[English] 日本語
Yorodumi
- EMDB-21493: cryo-EM map of Sth1-Arp7-Arp9-Rtt102 in the ADP BeF3 state bound ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-21493
Titlecryo-EM map of Sth1-Arp7-Arp9-Rtt102 in the ADP BeF3 state bound to the nucleosome with a peeled DNA conformation
Map dataCryo-EM map of Sth1-Arp7-Arp9-Rtt102 bound to the nucleosome with a peeled DNA conformation (ADP-BeF3 state); unsharpened map
Sample
  • Complex: cryo-EM map of Sth1-Arp7-Arp9-Rtt102 in the ADP BeF3 state bound to the nucleosome with a peeled DNA conformation
Function / homology
Function and homology information


chromatin remodeling at centromere / RHO GTPases activate IQGAPs / RHO GTPases Activate WASPs and WAVEs / Regulation of actin dynamics for phagocytic cup formation / Platelet degranulation / DNA translocase activity / : / nucleosome disassembly / RSC-type complex / SWI/SNF complex ...chromatin remodeling at centromere / RHO GTPases activate IQGAPs / RHO GTPases Activate WASPs and WAVEs / Regulation of actin dynamics for phagocytic cup formation / Platelet degranulation / DNA translocase activity / : / nucleosome disassembly / RSC-type complex / SWI/SNF complex / ATP-dependent chromatin remodeler activity / NuA4 histone acetyltransferase complex / chromosome, centromeric region / ATP-dependent activity, acting on DNA / cytoskeleton organization / meiotic cell cycle / helicase activity / chromosome segregation / transcription elongation by RNA polymerase II / base-excision repair / lysine-acetylated histone binding / structural constituent of chromatin / double-strand break repair / nucleosome / chromatin organization / DNA helicase / chromatin remodeling / protein heterodimerization activity / chromatin binding / chromatin / structural molecule activity / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / ATP hydrolysis activity / positive regulation of transcription by RNA polymerase II / DNA binding / ATP binding / nucleus
Similarity search - Function
Transcription regulator protein Rtt102 / Rtt102p-like transcription regulator protein / Snf2, ATP coupling domain / Snf2-ATP coupling, chromatin remodelling complex / Snf2-ATP coupling, chromatin remodelling complex / HSA domain / Helicase/SANT-associated domain / HSA domain profile. / : / SNF2-like, N-terminal domain superfamily ...Transcription regulator protein Rtt102 / Rtt102p-like transcription regulator protein / Snf2, ATP coupling domain / Snf2-ATP coupling, chromatin remodelling complex / Snf2-ATP coupling, chromatin remodelling complex / HSA domain / Helicase/SANT-associated domain / HSA domain profile. / : / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / Actin / Actin family / Actin / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A conserved site / Histone H2A signature. / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone H2A / Histone 2A / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Helicase conserved C-terminal domain / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / ATPase, nucleotide binding domain / Histone-fold / Bromodomain, conserved site / Bromodomain signature. / helicase superfamily c-terminal domain / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Histone H2B 1.1 / Histone H2A type 1 / Nuclear protein STH1/NPS1 / Regulator of Ty1 transposition protein 102 / Histone H4 / Actin-like protein ARP9 / Actin-related protein 7 / Histone H2A / Histone H2B / Histone H3
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.3 Å
AuthorsLeschziner AE / Baker RW
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5R01GM092895-08 United States
CitationJournal: Nat Struct Mol Biol / Year: 2021
Title: Structural insights into assembly and function of the RSC chromatin remodeling complex.
Authors: Richard W Baker / Janice M Reimer / Peter J Carman / Bengi Turegun / Tsutomu Arakawa / Roberto Dominguez / Andres E Leschziner /
Abstract: SWI/SNF chromatin remodelers modify the position and spacing of nucleosomes and, in humans, are linked to cancer. To provide insights into the assembly and regulation of this protein family, we ...SWI/SNF chromatin remodelers modify the position and spacing of nucleosomes and, in humans, are linked to cancer. To provide insights into the assembly and regulation of this protein family, we focused on a subcomplex of the Saccharomyces cerevisiae RSC comprising its ATPase (Sth1), the essential actin-related proteins (ARPs) Arp7 and Arp9 and the ARP-binding protein Rtt102. Cryo-EM and biochemical analyses of this subcomplex shows that ARP binding induces a helical conformation in the helicase-SANT-associated (HSA) domain of Sth1. Surprisingly, the ARP module is rotated 120° relative to the full RSC about a pivot point previously identified as a regulatory hub in Sth1, suggesting that large conformational changes are part of Sth1 regulation and RSC assembly. We also show that a conserved interaction between Sth1 and the nucleosome acidic patch enhances remodeling. As some cancer-associated mutations dysregulate rather than inactivate SWI/SNF remodelers, our insights into RSC complex regulation advance a mechanistic understanding of chromatin remodeling in disease states.
History
DepositionFeb 28, 2020-
Header (metadata) releaseDec 2, 2020-
Map releaseDec 2, 2020-
UpdateJan 27, 2021-
Current statusJan 27, 2021Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.02
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.02
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_21493.png

