[English] 日本語
Yorodumi
- EMDB-4240: Human Bact spliceosome state 8 unmasked -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-4240
TitleHuman Bact spliceosome state 8 unmasked
Map data
Sample
  • Complex: human Bact spliceosome state 1 unmasked
Function / homology
Function and homology information


post-spliceosomal complex / RES complex / negative regulation of chemokine-mediated signaling pathway / snoRNA splicing / U11/U12 snRNP / snRNP binding / post-mRNA release spliceosomal complex / U2 snRNP binding / regulation of retinoic acid receptor signaling pathway / U7 snRNA binding ...post-spliceosomal complex / RES complex / negative regulation of chemokine-mediated signaling pathway / snoRNA splicing / U11/U12 snRNP / snRNP binding / post-mRNA release spliceosomal complex / U2 snRNP binding / regulation of retinoic acid receptor signaling pathway / U7 snRNA binding / histone pre-mRNA DCP binding / 3'-5' RNA helicase activity / U7 snRNP / B-WICH complex / generation of catalytic spliceosome for first transesterification step / histone pre-mRNA 3'end processing complex / cis assembly of pre-catalytic spliceosome / regulation of vitamin D receptor signaling pathway / SLBP independent Processing of Histone Pre-mRNAs / SLBP Dependent Processing of Replication-Dependent Histone Pre-mRNAs / spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) / embryonic brain development / splicing factor binding / miRNA processing / protein methylation / U12-type spliceosomal complex / methylosome / 7-methylguanosine cap hypermethylation / nuclear retinoic acid receptor binding / U2-type catalytic step 1 spliceosome / U1 snRNP binding / pICln-Sm protein complex / Prp19 complex / RNA splicing, via transesterification reactions / blastocyst formation / poly(A) binding / positive regulation of androgen receptor activity / mRNA 3'-end processing / spliceosomal tri-snRNP complex / small nuclear ribonucleoprotein complex / P granule / pre-mRNA binding / sno(s)RNA-containing ribonucleoprotein complex / SMN-Sm protein complex / mRNA cis splicing, via spliceosome / U2-type spliceosomal complex / telomerase RNA binding / U2-type precatalytic spliceosome / positive regulation of mRNA splicing, via spliceosome / : / telomerase holoenzyme complex / C2H2 zinc finger domain binding / regulation of mRNA splicing, via spliceosome / U2-type prespliceosome assembly / U2-type catalytic step 2 spliceosome / commitment complex / positive regulation by host of viral transcription / U4 snRNP / positive regulation of vitamin D receptor signaling pathway / Transport of Mature mRNA derived from an Intron-Containing Transcript / Notch binding / transcription regulator inhibitor activity / U2 snRNP / nuclear vitamin D receptor binding / SAGA complex / Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells / RNA Polymerase II Transcription Termination / RUNX3 regulates NOTCH signaling / positive regulation of transcription by RNA polymerase III / U1 snRNP / RHOBTB1 GTPase cycle / NOTCH4 Intracellular Domain Regulates Transcription / U2-type prespliceosome / ubiquitin-ubiquitin ligase activity / K63-linked polyubiquitin modification-dependent protein binding / WD40-repeat domain binding / NOTCH3 Intracellular Domain Regulates Transcription / positive regulation of neurogenesis / pattern recognition receptor activity / lipid biosynthetic process / precatalytic spliceosome / nuclear androgen receptor binding / cyclosporin A binding / spliceosomal complex assembly / positive regulation of transcription by RNA polymerase I / Notch-HLH transcription pathway / mRNA Splicing - Minor Pathway / Formation of paraxial mesoderm / generation of catalytic spliceosome for second transesterification step / positive regulation of transforming growth factor beta receptor signaling pathway / regulation of RNA splicing / SMAD binding / protein K63-linked ubiquitination / mRNA 3'-splice site recognition / antiviral innate immune response / blastocyst development / protein localization to nucleus / spliceosomal tri-snRNP complex assembly / transcription-coupled nucleotide-excision repair / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator
