[English] 日本語
Yorodumi
- EMDB-8011: Foot region of the yeast spliceosomal U4/U6.U5 tri-snRNP -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-8011
TitleFoot region of the yeast spliceosomal U4/U6.U5 tri-snRNP
Map data
SampleFoot region of the yeast spliceosomal U4/U6.U5 tri-snRNP
  • (nucleic-acidNucleic acid) x 2
  • (Pre-mRNA-splicing factor ...) x 2
  • Small nuclear ribonucleoprotein-associated protein B
  • (Small nuclear ribonucleoprotein ...SnRNP) x 6
  • Unknown polypeptide
  • ligand
Function / homology
Function and homology information


generation of catalytic spliceosome for first transesterification step / spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) / splicing factor binding / pICln-Sm protein complex / U4 snRNP / small nuclear ribonucleoprotein complex / spliceosomal tri-snRNP complex / SMN-Sm protein complex / U2-type catalytic step 2 spliceosome / commitment complex ...generation of catalytic spliceosome for first transesterification step / spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) / splicing factor binding / pICln-Sm protein complex / U4 snRNP / small nuclear ribonucleoprotein complex / spliceosomal tri-snRNP complex / SMN-Sm protein complex / U2-type catalytic step 2 spliceosome / commitment complex / U2 snRNP / U12-type spliceosomal complex / generation of catalytic spliceosome for second transesterification step / U2-type prespliceosome / spliceosomal snRNP assembly / U1 snRNP / mRNA 3'-splice site recognition / mRNA 5'-splice site recognition / precatalytic spliceosome / spliceosomal tri-snRNP complex assembly / U5 snRNP / U5 snRNA binding / poly(U) RNA binding / U2 snRNA binding / U6 snRNA binding / pre-mRNA intronic binding / U4/U6 x U5 tri-snRNP complex / U1 snRNA binding / isopeptidase activity / catalytic step 2 spliceosome / metallopeptidase activity / mRNA splicing, via spliceosome / ribonucleoprotein complex / GTPase activity / mRNA binding / GTP binding / RNA binding / nucleus / cytosol / cytoplasm
Translational (tr)-type GTP-binding domain / PROCT domain / Translation elongation factor EFTu-like, domain 2 / RNA recognition motif, spliceosomal PrP8 / Pre-mRNA-processing-splicing factor 8, U5-snRNA-binding / Pre-mRNA-processing-splicing factor 8, U6-snRNA-binding / Sm-like protein Lsm6/SmF / Ribosomal protein S5 domain 2-type fold, subgroup / PROCN domain / Small nuclear ribonucleoprotein E ...Translational (tr)-type GTP-binding domain / PROCT domain / Translation elongation factor EFTu-like, domain 2 / RNA recognition motif, spliceosomal PrP8 / Pre-mRNA-processing-splicing factor 8, U5-snRNA-binding / Pre-mRNA-processing-splicing factor 8, U6-snRNA-binding / Sm-like protein Lsm6/SmF / Ribosomal protein S5 domain 2-type fold, subgroup / PROCN domain / Small nuclear ribonucleoprotein E / PRO8NT domain / Ribonuclease H-like superfamily / LSM domain superfamily / Translation protein, beta-barrel domain superfamily / JAB1/MPN/MOV34 metalloenzyme domain / Elongation factor EFG, domain V-like / Translation elongation factor EFG/EF2, domain IV / PRP8 domain IV core / Ribosomal protein S5 domain 2-type fold / Like-Sm (LSM) domain containing protein, LSm4/SmD1/SmD3 / Small nuclear ribonucleoprotein F / Snu114, GTP-binding domain / Prp8 RNase domain IV, fingers region / Prp8 RNase domain IV, palm region / Pre-mRNA-processing-splicing factor 8, U5-snRNA-binding domain superfamily / MPN domain / 116kDa U5 small nuclear ribonucleoprotein component, C-terminal / Small nuclear ribonucleoprotein Sm D2 / EF-G domain III/V-like / Small nuclear ribonucleoprotein Sm D3 / Small nuclear ribonucleoprotein G / 116kDa U5 small nuclear ribonucleoprotein component, N-terminal / Pre-mRNA-processing-splicing factor 8 / P-loop containing nucleoside triphosphate hydrolase / LSM domain, eukaryotic/archaea-type
Small nuclear ribonucleoprotein F / Small nuclear ribonucleoprotein Sm D2 / Small nuclear ribonucleoprotein Sm D1 / Pre-mRNA-splicing factor 8 / Small nuclear ribonucleoprotein Sm D3 / Small nuclear ribonucleoprotein G / Small nuclear ribonucleoprotein-associated protein B / Pre-mRNA-splicing factor SNU114 / Small nuclear ribonucleoprotein E