Downloads & links

-
Map

FileDownload / File: emd_21493.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM map of Sth1-Arp7-Arp9-Rtt102 bound to the nucleosome with a peeled DNA conformation (ADP-BeF3 state); unsharpened map
Voxel sizeX=Y=Z: 1.16 Å
Density
Contour LevelBy AUTHOR: 0.02 / Movie #1: 0.02
Minimum - Maximum-0.010518378 - 0.055904645
Average (Standard dev.)0.00013047986 (±0.0021754843)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 348.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.161.161.16
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z348.000348.000348.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ400400400
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-0.0110.0560.000

-
Supplemental data

-
Additional map: Cryo-EM map of Sth1-Arp7-Arp9-Rtt102 bound to the nucleosome...

Fileemd_21493_additional_1.map
AnnotationCryo-EM map of Sth1-Arp7-Arp9-Rtt102 bound to the nucleosome with a peeled DNA conformation (ADP-BeF3 state); sharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Cryo-EM map of Sth1-Arp7-Arp9-Rtt102 bound to the nucleosome...

Fileemd_21493_half_map_1.map
AnnotationCryo-EM map of Sth1-Arp7-Arp9-Rtt102 bound to the nucleosome with a peeled DNA conformation (ADP-BeF3 state); half map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Cryo-EM map of Sth1-Arp7-Arp9-Rtt102 bound to the nucleosome...

Fileemd_21493_half_map_2.map
AnnotationCryo-EM map of Sth1-Arp7-Arp9-Rtt102 bound to the nucleosome with a peeled DNA conformation (ADP-BeF3 state); half map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : cryo-EM map of Sth1-Arp7-Arp9-Rtt102 in the ADP BeF3 state bound ...

EntireName: cryo-EM map of Sth1-Arp7-Arp9-Rtt102 in the ADP BeF3 state bound to the nucleosome with a peeled DNA conformation
Components
  • Complex: cryo-EM map of Sth1-Arp7-Arp9-Rtt102 in the ADP BeF3 state bound to the nucleosome with a peeled DNA conformation

-
Supramolecule #1: cryo-EM map of Sth1-Arp7-Arp9-Rtt102 in the ADP BeF3 state bound ...

SupramoleculeName: cryo-EM map of Sth1-Arp7-Arp9-Rtt102 in the ADP BeF3 state bound to the nucleosome with a peeled DNA conformation
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#12
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Recombinant expressionOrganism: Escherichia coli (E. coli) / Recombinant strain: BL21 Rosetta
Molecular weightTheoretical: 440 KDa

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration1 mg/mL
BufferpH: 7.5
GridModel: UltrAuFoil / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR / Details: Glow discharge for 30 seconds at 25 mAmp
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: 4 second blot time, blot force 20.
DetailsSample was crosslinked using the GRAFIX protocol

-
Electron microscopy

MicroscopeFEI TALOS ARCTICA
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 36000
Sample stageCooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average exposure time: 7.0 sec. / Average electron dose: 53.0 e/Å2
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

-
Image processing

Particle selectionNumber selected: 2020734
CTF correctionSoftware - Name: CTFFIND (ver. 4)
Startup modelType of model: OTHER / Details: Ab initio model generation in cryoSPARC v2
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3) / Number images used: 112634
FSC plot (resolution estimation)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

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.
  • 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 Accession Codes are Changing Soon! / 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.
  • 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

-
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.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

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