[English] 日本語
Yorodumi
- PDB-6n7r: Saccharomyces cerevisiae spliceosomal E complex (ACT1) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6n7r
TitleSaccharomyces cerevisiae spliceosomal E complex (ACT1)
Components
  • (Small nuclear ribonucleoprotein ...SnRNP) x 6
  • (U1 small nuclear ribonucleoprotein ...) x 5
  • 56 kDa U1 small nuclear ribonucleoprotein component
  • ACT1 pre-mRNA
  • Pre-mRNA-processing factor 39
  • Protein LUC7
  • Protein NAM8
  • Small nuclear ribonucleoprotein-associated protein B
  • U1 snRNAU1 spliceosomal RNA
KeywordsRNA BINDING PROTEIN / pre-mRNA splicing / spliceosome / E complex
Function / homology
Function and homology information


positive regulation of RNA binding / mRNA splice site selection / splicing factor binding / positive regulation of mRNA splicing, via spliceosome / pICln-Sm protein complex / U4 snRNP / mRNA 5'-splice site recognition / small nuclear ribonucleoprotein complex / SMN-Sm protein complex / pre-mRNA 5'-splice site binding ...positive regulation of RNA binding / mRNA splice site selection / splicing factor binding / positive regulation of mRNA splicing, via spliceosome / pICln-Sm protein complex / U4 snRNP / mRNA 5'-splice site recognition / small nuclear ribonucleoprotein complex / SMN-Sm protein complex / pre-mRNA 5'-splice site binding / commitment complex / U12-type spliceosomal complex / U2 snRNP / small nucleolar ribonucleoprotein complex / U5 snRNP / spliceosomal snRNP assembly / U2-type prespliceosome / P granule / U1 snRNP / U4/U6 x U5 tri-snRNP complex / U1 snRNA binding / poly(U) RNA binding / catalytic step 2 spliceosome / mRNA splicing, via spliceosome / mRNA binding / mitochondrion / RNA binding / zinc ion binding / nucleus / cytosol / cytoplasm
Tetratricopeptide-like helical domain superfamily / Small nuclear ribonucleoprotein G / Sm-like protein Lsm6/SmF / LSM domain superfamily / Luc7-related / Matrin/U1-C-like, C2H2-type zinc finger / HAT (Half-A-TPR) repeat / PWI domain / LSM domain, eukaryotic/archaea-type / Matrin/U1-C, C2H2-type zinc finger ...Tetratricopeptide-like helical domain superfamily / Small nuclear ribonucleoprotein G / Sm-like protein Lsm6/SmF / LSM domain superfamily / Luc7-related / Matrin/U1-C-like, C2H2-type zinc finger / HAT (Half-A-TPR) repeat / PWI domain / LSM domain, eukaryotic/archaea-type / Matrin/U1-C, C2H2-type zinc finger / RNA recognition motif domain / U1 small nuclear ribonucleoprotein C / U1 small nuclear ribonucleoprotein of 70kDa N-terminal / Small nuclear ribonucleoprotein E / Like-Sm (LSM) domain containing protein, LSm4/SmD1/SmD3 / U1-C, C2H2-type zinc finger / Small nuclear ribonucleoprotein Sm D2 / Small nuclear ribonucleoprotein Sm D3 / U1 small nuclear ribonucleoprotein 70kDa / Zinc finger matrin-type profile. / Eukaryotic RNA Recognition Motif (RRM) profile. / U1 small nuclear ribonucleoprotein of 70kDa MW N terminal / U1 zinc finger / LUC7 N_terminus / LSM domain / RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) / Nucleotide-binding alpha-beta plait domain superfamily / Zinc finger C2H2 superfamily / RNA-binding domain superfamily / snRNP70, RNA recognition motif / Small nuclear ribonucleoprotein F
Small nuclear ribonucleoprotein Sm D1 / Small nuclear ribonucleoprotein E / Protein LUC7 / Small nuclear ribonucleoprotein Sm D2 / U1 small nuclear ribonucleoprotein C / 56 kDa U1 small nuclear ribonucleoprotein component / U1 small nuclear ribonucleoprotein component PRP42 / Small nuclear ribonucleoprotein F / U1 small nuclear ribonucleoprotein 70 kDa homolog / Protein NAM8 ...Small nuclear ribonucleoprotein Sm D1 / Small nuclear ribonucleoprotein E / Protein LUC7 / Small nuclear ribonucleoprotein Sm D2 / U1 small nuclear ribonucleoprotein C / 56 kDa U1 small nuclear ribonucleoprotein component / U1 small nuclear ribonucleoprotein component PRP42 / Small nuclear ribonucleoprotein F / U1 small nuclear ribonucleoprotein 70 kDa homolog / Protein NAM8 / U1 small nuclear ribonucleoprotein component SNU71 / Small nuclear ribonucleoprotein Sm D3 / Small nuclear ribonucleoprotein G / Small nuclear ribonucleoprotein-associated protein B / Pre-mRNA-processing factor 39 / U1 small nuclear ribonucleoprotein A / gb:1039023756:
Biological speciesSaccharomyces cerevisiae (baker's yeast)
Saccharomyces cerevisiae S288C (yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsLiu, S. / Li, X. / Zhou, Z.H. / Zhao, R.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research InstituteGM126157 United States
National Institutes of Health/National Human Genome Research InstituteGM114178 United States
National Institutes of Health/National Human Genome Research InstituteGM071940 United States
National Institutes of Health/National Human Genome Research InstituteAI094386 United States
CitationJournal: Nature / Year: 2019
Title: A unified mechanism for intron and exon definition and back-splicing.
Authors: Xueni Li / Shiheng Liu / Lingdi Zhang / Aaron Issaian / Ryan C Hill / Sara Espinosa / Shasha Shi / Yanxiang Cui / Kalli Kappel / Rhiju Das / Kirk C Hansen / Z Hong Zhou / Rui Zhao /
Abstract: The molecular mechanisms of exon definition and back-splicing are fundamental unanswered questions in pre-mRNA splicing. Here we report cryo-electron microscopy structures of the yeast spliceosomal E ...The molecular mechanisms of exon definition and back-splicing are fundamental unanswered questions in pre-mRNA splicing. Here we report cryo-electron microscopy structures of the yeast spliceosomal E complex assembled on introns, providing a view of the earliest event in the splicing cycle that commits pre-mRNAs to splicing. The E complex architecture suggests that the same spliceosome can assemble across an exon, and that it either remodels to span an intron for canonical linear splicing (typically on short exons) or catalyses back-splicing to generate circular RNA (on long exons). The model is supported by our experiments, which show that an E complex assembled on the middle exon of yeast EFM5 or HMRA1 can be chased into circular RNA when the exon is sufficiently long. This simple model unifies intron definition, exon definition, and back-splicing through the same spliceosome in all eukaryotes and should inspire experiments in many other systems to understand the mechanism and regulation of these processes.
Validation Report
SummaryFull reportAbout validation report
History
DepositionNov 28, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 18, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 2, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-0361
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: U1 small nuclear ribonucleoprotein 70 kDa homolog
B: U1 small nuclear ribonucleoprotein C
C: U1 small nuclear ribonucleoprotein A
D: U1 small nuclear ribonucleoprotein component PRP42
E: Pre-mRNA-processing factor 39
F: Protein NAM8
G: 56 kDa U1 small nuclear ribonucleoprotein component
H: U1 small nuclear ribonucleoprotein component SNU71,U1 small nuclear ribonucleoprotein component SNU71,Snu71
I: Protein LUC7
K: Small nuclear ribonucleoprotein-associated protein B
L: Small nuclear ribonucleoprotein Sm D1
M: Small nuclear ribonucleoprotein Sm D2
N: Small nuclear ribonucleoprotein Sm D3
O: Small nuclear ribonucleoprotein E
P: Small nuclear ribonucleoprotein F
Q: Small nuclear ribonucleoprotein G
R: U1 snRNA
r: ACT1 pre-mRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)738,77519
Polymers738,71018
Non-polymers651
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