Biological speciesSaccharomyces cerevisiae (baker's yeast) / Baker's yeast (baker's yeast)
Methodsingle particle reconstruction / Resolution: 3.7 Å
AuthorsNguyen THD / Galej WP / Bai XC / Oubridge C / Scheres SHW / Newman AJ / Nagai K
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom) United Kingdom
Citation
Journal: Nature / Year: 2016
Title: Cryo-EM structure of the yeast U4/U6.U5 tri-snRNP at 3.7 Å resolution.
Authors: Thi Hoang Duong Nguyen / Wojciech P Galej / Xiao-Chen Bai / Chris Oubridge / Andrew J Newman / Sjors H W Scheres / Kiyoshi Nagai /
Abstract: U4/U6.U5 tri-snRNP represents a substantial part of the spliceosome before activation. A cryo-electron microscopy structure of Saccharomyces cerevisiae U4/U6.U5 tri-snRNP at 3.7 Å resolution led ...U4/U6.U5 tri-snRNP represents a substantial part of the spliceosome before activation. A cryo-electron microscopy structure of Saccharomyces cerevisiae U4/U6.U5 tri-snRNP at 3.7 Å resolution led to an essentially complete atomic model comprising 30 proteins plus U4/U6 and U5 small nuclear RNAs (snRNAs). The structure reveals striking interweaving interactions of the protein and RNA components, including extended polypeptides penetrating into subunit interfaces. The invariant ACAGAGA sequence of U6 snRNA, which base-pairs with the 5'-splice site during catalytic activation, forms a hairpin stabilized by Dib1 and Prp8 while the adjacent nucleotides interact with the exon binding loop 1 of U5 snRNA. Snu114 harbours GTP, but its putative catalytic histidine is held away from the γ-phosphate by hydrogen bonding to a tyrosine in the amino-terminal domain of Prp8. Mutation of this histidine to alanine has no detectable effect on yeast growth. The structure provides important new insights into the spliceosome activation process leading to the formation of the catalytic centre.
#1: Journal: Nature / Year: 2015
Title: The architecture of the spliceosomal U4/U6.U5 tri-snRNP.
Authors: Thi Hoang Duong Nguyen / Wojciech P Galej / Xiao-chen Bai / Christos G Savva / Andrew J Newman / Sjors H W Scheres / Kiyoshi Nagai /
Abstract: U4/U6.U5 tri-snRNP is a 1.5-megadalton pre-assembled spliceosomal complex comprising U5 small nuclear RNA (snRNA), extensively base-paired U4/U6 snRNAs and more than 30 proteins, including the key ...U4/U6.U5 tri-snRNP is a 1.5-megadalton pre-assembled spliceosomal complex comprising U5 small nuclear RNA (snRNA), extensively base-paired U4/U6 snRNAs and more than 30 proteins, including the key components Prp8, Brr2 and Snu114. The tri-snRNP combines with a precursor messenger RNA substrate bound to U1 and U2 small nuclear ribonucleoprotein particles (snRNPs), and transforms into a catalytically active spliceosome after extensive compositional and conformational changes triggered by unwinding of the U4 and U6 (U4/U6) snRNAs. Here we use cryo-electron microscopy single-particle reconstruction of Saccharomyces cerevisiae tri-snRNP at 5.9 Å resolution to reveal the essentially complete organization of its RNA and protein components. The single-stranded region of U4 snRNA between its 3' stem-loop and the U4/U6 snRNA stem I is loaded into the Brr2 helicase active site ready for unwinding. Snu114 and the amino-terminal domain of Prp8 position U5 snRNA to insert its loop I, which aligns the exons for splicing, into the Prp8 active site cavity. The structure provides crucial insights into the activation process and the active site of the spliceosome.
Validation ReportSummary, Full report, XML, About validation report
History
DepositionDec 15, 2015-
Header (metadata) releaseFeb 3, 2016-
Map releaseFeb 3, 2016-
UpdateOct 2, 2019-
Current statusOct 2, 2019Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.03
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.03
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-5gam
  • Surface level: 0.03
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

