[English] 日本語
Yorodumi
- EMDB-7131: Chromatin-modifying complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-7131
TitleChromatin-modifying complex
Map dataStructure of the Saccharomyces cerevisiae NuA4 histone acetyltransferase complex
Sample
  • Complex: Chromatin-modifying complex
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / negative staining / Resolution: 26.5 Å
AuthorsSetiaputra DT / Dalwadi U / Yip CK
CitationJournal: Mol Cell Biol / Year: 2018
Title: Molecular Architecture of the Essential Yeast Histone Acetyltransferase Complex NuA4 Redefines Its Multimodularity.
Authors: Dheva Setiaputra / Salar Ahmad / Udit Dalwadi / Anne-Lise Steunou / Shan Lu / James D Ross / Meng-Qiu Dong / Jacques Côté / Calvin K Yip /
Abstract: Conserved from yeast to humans, the NuA4 histone acetyltransferase is a large multisubunit complex essential for cell viability through the regulation of gene expression, genome maintenance, ...Conserved from yeast to humans, the NuA4 histone acetyltransferase is a large multisubunit complex essential for cell viability through the regulation of gene expression, genome maintenance, metabolism, and cell fate during development and stress. How the different NuA4 subunits work in concert with one another to perform these diverse functions remains unclear, and addressing this central question requires a comprehensive understanding of NuA4's molecular architecture and subunit organization. We have determined the structure of fully assembled native yeast NuA4 by single-particle electron microscopy. Our data revealed that NuA4 adopts a trilobal overall architecture, with each of the three lobes constituted by one or two functional modules. By performing cross-linking coupled to mass spectrometry analysis and protein interaction studies, we further mapped novel intermolecular interfaces within NuA4. Finally, we combined these new data with other known structural information of NuA4 subunits and subassemblies to construct a multiscale model to illustrate how the different NuA4 subunits and modules are spatially arranged. This model shows that the multiple chromatin reader domains are clustered together around the catalytic core, suggesting that NuA4's multimodular architecture enables it to engage in multivalent interactions with its nucleosome substrate.
History
DepositionNov 28, 2017-
Header (metadata) releaseJan 31, 2018-
Map releaseDec 19, 2018-
UpdateJul 3, 2019-
Current statusJul 3, 2019Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0532
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.0532
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_7131.png

Downloads & links

-
Map

FileDownload / File: emd_7131.map.gz / Format: CCP4 / Size: 1.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationStructure of the Saccharomyces cerevisiae NuA4 histone acetyltransferase complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
7 Å/pix.
x 72 pix.
= 504. Å		7 Å/pix.
x 72 pix.
= 504. Å		7 Å/pix.
x 72 pix.
= 504. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 7 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0532 / Movie #1: 0.0532
Minimum - Maximum-0.18335663 - 0.24313597
Average (Standard dev.)-0.0014149046 (±0.017195124)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions727272
Spacing727272
CellA=B=C: 504.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z777
M x/y/z727272
origin x/y/z0.0000.0000.000
length x/y/z504.000504.000504.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ480480480
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS727272
D min/max/mean-0.1830.243-0.001

-
Supplemental data

-
Sample components

-
Entire : Chromatin-modifying complex

EntireName: Chromatin-modifying complex
Components
  • Complex: Chromatin-modifying complex

-
Supramolecule #1: Chromatin-modifying complex

SupramoleculeName: Chromatin-modifying complex / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: BJ1991 / Location in cell: Nucleus
Molecular weightTheoretical: 1 MDa

-
Experimental details

-
Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
Component:
ConcentrationFormulaName
350.0 mMNaClSodium chloride
40.0 mMC8H18N2O4SHEPES
20.0 %C3H8O3Glycerol
2.0 mMMg(CH3COO)2Magnesium acetate
0.02 %C5H8O2Glutaraldehyde
0.1 %C32H58N2O7SCHAPS
StainingType: NEGATIVE / Material: Uranyl formate
Details: Negatively-stained EM specimens were prepared by uranyl formate staining on continuous carbon-overlaid copper grids.
GridModel: Ted Pella / Material: COPPER / Mesh: 400 / Support film - Material: FORMVAR / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 101.325 kPa
DetailsComplexes were purified from yeast via affinity purification for a FLAG-tagged subunit. Purified complexes were subjected to glycerol gradient ultracentrifugation, fractionated, and analyzed by negative-stain electron microscopy.

-
Electron microscopy

MicroscopeFEI TECNAI SPIRIT
Image recordingFilm or detector model: FEI EAGLE (4k x 4k) / Digitization - Dimensions - Width: 1365 pixel / Digitization - Dimensions - Height: 1365 pixel / Number grids imaged: 1 / Number real images: 251 / Average exposure time: 1.0 sec. / Average electron dose: 25.0 e/Å2
Electron beamAcceleration voltage: 120 kV / Electron source: LAB6
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 49000
Sample stageSpecimen holder model: SIDE ENTRY, EUCENTRIC / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Tecnai Spirit / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 26402
Details: A subset of 200 particles were picked manually using the RELION software and used to generate reference-free 2D class averages. Representative class averages were used as templates for ...Details: A subset of 200 particles were picked manually using the RELION software and used to generate reference-free 2D class averages. Representative class averages were used as templates for automatic picking using RELION.
CTF correctionSoftware:
Namedetails
CTFFIND (ver. 3)CTFFIND3 was used to fit CTFs to raw micrographs using the SPIDER interface.
SPIDER (ver. 22.10)SPIDER was used to phase flip images for CTF correction.

Details: CTFs of raw images were determined using CTFFIND3 and the images were phase-flipped using the SPIDER image suite.
Startup modelType of model: RANDOM CONICAL TILT / Random conical tilt - Tilt angle: 60 degrees
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 26.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2) / Number images used: 7976
Initial angle assignmentType: NOT APPLICABLE / Software - Name: EMAN (ver. 2.12)
Final angle assignmentType: PROJECTION MATCHING
Projection matching processing - Number reference projections: 3072
Projection matching processing - Angular sampling: 1.875 degrees
Software - Name: RELION (ver. 2)
Software - details: RCT model was used as starting model for 3D classification and refinement using untilted dataset.
Final 3D classificationNumber classes: 4 / Avg.num./class: 5791 / Software - Name: RELION (ver. 2)
Software - details: RCT model was used as starting model for 3D classification using untilted dataset.

+
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