+
U1 small nuclear ribonucleoprotein ... , 5 types, 5 molecules ABCDH

#1: Protein/peptide U1 small nuclear ribonucleoprotein 70 kDa homolog / U1-70K / U1 small nuclear ribonucleoprotein SNP1 / U1 snRNP protein SNP1


Mass: 34506.148 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q00916
#2: Protein/peptide U1 small nuclear ribonucleoprotein C / U1C


Mass: 27106.016 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q05900
#3: Protein/peptide U1 small nuclear ribonucleoprotein A / U1A / Mutant U1 die protein 1


Mass: 40413.961 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Production host: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain (production host): ATCC 204508 / S288c / References: UniProt: P32605
#4: Protein/peptide U1 small nuclear ribonucleoprotein component PRP42 / U1 snRNP protein PRP42 / 65 kDa snRNP protein / Pre-mRNA-processing factor 42


Mass: 65222.020 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q03776
#8: Protein/peptide U1 small nuclear ribonucleoprotein component SNU71,U1 small nuclear ribonucleoprotein component SNU71,Snu71


Mass: 9123.642 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast), (natural) Saccharomyces cerevisiae S288C (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P53207

+
Protein/peptide , 5 types, 5 molecules EFGIK

#5: Protein/peptide Pre-mRNA-processing factor 39


Mass: 74834.742 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P39682
#6: Protein/peptide Protein NAM8


Mass: 57010.840 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q00539
#7: Protein/peptide 56 kDa U1 small nuclear ribonucleoprotein component


Mass: 56575.277 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q03782
#9: Protein/peptide Protein LUC7


Mass: 30245.885 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q07508
#10: Protein/peptide Small nuclear ribonucleoprotein-associated protein B / snRNP-B / Sm protein B / SmB


Mass: 22426.990 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P40018

+
Small nuclear ribonucleoprotein ... , 6 types, 6 molecules LMNOPQ

#11: Protein/peptide Small nuclear ribonucleoprotein Sm D1 / Sm-D1 / snRNP core protein D1


Mass: 16296.798 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q02260
#12: Protein/peptide Small nuclear ribonucleoprotein Sm D2 / Sm-D2 / snRNP core protein D2


Mass: 12876.066 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q06217
#13: Protein/peptide Small nuclear ribonucleoprotein Sm D3 / Sm-D3 / snRNP core protein D3


Mass: 11240.139 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P43321
#14: Protein/peptide Small nuclear ribonucleoprotein E / snRNP-E / Sm protein E / SmE


Mass: 10385.098 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q12330
#15: Protein/peptide Small nuclear ribonucleoprotein F / snRNP-F / Sm protein F / SmF


Mass: 9669.945 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P54999
#16: Protein/peptide Small nuclear ribonucleoprotein G / snRNP-G / Sm protein G / SmG


Mass: 8490.809 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P40204

+
RNA chain , 2 types, 2 molecules Rr

#17: RNA chain U1 snRNA / U1 spliceosomal RNA


Mass: 182114.516 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: GenBank: 1039023756
#18: RNA chain ACT1 pre-mRNA


Mass: 70171.188 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae S288C (yeast)

+
Non-polymers , 1 types, 1 molecules

#19: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Zinc

+
Details

Has ligand of interestN

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: Saccharomyces cerevisiae spliceosomal E complex (ACT1)
Type: COMPLEX
Entity ID: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18
Source: MULTIPLE SOURCES
Molecular weightExperimental value: NO
Source (natural)Organism: Saccharomyces cerevisiae (baker's yeast)
Buffer solutionpH: 7.9
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: unspecified
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 30 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

-
Processing

EM software
IDNameVersionCategory
2Leginonimage acquisition
4CTFFIND4CTF correction
10RELION2.1initial Euler assignment
11RELION2.1final Euler assignment
12RELION2.1classification
13RELION2.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 270587 / Symmetry type: POINT

+
About Yorodumi

-
News

-
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

External links: EMDB at PDBe / 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. 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.

External links: wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

+
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

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

Read more

-
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.

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