-
Map

FileDownload / File: emd_8011.map.gz / Format: CCP4 / Size: 209.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.43 Å/pix.
x 380 pix.
= 543.4 Å
1.43 Å/pix.
x 380 pix.
= 543.4 Å
1.43 Å/pix.
x 380 pix.
= 543.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.43 Å
Density
Contour LevelBy ANNOTATOR: 0.012 / Movie #1: 0.03
Minimum - Maximum-0.07631316 - 0.19373968
Average (Standard dev.)-0.0002308518 (±0.0031405948)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions380380380
Spacing380380380
CellA=B=C: 543.39996 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.431.431.43
M x/y/z380380380
origin x/y/z0.0000.0000.000
length x/y/z543.400543.400543.400
α/β/γ90.00090.00090.000
start NX/NY/NZ-190-190-190
NX/NY/NZ380380380
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS380380380
D min/max/mean-0.0760.194-0.000

-
Supplemental data

-
Sample components

+
Entire Foot region of the yeast spliceosomal U4/U6.U5 tri-snRNP

EntireName: Foot region of the yeast spliceosomal U4/U6.U5 tri-snRNP
Number of components: 14

+
Component #1: protein, Foot region of the yeast spliceosomal U4/U6.U5 tri-snRNP

ProteinName: Foot region of the yeast spliceosomal U4/U6.U5 tri-snRNP
Recombinant expression: No
MassTheoretical: 350 kDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast) / Strain: BCY123

+
Component #2: nucleic-acid, U5 snRNA

nucleic acidName: U5 snRNAU5 spliceosomal RNA / Class: RNA / Details: Short form of U5 snRNA (179 nt) / Structure: OTHER / Synthetic: No
Sequence:
AAGCAGCUUU ACAGAUCAAU GGCGGAGGGA GGUCAACAUC AAGAACUGUG GGCCUUUUAU UGCCUAUAGA ACUUAUAACG AACAUGGUUC UUGCCUUUUA CCAGAACCAU CCGGGUGUUG UCUCCAUAGA AACAGGUAAA GCUGUCCGUU ACUGUGGGCU UGCCAUAUUU UUUGGAAC
MassTheoretical: 57.138711 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: BCY123

+
Component #3: protein, Pre-mRNA-splicing factor 8

ProteinName: Pre-mRNA-splicing factor 8 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 85.826102 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: BCY123

+
Component #4: protein, Pre-mRNA-splicing factor SNU114

ProteinName: Pre-mRNA-splicing factor SNU114 / Details: Full length Snu114 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 114.132086 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: BCY123

+
Component #5: nucleic-acid, U6 snRNA, 5' end

nucleic acidName: U6 snRNA, 5' endU6 spliceosomal RNA / Class: RNA / Details: The 5' end 31 nucleotides of U6 snRNA / Structure: OTHER / Synthetic: No
Sequence:
GUUCGCGAAG UAACCCUUCG UGGACAUUUG G
MassTheoretical: 9.928893 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: BCY123

+
Component #6: protein, Small nuclear ribonucleoprotein-associated protein B

ProteinName: Small nuclear ribonucleoprotein-associated protein B / Details: The SmB protein from the U5 snRNP Sm protein ring. / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 22.42699 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: BCY123

+
Component #7: protein, Small nuclear ribonucleoprotein E

ProteinName: Small nuclear ribonucleoprotein E / Details: The SmE protein from the U5 snRNP Sm protein ring. / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 10.385098 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: BCY123

+
Component #8: protein, Small nuclear ribonucleoprotein F

ProteinName: Small nuclear ribonucleoprotein F / Details: The SmF protein from the U5 snRNP Sm protein ring. / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 9.669945 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: BCY123

+
Component #9: protein, Small nuclear ribonucleoprotein G

ProteinName: Small nuclear ribonucleoprotein G / Details: The SmG protein from the U5 snRNP Sm protein ring. / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 8.490809 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: BCY123

+
Component #10: protein, Unknown polypeptide

ProteinName: Unknown polypeptide / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 1.549902 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: BCY123

+
Component #11: protein, Small nuclear ribonucleoprotein Sm D3

ProteinName: Small nuclear ribonucleoprotein Sm D3
Details: The SmD3 protein from the U5 snRNP Sm protein ring.
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.240139 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: BCY123

+
Component #12: protein, Small nuclear ribonucleoprotein Sm D1

ProteinName: Small nuclear ribonucleoprotein Sm D1
Details: The SmD1 protein from the U5 snRNP Sm protein ring.
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 16.296798 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: BCY123

+
Component #13: protein, Small nuclear ribonucleoprotein Sm D2

ProteinName: Small nuclear ribonucleoprotein Sm D2
Details: The SmD2 protein from the U5 snRNP Sm protein ring.
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 12.876066 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: BCY123

+
Component #14: ligand, GUANOSINE-5'-TRIPHOSPHATE

LigandName: GUANOSINE-5'-TRIPHOSPHATEGuanosine triphosphate / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.52318 kDa

-
Experimental details

-
Sample preparation

SpecimenSpecimen state: Particle
Sample solutionSpecimen conc.: 0.2 mg/mL / pH: 7.9
Support filmGrids are made of holey carbon, carbon-coated and glow discharged in N-amylamine.
VitrificationCryogen name: NONE

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 38 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 81000.0 X (nominal), 35714.0 X (calibrated) / Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 500.0 - 3500.0 nm / Energy filter: GIF Quantum
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

-
Image acquisition

Image acquisitionNumber of digital images: 2477

-
Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 140155
3D reconstructionSoftware: RELION / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

-
Atomic model buiding

Modeling #1Refinement space: RECIPROCAL
Output model

+
About Yorodumi

-
News

-
Aug 12, 2020. New: Covid-19 info

New: Covid-19 info

  • 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. New: 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. (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

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