[English] 日本語
Yorodumi
- EMDB-1852: EM map of the negative stained SMG-1-8-9 complex. -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-1852
TitleEM map of the negative stained SMG-1-8-9 complex.
Map dataThis is the EM map of the negatively stained SMG-1-8-9 complex
Sample
  • Sample: Human SMG-1 kinase bound to SMG-9 and SMG-8
  • Protein or peptide: SMG-1
  • Protein or peptide: SMG-9
  • Protein or peptide: SMG-8
KeywordsNonsense-mediated mRNA decay / NMD / SMG-1 / SMG-8 / SMG-9 / SMG1C
Function / homologynuclear-transcribed mRNA catabolic process, nonsense-mediated decay
Function and homology information
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / negative staining / Resolution: 24.0 Å
AuthorsArias-Palomo E / Yamashita A / Fernandez IS / Nunez-Ramirez R / Bamba Y / Izumi N / Ohno S / Llorca O
CitationJournal: Genes Dev / Year: 2011
Title: The nonsense-mediated mRNA decay SMG-1 kinase is regulated by large-scale conformational changes controlled by SMG-8.
Authors: Ernesto Arias-Palomo / Akio Yamashita / Israel S Fernández / Rafael Núñez-Ramírez / Yumi Bamba / Natsuko Izumi / Shigeo Ohno / Oscar Llorca /
Abstract: Nonsense-mediated mRNA decay (NMD) is a eukaryotic surveillance pathway that regulates the degradation of mRNAs harboring premature translation termination codons. NMD also influences the expression ...Nonsense-mediated mRNA decay (NMD) is a eukaryotic surveillance pathway that regulates the degradation of mRNAs harboring premature translation termination codons. NMD also influences the expression of many physiological transcripts. SMG-1 is a large kinase essential to NMD that phosphorylates Upf1, which seems to be the definitive signal triggering mRNA decay. However, the regulation of the kinase activity of SMG-1 remains poorly understood. Here, we reveal the three-dimensional architecture of SMG-1 in complex with SMG-8 and SMG-9, and the structural mechanisms regulating SMG-1 kinase. A bent arm comprising a long region of HEAT (huntington, elongation factor 3, a subunit of PP2A and TOR1) repeats at the N terminus of SMG-1 functions as a scaffold for SMG-8 and SMG-9, and projects from the C-terminal core containing the phosphatidylinositol 3-kinase domain. SMG-9 seems to control the activity of SMG-1 indirectly through the recruitment of SMG-8 to the N-terminal HEAT repeat region of SMG-1. Notably, SMG-8 binding to the SMG-1:SMG-9 complex specifically down-regulates the kinase activity of SMG-1 on Upf1 without contacting the catalytic domain. Assembly of the SMG-1:SMG-8:SMG-9 complex induces a significant motion of the HEAT repeats that is signaled to the kinase domain. Thus, large-scale conformational changes induced by SMG-8 after SMG-9-mediated recruitment tune SMG-1 kinase activity to modulate NMD.
History
DepositionDec 17, 2010-
Header (metadata) releaseJan 21, 2011-
Map releaseDec 23, 2011-
UpdateDec 23, 2011-
Current statusDec 23, 2011Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.05
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.05
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMD1852.png

Downloads & links

-
Map

FileDownload / File: emd_1852.map.gz / Format: CCP4 / Size: 1.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis is the EM map of the negatively stained SMG-1-8-9 complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
4.2 Å/pix.
x 80 pix.
= 336. Å		4.2 Å/pix.
x 80 pix.
= 336. Å		4.2 Å/pix.
x 80 pix.
= 336. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 4.2 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05 / Movie #1: 0.05
Minimum - Maximum-0.0221306 - 0.179076
Average (Standard dev.)0.00185082 (±0.0110756)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-40-40-40
Dimensions808080
Spacing808080
CellA=B=C: 336 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.24.24.2
M x/y/z808080
origin x/y/z0.0000.0000.000
length x/y/z336.000336.000336.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-30-24-70
NX/NY/NZ6149141
MAP C/R/S123
start NC/NR/NS-40-40-40
NC/NR/NS808080
D min/max/mean-0.0220.1790.002

