like helicase 1 / AAA+ ATPase domain / RuvB-like / P-loop containing nucleoside triphosphate hydrolase / TIP49, P-loop domain / RuvB-like helicase 2 / RuvB-like, AAA-lid domain / RuvB-like helicase 2, domain II / TIP49 P-loop domain
RuvB-like 2 / RuvB-like 1
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.63 Å
AuthorsMunoz-Hernandez, H. / Rodriguez, C.F. / Llorca, O.
Funding support Spain, 3items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and UniversitiesSAF2014-52301-R Spain
Spanish Ministry of Science, Innovation, and UniversitiesSAF2017-82632-P Spain
Spanish Ministry of Economy and CompetitivenessBES-2015-071348 Spain
CitationJournal: Sci Adv / Year: 2019
Title: Structural mechanism for regulation of the AAA-ATPases RUVBL1-RUVBL2 in the R2TP co-chaperone revealed by cryo-EM.
Authors: Hugo Muñoz-Hernández / Mohinder Pal / Carlos F Rodríguez / Rafael Fernandez-Leiro / Chrisostomos Prodromou / Laurence H Pearl / Oscar Llorca /
Abstract: The human R2TP complex (RUVBL1-RUVBL2-RPAP3-PIH1D1) is an HSP90 co-chaperone required for the maturation of several essential multiprotein complexes, including RNA polymerase II, small nucleolar ...The human R2TP complex (RUVBL1-RUVBL2-RPAP3-PIH1D1) is an HSP90 co-chaperone required for the maturation of several essential multiprotein complexes, including RNA polymerase II, small nucleolar ribonucleoproteins, and PIKK complexes such as mTORC1 and ATR-ATRIP. RUVBL1-RUVBL2 AAA-ATPases are also primary components of other essential complexes such as INO80 and Tip60 remodelers. Despite recent efforts, the molecular mechanisms regulating RUVBL1-RUVBL2 in these complexes remain elusive. Here, we report cryo-EM structures of R2TP and show how access to the nucleotide-binding site of RUVBL2 is coupled to binding of the client recruitment component of R2TP (PIH1D1) to its DII domain. This interaction induces conformational rearrangements that lead to the destabilization of an N-terminal segment of RUVBL2 that acts as a gatekeeper to nucleotide exchange. This mechanism couples protein-induced motions of the DII domains with accessibility of the nucleotide-binding site in RUVBL1-RUVBL2, and it is likely a general mechanism shared with other RUVBL1-RUVBL2-containing complexes.
Validation Report
SummaryFull reportAbout validation report
History
DepositionJan 18, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 15, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Other / Category: atom_sites
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3]

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Structure visualization

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Assembly

Deposited unit
A: RuvB-like 1
B: RuvB-like 1
C: RuvB-like 1
D: RuvB-like 2
E: RuvB-like 2
F: RuvB-like 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)306,69411
Polymers304,5586
Non-polymers2,1365
Water0
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27450 Å2
ΔGint-161 kcal/mol
Surface area87820 Å2
MethodPISA

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Components

#1: Protein RuvB-like 1 / / 49 kDa TATA box-binding protein-interacting protein / 49 kDa TBP-interacting protein / 54 kDa ...49 kDa TATA box-binding protein-interacting protein / 49 kDa TBP-interacting protein / 54 kDa erythrocyte cytosolic protein / ECP-54 / INO80 complex subunit H / Nuclear matrix protein 238 / NMP 238 / Pontin 52 / TIP49a / TIP60-associated protein 54-alpha / TAP54-alpha


Mass: 50296.914 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RUVBL1, INO80H, NMP238, TIP49, TIP49A / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9Y265, DNA helicase
#2: Protein RuvB-like 2 / 48 kDa TATA box-binding protein-interacting protein / 48 kDa TBP-interacting protein / 51 kDa ...48 kDa TATA box-binding protein-interacting protein / 48 kDa TBP-interacting protein / 51 kDa erythrocyte cytosolic protein / ECP-51 / INO80 complex subunit J / Repressing pontin 52 / Reptin 52 / TIP49b / TIP60-associated protein 54-beta / TAP54-beta


Mass: 51222.465 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RUVBL2, INO80J, TIP48, TIP49B, CGI-46 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9Y230, DNA helicase
#3: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: RUVBL1-RUVBL2 in an open conformation (ADP-empty) / Type: COMPLEX / Entity ID: 1,2 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 7.8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 1.18 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.14_3260: / Classification: refinement
EM software
IDNameVersionCategory
9PHENIXmodel refinement
13RELION33D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 408781
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 4.63 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 33466 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model buildingPDB-ID: 6FO1
Refine LS restraints
Refinement-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00714746
ELECTRON MICROSCOPYf_angle_d0.98619910
ELECTRON MICROSCOPYf_dihedral_angle_d9.8959072
ELECTRON MICROSCOPYf_chiral_restr0.0592362
ELECTRON MICROSCOPYf_plane_restr0.0072538

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