[English] 日本語
Yorodumi
- EMDB-1062: Three-dimensional structure of C complex spliceosomes by electron... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-1062
TitleThree-dimensional structure of C complex spliceosomes by electron microscopy.
Map dataMap of C-complex of the human spliceosome.
Sample
  • Sample: C-complex of the human spliceosome
  • Organelle or cellular component: C-complex Spliceosome
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / negative staining / Resolution: 30.0 Å
AuthorsJurica MS / Sousa D / Moore MJ / Grigorieff N
CitationJournal: Nat Struct Mol Biol / Year: 2004
Title: Three-dimensional structure of C complex spliceosomes by electron microscopy.
Authors: Melissa S Jurica / Duncan Sousa / Melissa J Moore / Nikolaus Grigorieff /
Abstract: The spliceosome is a multimegadalton RNA-protein machine that removes noncoding sequences from nascent pre-mRNAs. Recruitment of the spliceosome to splice sites and subsequent splicing require a ...The spliceosome is a multimegadalton RNA-protein machine that removes noncoding sequences from nascent pre-mRNAs. Recruitment of the spliceosome to splice sites and subsequent splicing require a series of dynamic interactions among the spliceosome's component U snRNPs and many additional protein factors. These dynamics present several challenges for structural analyses, including purification of stable complexes to compositional homogeneity and assessment of conformational heterogeneity. We have isolated spliceosomes arrested before the second chemical step of splicing (C complex) in which U2, U5 and U6 snRNAs are stably associated. Using electron microscopy, we obtained images of C complex spliceosomes under cryogenic conditions and determined a three-dimensional structure of a core complex to a resolution of 30 A. The structure reveals a particle of dimensions 27 x 22 x 24 nm with a relatively open arrangement of three primary domains.
History
DepositionDec 10, 2003-
Header (metadata) releaseDec 16, 2003-
Map releaseFeb 23, 2004-
UpdateOct 24, 2012-
Current statusOct 24, 2012Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.411471886
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.411471886
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1062.gif

Downloads & links

-
Map

FileDownload / File: emd_1062.map.gz / Format: CCP4 / Size: 7.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMap of C-complex of the human spliceosome.
Voxel sizeX=Y=Z: 4.6667 Å
Density
Contour Level1: 0.27 / Movie #1: 0.4114719
Minimum - Maximum0.0 - 1.64744
Average (Standard dev.)0.0171454 (±0.100784)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-64-64-64
Dimensions128128128
Spacing128128128
CellA=B=C: 597.338 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.6667031254.6667031254.666703125
M x/y/z128128128
origin x/y/z0.0000.0000.000
length x/y/z597.338597.338597.338
α/β/γ90.00090.00090.000
start NX/NY/NZ0052
NX/NY/NZ12812855
MAP C/R/S123
start NC/NR/NS-64-64-64
NC/NR/NS128128128
D min/max/mean0.0001.6470.017

-
Supplemental data

-
Sample components

-
Entire : C-complex of the human spliceosome

EntireName: C-complex of the human spliceosome
Components
  • Sample: C-complex of the human spliceosome
  • Organelle or cellular component: C-complex Spliceosome

-
Supramolecule #1000: C-complex of the human spliceosome

SupramoleculeName: C-complex of the human spliceosome / type: sample / ID: 1000 / Number unique components: 1
Molecular weightTheoretical: 2.6 MDa
Method: The molecular weight of core C-complex components were added together. The map becomes discontinous at either higher or lower weights.

-
Supramolecule #1: C-complex Spliceosome

SupramoleculeName: C-complex Spliceosome / type: organelle_or_cellular_component / ID: 1 / Name.synonym: Spliceosome / Number of copies: 1 / Oligomeric state: monomer / Recombinant expression: No
Source (natural)Organism: Homo sapiens (human) / synonym: Human / Cell: HeLa / Organelle: Nucleus / Location in cell: Nucleus
Molecular weightExperimental: 2.6 MDa

-
Experimental details

-
Structure determination

Methodnegative staining, cryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
Details: 150mM KCl, 5mM EDTA, 20mM Tris, 10mM maltose, and 5% glycerol
StainingType: NEGATIVE
Details: Thin carbon is floated for 1 minute on the sample. The carbon is transferred onto a solution of 1% uranyl formate, sample side down, and then picked up with a holey carbon grid (Quantifoil). ...Details: Thin carbon is floated for 1 minute on the sample. The carbon is transferred onto a solution of 1% uranyl formate, sample side down, and then picked up with a holey carbon grid (Quantifoil). A second layer of thin carbon is sandwiched on top of the sample.
GridDetails: 400 mesh copper grid
VitrificationCryogen name: NITROGEN / Instrument: HOMEMADE PLUNGER / Details: Vitrification instrument: human hand. none / Method: See experimental details.

-
Electron microscopy

MicroscopeFEI/PHILIPS CM12
Electron beamAcceleration voltage: 120 kV / Electron source: LAB6
Electron opticsCalibrated magnification: 60000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2 mm / Nominal defocus max: 20.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 60000
Sample stageSpecimen holder: Side entry liquid nitrogen-cooled cryo specimen holder.
Specimen holder model: OTHER / Tilt angle min: 35 / Tilt angle max: 45
TemperatureMin: 90 K / Max: 100 K / Average: 95 K
Alignment procedureLegacy - Astigmatism: objective lens astigmatism was corrected at 200,000 times magnification
DetailsMICROSCOPE Philips CM12
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7 µm / Number real images: 72 / Average electron dose: 10 e/Å2 / Bits/pixel: 8

-
Image processing

CTF correctionDetails: CTF correction of each particle
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 30.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: Spider and Frealign
Details: The final map was calculated from one dataset and filtered to 20 angstroms resolution.
Number images used: 1834
DetailsImage tilt pairs were collected manually and processed using Spider and Frealign.

+
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