Similarity search - Function
Pre-mRNA-splicing factor CWC24-like / Ist3-like, RNA recognition motif / Pre-mRNA-splicing factor Isy1 / Bud13 / Pre-mRNA-splicing factor Isy1 superfamily / Isy1-like splicing family / Pre-mRNA-splicing factor of RES complex / : / : / Intron-binding protein aquarius, beta-barrel ...Pre-mRNA-splicing factor CWC24-like / Ist3-like, RNA recognition motif / Pre-mRNA-splicing factor Isy1 / Bud13 / Pre-mRNA-splicing factor Isy1 superfamily / Isy1-like splicing family / Pre-mRNA-splicing factor of RES complex / : / : / Intron-binding protein aquarius, beta-barrel / Intron-binding protein aquarius insert domain / : / Pre-mRNA-splicing factor SPF27 / Breast carcinoma amplified sequence 2 (BCAS2) / PWI domain superfamily / PWI domain / PWI domain profile. / CWF11 family / Intron-binding protein aquarius, N-terminal / SF3B6, RNA recognition motif / Intron-binding protein aquarius N-terminal / Peptidyl-prolyl cis-trans isomerase E / Peptidyl-prolyl cis-trans isomerase E, RNA recognition motif / Splicing factor 3A subunit 1, ubiquitin domain / Splicing factor SF3a60 binding domain / Splicing factor SF3a60 binding domain / : / Replication stress response SDE2 C-terminal / Cactus-binding C-terminus of cactin protein / PWI domain / PWI, domain in splicing factors / U2 small nuclear ribonucleoprotein B'', RNA recognition motif 2 / U2 small nuclear ribonucleoprotein B'', RNA recognition motif 1 / Cyclophilin-type peptidyl-prolyl cis-trans isomerase, cyclophilin A-like / Splicing factor 3A subunit 1 / Splicing factor 3A subunit 1, conserved domain / Helix hairpin bin domain superfamily / Pre-mRNA splicing factor PRP21 like protein / SF3A2 domain / Pre-mRNA-splicing factor SF3a complex subunit 2 (Prp11) / mRNA splicing factor Cwf21 domain / Splicing factor SF3a60 /Prp9 subunit, C-terminal / SF3A3 domain / cwf21 domain / SF3a60/Prp9 C-terminal / Pre-mRNA-splicing factor SF3A3, of SF3a complex, Prp9 / Pre-mRNA-processing factor 17 / Splicing factor 3B, subunit 5 / : / STL11, N-terminal / SWAP/Surp / SWAP/Surp superfamily / Surp module / SURP motif repeat profile. / Suppressor-of-White-APricot splicing regulator / Pre-mRNA-splicing factor 19 / Pre-mRNA-processing factor 19 / : / Prp19/Pso4-like / Splicing factor 3B subunit 1 / DNA2/NAM7 helicase, helicase domain / DNA2/NAM7-like helicase / Splicing factor 3B subunit 1 / AAA domain / Domain of unknown function DUF382 / WD repeat Prp46/PLRG1-like / Domain of unknown function (DUF382) / U-box domain / BUD31/G10-related, conserved site / : / : / G10 protein signature 1. / G10 protein signature 2. / SKI-interacting protein SKIP, SNW domain / SKI-interacting protein, SKIP / SKIP/SNW domain / Myb-like DNA-binding domain / Pre-mRNA-splicing factor Cwf15/Cwc15 / HAT (Half-A-TPR) repeat / Cwf15/Cwc15 cell cycle control protein / Zinc-finger of C2H2 type / Zinc finger C-x8-C-x5-C-x3-H type (and similar) / Pre-mRNA-splicing factor Cwc2/Slt11 / G10 protein / PHF5-like / Pre-mRNA-splicing factor BUD31 / PHF5-like protein / PSP, proline-rich / Pre-mRNA splicing factor component Cdc5p/Cef1, C-terminal / PSP / pre-mRNA splicing factor component / proline-rich domain in spliceosome associated proteins / Splicing factor 3B subunit 5/RDS3 complex subunit 10 / Splicing factor 3B subunit 10 (SF3b10) / Small ribonucleoprotein associated, SmB/SmN / Splicing factor 3B subunit 1-like / Matrin/U1-C, C2H2-type zinc finger / Zinc finger matrin-type profile. / Initiation factor eIF-4 gamma, MA3 / MA3 domain
Similarity search - Domain/homology