-
Supplemental data

-
Sample components

-
Entire : Human SMG-1 kinase bound to SMG-9 and SMG-8

EntireName: Human SMG-1 kinase bound to SMG-9 and SMG-8
Components
  • Sample: Human SMG-1 kinase bound to SMG-9 and SMG-8
  • Protein or peptide: SMG-1
  • Protein or peptide: SMG-9
  • Protein or peptide: SMG-8

-
Supramolecule #1000: Human SMG-1 kinase bound to SMG-9 and SMG-8

SupramoleculeName: Human SMG-1 kinase bound to SMG-9 and SMG-8 / type: sample / ID: 1000
Oligomeric state: One molecule of SMG-1 binds to one molecule of SMG-9 and one molecule of SMG-8
Number unique components: 3
Molecular weightTheoretical: 580 KDa

-
Macromolecule #1: SMG-1

MacromoleculeName: SMG-1 / type: protein_or_peptide / ID: 1 / Name.synonym: SMG-1 / Number of copies: 1 / Oligomeric state: Monomer / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human) / synonym: Human
Molecular weightTheoretical: 410 KDa
Recombinant expressionOrganism: 293T cells / Recombinant plasmid: pEF_Flag-HA-SBP
SequenceGO: nuclear-transcribed mRNA catabolic process, nonsense-mediated decay

-
Macromolecule #2: SMG-9

MacromoleculeName: SMG-9 / type: protein_or_peptide / ID: 2 / Name.synonym: SMG-9 / Number of copies: 1 / Oligomeric state: Monomer / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human) / synonym: Human
Molecular weightTheoretical: 60 KDa
Recombinant expressionOrganism: 293T Cells / Recombinant plasmid: pSR_Strep-HA
SequenceGO: nuclear-transcribed mRNA catabolic process, nonsense-mediated decay

-
Macromolecule #3: SMG-8

MacromoleculeName: SMG-8 / type: protein_or_peptide / ID: 3 / Name.synonym: SMG-8 / Number of copies: 1 / Oligomeric state: Monomer / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human) / synonym: Human
Molecular weightTheoretical: 110 KDa
Recombinant expressionOrganism: 293T Cells / Recombinant plasmid: pSR_Strep-HA
SequenceGO: nuclear-transcribed mRNA catabolic process, nonsense-mediated decay

-
Experimental details

-
Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
Details: 10 mM HEPES-KOH at pH7.5, 150 mM NaCl, 20% glycerol, 10 mM MgCl2
StainingType: NEGATIVE
Details: Protein was adsorbed for 1 minute, washed in two water drops and stained with 2% w/v uranyl formate for 1 minute.
GridDetails: 400 mesh copper grid
VitrificationCryogen name: NONE / Instrument: OTHER

-
Electron microscopy

MicroscopeJEOL 1230
TemperatureAverage: 294 K
Alignment procedureLegacy - Astigmatism: Objective lens astigmatism was corrected at 80,000 times magnification
DetailsMicroscope JEOL JEM-1230
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: OTHER / Digitization - Sampling interval: 10.5 µm / Details: Minolta Dimage Scan Multi PRO scanner / Bits/pixel: 16
Tilt angle min0
Electron beamAcceleration voltage: 100 kV / Electron source: TUNGSTEN HAIRPIN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.9 mm / Nominal defocus max: 1.2 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 50000
Sample stageSpecimen holder: Side entry single tilt holder / Specimen holder model: JEOL / Tilt angle max: 20

-
Image processing

DetailsParticles were collected manually.
CTF correctionDetails: Each micrograph
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 24.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EMAN, Xmipp / Number images used: 13853

+
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