|Entry||Database: EMDB / ID: EMD-4240|
|Title||Human Bact spliceosome state 8 unmasked|
|Sample||human Bact spliceosome state 1 unmasked|
|Function / homology|
Function and homology information
isopeptide cross-linking via N6-glycyl-L-lysine / positive regulation of vitamin D receptor signaling pathway / post-spliceosomal complex / RES complex / U2-type prespliceosome assembly / cellular response to interleukin-2 / cellular response to wortmannin / cellular response to prolactin / U11/U12 snRNP / snoRNA splicing ...isopeptide cross-linking via N6-glycyl-L-lysine / positive regulation of vitamin D receptor signaling pathway / post-spliceosomal complex / RES complex / U2-type prespliceosome assembly / cellular response to interleukin-2 / cellular response to wortmannin / cellular response to prolactin / U11/U12 snRNP / snoRNA splicing / negative regulation of chemokine-mediated signaling pathway / U2 snRNP binding / snRNP binding / U7 snRNA binding / histone pre-mRNA DCP binding / leucine zipper domain binding / signal transduction involved in DNA damage checkpoint / U7 snRNP / transcription corepressor binding / histone pre-mRNA 3'end processing complex / cis assembly of pre-catalytic spliceosome / production of miRNAs involved in gene silencing by miRNA / methylosome / blastocyst formation / regulation of vitamin D receptor signaling pathway / histone mRNA metabolic process / post-mRNA release spliceosomal complex / generation of catalytic spliceosome for first transesterification step / RNA splicing, via transesterification reactions / U2-type spliceosomal complex / inner cell mass cell proliferation / spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) / splicing factor binding / positive regulation of androgen receptor activity / hair cycle / positive regulation of neurogenesis / telomerase holoenzyme complex / positive regulation of astrocyte differentiation / U2-type catalytic step 1 spliceosome / protein phosphatase 1 binding / U1 snRNP binding / U2-type precatalytic spliceosome / WD40-repeat domain binding / pICln-Sm protein complex / positive regulation of mRNA splicing, via spliceosome / positive regulation by host of viral transcription / regulation of retinoic acid receptor signaling pathway / U4 snRNP / ubiquitin-ubiquitin ligase activity / P granule / C2H2 zinc finger domain binding / small nuclear ribonucleoprotein complex / retinoic acid receptor binding / telomerase RNA binding / spliceosomal tri-snRNP complex / positive regulation of gene expression, epigenetic / poly(A) binding / import into nucleus / SMN-Sm protein complex / pre-mRNA binding / protein methylation / mRNA cis splicing, via spliceosome / U2-type catalytic step 2 spliceosome / commitment complex / Prp19 complex / regulation of mRNA splicing, via spliceosome / U2 snRNP / Cul4-RING E3 ubiquitin ligase complex / vitamin D receptor binding / U12-type spliceosomal complex / Notch binding / K63-linked polyubiquitin modification-dependent protein binding / positive regulation of transcription of Notch receptor target / spliceosomal complex assembly / small nucleolar ribonucleoprotein complex / blastocyst development / generation of catalytic spliceosome for second transesterification step / mRNA 3'-end processing / U2-type prespliceosome / spliceosomal snRNP assembly / cellular response to fibroblast growth factor stimulus / precatalytic spliceosome / U1 snRNP / mRNA 3'-splice site recognition / lipid biosynthetic process / protein K63-linked ubiquitination / RNA export from nucleus / spliceosomal tri-snRNP complex assembly / positive regulation of transforming growth factor beta receptor signaling pathway / cyclosporin A binding / positive regulation of histone H3-K4 methylation / U5 snRNP / retinoic acid receptor signaling pathway / U5 snRNA binding / U2 snRNA binding / positive regulation of Notch signaling pathway / pre-mRNA intronic binding / protein localization to nucleus / RNA processing / U4/U6 x U5 tri-snRNP complex