E3 ubiquitin-protein ligase RNF113A / Pleiotropic regulator 1 / Pre-mRNA-splicing factor ATP-dependent RNA helicase DHX16 / RNA helicase aquarius / Pre-mRNA-processing factor 17 / Splicing factor 3B subunit 1 / U5 small nuclear ribonucleoprotein 200 kDa helicase / Pre-mRNA-splicing factor SPF27 / U2 small nuclear ribonucleoprotein B'' / U2 small nuclear ribonucleoprotein A' ...E3 ubiquitin-protein ligase RNF113A / Pleiotropic regulator 1 / Pre-mRNA-splicing factor ATP-dependent RNA helicase DHX16 / RNA helicase aquarius / Pre-mRNA-processing factor 17 / Splicing factor 3B subunit 1 / U5 small nuclear ribonucleoprotein 200 kDa helicase / Pre-mRNA-splicing factor SPF27 / U2 small nuclear ribonucleoprotein B'' / U2 small nuclear ribonucleoprotein A' / Small nuclear ribonucleoprotein-associated proteins B and B' / Protein BUD31 homolog / Small nuclear ribonucleoprotein E / Small nuclear ribonucleoprotein F / Small nuclear ribonucleoprotein G / Small nuclear ribonucleoprotein Sm D1 / Small nuclear ribonucleoprotein Sm D2 / Small nuclear ribonucleoprotein Sm D3 / Splicing factor 3A subunit 3 / Splicing factor 3B subunit 2 / SNW domain-containing protein 1 / 116 kDa U5 small nuclear ribonucleoprotein component / Splicing factor 3B subunit 3 / Splicing factor 3A subunit 2 / Splicing factor 3A subunit 1 / Pre-mRNA-processing-splicing factor 8 / Spliceosome-associated protein CWC27 homolog / PHD finger-like domain-containing protein 5A / Serine/arginine repetitive matrix protein 1 / Smad nuclear-interacting protein 1 / U5 small nuclear ribonucleoprotein 40 kDa protein / Cell division cycle 5-like protein / BUD13 homolog / Splicing factor 3B subunit 5 / Crooked neck-like protein 1 / Pre-mRNA-splicing factor CWC22 homolog / Pre-mRNA-splicing factor SYF1 / Pre-mRNA-splicing factor RBM22 / Spliceosome-associated protein CWC15 homolog / Pre-mRNA-splicing factor ISY1 homolog / Pre-mRNA-processing factor 19 / Peptidyl-prolyl cis-trans isomerase E / Serine/arginine repetitive matrix protein 2 / RNA-binding motif protein, X-linked 2 / Splicing factor 3B subunit 6 / Peptidyl-prolyl cis-trans isomerase-like 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.5 Å
AuthorsHaselbach D / Komarov I / Agafonov D / Kastner B / Luehrmann R / Stark H
CitationJournal: Cell / Year: 2018
Title: Structure and Conformational Dynamics of the Human Spliceosomal B Complex.
Authors: David Haselbach / Ilya Komarov / Dmitry E Agafonov / Klaus Hartmuth / Benjamin Graf / Olexandr Dybkov / Henning Urlaub / Berthold Kastner / Reinhard Lührmann / Holger Stark /
Abstract: The spliceosome is a highly dynamic macromolecular complex that precisely excises introns from pre-mRNA. Here we report the cryo-EM 3D structure of the human B spliceosome at 3.4 Å resolution. In ...The spliceosome is a highly dynamic macromolecular complex that precisely excises introns from pre-mRNA. Here we report the cryo-EM 3D structure of the human B spliceosome at 3.4 Å resolution. In the B state, the spliceosome is activated but not catalytically primed, so that it is functionally blocked prior to the first catalytic step of splicing. The spliceosomal core is similar to the yeast B spliceosome; important differences include the presence of the RNA helicase aquarius and peptidyl prolyl isomerases. To examine the overall dynamic behavior of the purified spliceosome, we developed a principal component analysis-based approach. Calculating the energy landscape revealed eight major conformational states, which we refined to higher resolution. Conformational differences of the highly flexible structural components between these eight states reveal how spliceosomal components contribute to the assembly of the spliceosome, allowing it to generate a dynamic interaction network required for its subsequent catalytic activation.
History
DepositionDec 22, 2017-
Header (metadata) releaseFeb 7, 2018-
Map releaseFeb 7, 2018-
UpdateFeb 7, 2018-
Current statusFeb 7, 2018Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.013
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.013
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6ff7
  • Surface level: 0.013
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4240.png

