[English] 日本語
Yorodumi
- EMDB-4553: Truncated human R2TP complex, structure 4 (ADP-empty) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-4553
TitleTruncated human R2TP complex, structure 4 (ADP-empty)
Map data
SampleRUVBL1-RUVBL2 in an open conformation (ADP-empty):
RuvB-like 1 / RuvB-like 2 / ligand
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
RuvB-like, AAA-lid domain / RuvB-like helicase 2, domain II / RuvB-like helicase 2 / RuvB-like helicase 1 / P-loop containing nucleoside triphosphate hydrolase / RuvB-like / TIP49, P-loop domain / AAA+ ATPase domain
RuvB-like 2 / RuvB-like 1
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.63 Å
AuthorsMunoz-Hernandez H / Rodriguez CF / Llorca O
Funding support Spain, 3 items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and UniversitiesSAF2014-52301-R Spain
Spanish Ministry of Economy and CompetitivenessBES-2015-071348 Spain
Spanish Ministry of Science, Innovation, and UniversitiesSAF2017-82632-P 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 ReportPDB-ID: 6qi9

SummaryFull reportAbout validation report
History
DepositionJan 18, 2019-
Header (metadata) releaseFeb 13, 2019-
Map releaseMay 15, 2019-
UpdateDec 18, 2019-
Current statusDec 18, 2019Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.01
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.01
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6qi9
  • Surface level: 0.01
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

-
Map

FileDownload / File: emd_4553.map.gz / Format: CCP4 / Size: 67 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 260 pix.
= 278.2 Å
1.07 Å/pix.
x 260 pix.
= 278.2 Å
1.07 Å/pix.
x 260 pix.
= 278.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density
Contour LevelBy AUTHOR: 0.01 / Movie #1: 0.01
Minimum - Maximum-0.032253817 - 0.059564065
Average (Standard dev.)0.00015664156 (±0.0017792217)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions260260260
Spacing260260260
CellA=B=C: 278.2 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.071.071.07
M x/y/z260260260
origin x/y/z0.0000.0000.000
length x/y/z278.200278.200278.200
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ208208208
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS260260260
D min/max/mean-0.0320.0600.000

-
Supplemental data

-
Sample components

-
Entire RUVBL1-RUVBL2 in an open conformation (ADP-empty)

EntireName: RUVBL1-RUVBL2 in an open conformation (ADP-empty) / Number of components: 4

-
Component #1: protein, RUVBL1-RUVBL2 in an open conformation (ADP-empty)

ProteinName: RUVBL1-RUVBL2 in an open conformation (ADP-empty) / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli BL21(DE3) (bacteria)

-
Component #2: protein, RuvB-like 1

ProteinName: RuvB-like 1 / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 50.296914 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli BL21(DE3) (bacteria)

-
Component #3: protein, RuvB-like 2

ProteinName: RuvB-like 2 / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 51.222465 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli BL21(DE3) (bacteria)

-
Component #4: ligand, ADENOSINE-5'-DIPHOSPHATE

LigandName: ADENOSINE-5'-DIPHOSPHATE / Number of Copies: 5 / Recombinant expression: No
MassTheoretical: 0.427201 kDa

-
Experimental details

-
Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionpH: 7.8
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 277 K / Humidity: 100 %

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 1.18 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

-
Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 33466
3D reconstructionSoftware: RELION / Resolution: 4.63 Å / Resolution method: FSC 0.143 CUT-OFF

-
Atomic model buiding

Modeling #1Refinement protocol: rigid body / Refinement space: REAL
Input PDB model: 6FO1
Output model

+
About Yorodumi

-
News

-
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

-
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force. (see PDBe EMDB page)
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is "EMD"? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB at PDBe / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.:Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.:Changes in new EM Navigator and Yorodumi

Read more

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more