Helicase superfamily 1/2, ATP-binding domain / SAP domain / MIF4G-like, type 3 / Splicing factor 3A subunit 1 / U box domain / Matrin/U1-C-like, C2H2-type zinc finger / U2A'/phosphoprotein 32 family A, C-terminal / HAT (Half-A-TPR) repeat / PRP8 domain IV core / Initiation factor eIF-4 gamma, MA3 ...Helicase superfamily 1/2, ATP-binding domain / SAP domain / MIF4G-like, type 3 / Splicing factor 3A subunit 1 / U box domain / Matrin/U1-C-like, C2H2-type zinc finger / U2A'/phosphoprotein 32 family A, C-terminal / HAT (Half-A-TPR) repeat / PRP8 domain IV core / Initiation factor eIF-4 gamma, MA3 / PWI domain / DNA/RNA helicase, ATP-dependent, DEAH-box type, conserved site / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain / Zinc finger, RING-type / Splicing factor SF3a60 binding domain / G10 protein / Pre-mRNA splicing factor component Cdc5p/Cef1 / Cyclophilin-type peptidyl-prolyl cis-trans isomerase / Spt5 C-terminal domain / Cyclophilin-type peptidyl-prolyl cis-trans isomerase, conserved site / Cleavage/polyadenylation specificity factor, A subunit, C-terminal / SF3A3 domain / Ubiquitin-like domain superfamily / Helix hairpin bin domain superfamily / Cyclophilin-like domain superfamily / PHF5-like / Small GTP-binding protein domain / Sec63 domain / CWF11 family / Translation elongation factor EFTu-like, domain 2 / SKI-interacting protein SKIP, SNW domain / Pre-mRNA-processing-splicing factor 8 / P-loop containing nucleoside triphosphate hydrolase / Small nuclear ribonucleoprotein Sm D2 / Like-Sm (LSM) domain containing protein, LSm4/SmD1/SmD3 / Small nuclear ribonucleoprotein E / WD40 repeat / Helicase, C-terminal / PSP, proline-rich / Splicing factor 3B, subunit 5 / SKI-interacting protein, SKIP / Zinc finger, CCCH-type / Small ribonucleoprotein associated, SmB/SmN / JAB1/MPN/MOV34 metalloenzyme domain / RNA recognition motif domain / Forkhead-associated (FHA) domain / Sm-like protein Lsm6/SmF / Myb domain / SWAP/Surp / Immunoglobulin E-set / Peptidyl-prolyl cis-trans isomerase E / Armadillo-type fold / MIF4G-like domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Splicing factor 3B subunit 1 / Zinc finger, RING-type, conserved site / WD40-repeat-containing domain / Ribosomal protein S5 domain 2-type fold / SANT/Myb domain / Leucine-rich repeat / G-protein beta WD-40 repeat / LSM domain, eukaryotic/archaea-type / WD40 repeat, conserved site / Ribosomal protein S5 domain 2-type fold, subgroup / Tetratricopeptide repeat / RNA recognition motif, spliceosomal PrP8 / Pre-mRNA-processing-splicing factor 8, U5-snRNA-binding / Ubiquitin-like domain / Transcription factor, GTP-binding domain / Ricin B, lectin domain / Matrin/U1-C, C2H2-type zinc finger / Pre-mRNA-processing-splicing factor 8, U6-snRNA-binding / Bud13 / BUD31/G10-related, conserved site / Elongation factor EFG, domain V-like / Translation elongation factor EFG/EF2, domain IV / Splicing factor SF3a60 subunit C-terminal / Pre-mRNA-processing factor 19 / Zinc finger C2H2 superfamily / Splicing factor 3B subunit 5/RDS3 complex subunit 10 / LSM domain superfamily / PROCT domain / Nucleotide-binding alpha-beta plait domain superfamily / 116kDa U5 small nuclear ribonucleoprotein component, C-terminal / C2 domain superfamily / DNA2/NAM7 helicase-like, C-terminal / PROCN domain / DNA2/NAM7 helicase, helicase domain / Elongation Factor G, domain II / SWAP/Surp superfamily / Brr2, N-terminal helicase PWI domain / RNA-binding domain superfamily / DEAD/DEAH box helicase domain / Pre-mRNA-splicing factor Cwc2/Slt11 / WD40-repeat-containing domain superfamily / PRO8NT domain / Domain of unknown function DUF1605 / Winged helix DNA-binding domain superfamily / Armadillo-like helical / PWI domain superfamily
Crooked neck-like protein 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-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 / Serine/arginine repetitive matrix protein 2 / 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 / RNA-binding motif protein, X-linked 2 / Splicing factor 3B subunit 6 / Splicing factor 3A subunit 2 / Splicing factor 3A subunit 1 / U5 small nuclear ribonucleoprotein 200 kDa helicase / Splicing factor 3B subunit 3 / Small nuclear ribonucleoprotein-associated proteins B and B' / 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 / Pre-mRNA-splicing factor SPF27 / U2 small nuclear ribonucleoprotein B'' / U2 small nuclear ribonucleoprotein A' / Protein BUD31 homolog / 116 kDa U5 small nuclear ribonucleoprotein component / 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 / Peptidyl-prolyl cis-trans isomerase-like 1
|Biological species||Homo sapiens (human)|
|Method||single particle reconstruction / cryo EM / Resolution: 4.5 Å|
|Authors||Haselbach D / Komarov I / Agafonov D / Kastner B / Luehrmann R / Stark H|
|Citation||Journal: 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.