Downloads & links

-
Map

FileDownload / File: emd_4240.map.gz / Format: CCP4 / Size: 282.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.16 Å
Density
Contour LevelBy AUTHOR: 0.013 / Movie #1: 0.013
Minimum - Maximum-0.014408626 - 0.06181489
Average (Standard dev.)0.00064544595 (±0.004007307)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions420420420
Spacing420420420
CellA=B=C: 487.19998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.161.161.16
M x/y/z420420420
origin x/y/z0.0000.0000.000
length x/y/z487.200487.200487.200
α/β/γ90.00090.00090.000
start NX/NY/NZ-128-128-128
NX/NY/NZ256256256
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS420420420
D min/max/mean-0.0140.0620.001

-
Supplemental data

-
Sample components

-
Entire : human Bact spliceosome state 1 unmasked

EntireName: human Bact spliceosome state 1 unmasked
Components
  • Complex: human Bact spliceosome state 1 unmasked

-
Supramolecule #1: human Bact spliceosome state 1 unmasked

SupramoleculeName: human Bact spliceosome state 1 unmasked / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Homo sapiens (human) / Strain: HELA
Molecular weightTheoretical: 4.5 MDa

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.05 mg/mL
BufferpH: 7.9
Component:
ConcentrationNameFormula
20.0 mMHEPES
150.0 mMNaClSodium chloride
1.5 mMMgCl2
GridModel: Quantifoil R3.5/1 / Material: COPPER / Mesh: 400 / Support film - #0 - Film type ID: 1 / Support film - #0 - Material: CARBON / Support film - #0 - topology: HOLEY / Support film - #1 - Film type ID: 2 / Support film - #1 - Material: CARBON / Support film - #1 - topology: CONTINUOUS
VitrificationCryogen name: ETHANE / Chamber humidity: 75 % / Chamber temperature: 277 K / Instrument: LEICA EM GP / Details: blot with blotting sensor.

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 0.001 mm / Nominal defocus max: 4.5 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 59000
Specialist opticsSpherical aberration corrector: Microscope was modified with a Cs corrector with two hexapoles elements
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Alignment procedureComa free - Residual tilt: 14.0 mrad
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Digitization - Sampling interval: 14.0 µm / Number grids imaged: 1 / Number real images: 32000 / Average exposure time: 1.0 sec. / Average electron dose: 40.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Particle selectionNumber selected: 3300000
CTF correctionSoftware - Name: Gctf
Initial angle assignmentType: OTHER / Software - Name: EMAN2
Final 3D classificationNumber classes: 220 / Software - Name: RELION
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1) / Number images used: 165853

-
Atomic model buiding 1

RefinementProtocol: RIGID BODY FIT
Output model

PDB-6ff7:
human Bact spliceosome core structure

+
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