[English] 日本語
Yorodumi
- EMDB-7812: Human nuclear exosome-MTR4 RNA complex - focused reconstruction o... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-7812
TitleHuman nuclear exosome-MTR4 RNA complex - focused reconstruction on the DIS-PIN domain
Map dataHuman nuclear exosome-MTR4 RNA complex - composite map after focused reconstruction
Sample
  • Complex: Human nuclear exosome-MTR4 helicase captured after unwinding a DNA/RNA substrate
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsWeick E-M / Lima CD
CitationJournal: Cell / Year: 2018
Title: Helicase-Dependent RNA Decay Illuminated by a Cryo-EM Structure of a Human Nuclear RNA Exosome-MTR4 Complex.
Authors: Eva-Maria Weick / M Rhyan Puno / Kurt Januszyk / John C Zinder / Michael A DiMattia / Christopher D Lima /
Abstract: The ribonucleolytic RNA exosome interacts with RNA helicases to degrade RNA. To understand how the 3' to 5' Mtr4 helicase engages RNA and the nuclear exosome, we reconstituted 14-subunit Mtr4- ...The ribonucleolytic RNA exosome interacts with RNA helicases to degrade RNA. To understand how the 3' to 5' Mtr4 helicase engages RNA and the nuclear exosome, we reconstituted 14-subunit Mtr4-containing RNA exosomes from Saccharomyces cerevisiae, Schizosaccharomyces pombe, and human and show that they unwind structured substrates to promote degradation. We loaded a human exosome with an optimized DNA-RNA chimera that stalls MTR4 during unwinding and determined its structure to an overall resolution of 3.45 Å by cryoelectron microscopy (cryo-EM). The structure reveals an RNA-engaged helicase atop the non-catalytic core, with RNA captured within the central channel and DIS3 exoribonuclease active site. MPP6 tethers MTR4 to the exosome through contacts to the RecA domains of MTR4. EXOSC10 remains bound to the core, but its catalytic module and cofactor C1D are displaced by RNA-engaged MTR4. Competition for the exosome core may ensure that RNA is committed to degradation by DIS3 when engaged by MTR4.
History
DepositionApr 22, 2018-
Header (metadata) releaseMay 9, 2018-
Map releaseJun 20, 2018-
UpdateJun 27, 2018-
Current statusJun 27, 2018Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.03
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.03
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_7812.png

Downloads & links

-
Map

FileDownload / File: emd_7812.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHuman nuclear exosome-MTR4 RNA complex - composite map after focused reconstruction
Voxel sizeX=Y=Z: 1.07 Å
Density
Contour LevelBy AUTHOR: 0.03 / Movie #1: 0.03
Minimum - Maximum-0.120548755 - 0.19239767
Average (Standard dev.)0.00004187069 (±0.0019666187)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZXY
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 410.88 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.071.071.07
M x/y/z384384384
origin x/y/z0.0000.0000.000
length x/y/z410.880410.880410.880
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ384384384
MAP C/R/S312
start NC/NR/NS000
NC/NR/NS384384384
D min/max/mean-0.1210.1920.000

-
Supplemental data

-
Sample components

-
Entire : Human nuclear exosome-MTR4 helicase captured after unwinding a DN...

EntireName: Human nuclear exosome-MTR4 helicase captured after unwinding a DNA/RNA substrate
Components
  • Complex: Human nuclear exosome-MTR4 helicase captured after unwinding a DNA/RNA substrate

-
Supramolecule #1: Human nuclear exosome-MTR4 helicase captured after unwinding a DN...

SupramoleculeName: Human nuclear exosome-MTR4 helicase captured after unwinding a DNA/RNA substrate
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#15
Details: Human C1D/Rrp47 also in the sample, but was not observed in density
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
Molecular weightTheoretical: 690 KDa

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration1.0 mg/mL
BufferpH: 8
Component:
ConcentrationNameFormula
20.0 mMTris-HClTris
100.0 mMsodium chlorideNaClSodium chloride
0.5 mMmagnesium chlorideMgCl2
2.0 mMAMPPNP
1.0 mMBME
0.05 %CHAPSOCHAPS detergent
GridModel: Quantifoil R2/2 / Material: GOLD / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.037 kPa
VitrificationCryogen name: ETHANE / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV / Details: 30 sec wait time, 2.5 sec blot time.
DetailsSample was monodisperse upon elution from gel filtration prior to vitrification.

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Number real images: 1439 / Average electron dose: 85.23 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Particle selectionNumber selected: 278185
CTF correctionSoftware:
Namedetails
Gctf (ver. 1.06)determine
RELION (ver. 2.1.b1)apply
Startup modelType of model: NONE / Details: Ab initio model determination
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: cryoSPARC (ver. 0.6.1) / Software - details: from 0.6.1 to 0.6.5
Final 3D classificationNumber classes: 4 / Avg.num./class: 271036 / Software - Name: RELION (ver. 2.1b1)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 2.1b1)
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1b1) / Details: Focused refinement on DIS3-PIN and part of PH-ring / Number images used: 122284
FSC plot (resolution estimation)

-
Atomic model buiding 1

DetailsModels were rebuilt manually using Coot, with real space refinement with local scaling followed by Phenix real space refinement with suboptimal global scaling.
RefinementSpace: REAL / Protocol: BACKBONE TRACE / Overall B value: 64.3 / Target criteria: Correlation coefficient

+
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