|Validation Report||PDB-ID: 6ff7|
SummaryFull reportAbout validation report
|Structure viewer||EM map: |
Downloads & links
|File||Download / File: emd_4240.map.gz / Format: CCP4 / Size: 282.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)|
|Projections & slices|
Images are generated by Spider.
|Voxel size||X=Y=Z: 1.16 Å|
|Symmetry||Space group: 1|
CCP4 map header:
-Entire human Bact spliceosome state 1 unmasked
|Entire||Name: human Bact spliceosome state 1 unmasked / Number of components: 1|
-Component #1: protein, human Bact spliceosome state 1 unmasked
|Protein||Name: human Bact spliceosome state 1 unmasked / Recombinant expression: No|
|Mass||Theoretical: 4.5 MDa|
|Source||Species: Homo sapiens (human) / Strain: HELA|
|Specimen||Specimen state: Particle / Method: cryo EM|
|Sample solution||Specimen conc.: 0.05 mg/mL / pH: 7.9|
|Vitrification||Instrument: LEICA EM GP / Cryogen name: ETHANE / Temperature: 277 K / Humidity: 75 % / Details: blot with blotting sensor.|
-Electron microscopy imaging
Model: Titan Krios / Image courtesy: FEI Company
|Imaging||Microscope: FEI TITAN KRIOS|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 40 e/Å2 / Illumination mode: SPOT SCAN|
|Lens||Magnification: 59000.0 X (nominal) / Cs: 0.001 mm / Imaging mode: BRIGHT FIELD / Defocus: 800.0 - 4500.0 nm|
|Specimen Holder||Model: FEI TITAN KRIOS AUTOGRID HOLDER|
|Camera||Detector: FEI FALCON III (4k x 4k)|
|Image acquisition||Number of digital images: 32000 / Sampling size: 14 µm|
|Processing||Method: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 165853|
|3D reconstruction||Software: RELION / Resolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF|
-Atomic model buiding
|Modeling #1||Refinement protocol: rigid body|
-Aug 12, 2020. New: Covid-19 info
New: Covid-19 info
Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data
-Mar 5, 2020. Novel coronavirus structure data
Novel coronavirus structure data
- International Committee on Taxonomy of Viruses (ICTV) defined the short name of the 2019 coronavirus as "SARS-CoV-2".
The species Severe acute respiratory syndrome-related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2 - nature microbiology
- In the structure databanks used in Yorodumi, some data are registered as the other names, "COVID-19 virus" and "2019-nCoV". Here are the details of the virus and the list of structure data.
Related info.:Yorodumi Speices / Aug 12, 2020. New: Covid-19 info
+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. (see PDBe EMDB page)
- The EM Navigator/Yorodumi systems omit the EMD- prefix.
Related info.:Q: What is "EMD"? / ID/Accession-code notation in Yorodumi/EM Navigator
+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. See below links for details.
- 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.
+Jun 16, 2017. Omokage search with filter
Omokage search with filter
- Result of Omokage search can be filtered by keywords and the database types
Related info.:Omokage search
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.
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