[English] 日本語
Yorodumi
- EMDB-8014: Body region of the U4/U6.U5 tri-snRNP -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-8014
TitleBody region of the U4/U6.U5 tri-snRNP
Map data
SampleBody region of the U4/U6.U5 tri-snRNP complex
  • (nucleic-acidNucleic acid) x 3
  • unknown protein
  • (Pre-mRNA-splicing factor ...) x 2
  • (U4/U6 small nuclear ribonucleoprotein ...) x 2
  • Spliceosomal protein DIB1Spliceosome
  • Pre-mRNA-processing factor 31
  • 13 kDa ribonucleoprotein-associated protein
  • Pre-mRNA-splicing helicase BRR2
Function / homology
Function and homology information


spliceosomal conformational changes to generate catalytic conformation / U4/U6 snRNP / snoRNA splicing / rRNA 2'-O-methylation / positive regulation of RNA binding / spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) / box C/D RNP complex / U4 snRNP / spliceosomal tri-snRNP complex / U4 snRNA binding ...spliceosomal conformational changes to generate catalytic conformation / U4/U6 snRNP / snoRNA splicing / rRNA 2'-O-methylation / positive regulation of RNA binding / spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) / box C/D RNP complex / U4 snRNP / spliceosomal tri-snRNP complex / U4 snRNA binding / U3 snoRNA binding / generation of catalytic spliceosome for second transesterification step / spliceosomal snRNP assembly / mRNA 3'-splice site recognition / mRNA 5'-splice site recognition / precatalytic spliceosome / spliceosomal tri-snRNP complex assembly / rRNA methylation / U5 snRNP / U5 snRNA binding / U2 snRNA binding / U6 snRNA binding / pre-mRNA intronic binding / U4/U6 x U5 tri-snRNP complex / maturation of SSU-rRNA / U1 snRNA binding / small-subunit processome / isopeptidase activity / catalytic step 2 spliceosome / maturation of LSU-rRNA / spliceosomal complex / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / metallopeptidase activity / mRNA splicing, via spliceosome / RNA helicase / RNA helicase activity / mRNA binding / nucleolus / mitochondrion / RNA binding / nucleoplasm / ATP binding / identical protein binding / nucleus
Dim1 family / Domain of unknown function DUF1115 / PROCT domain / NOSIC / PROCN domain / PRO8NT domain / Ribonuclease H-like superfamily / Tetratricopeptide-like helical domain superfamily / DEAD/DEAH box helicase domain / PRP1 splicing factor, N-terminal ...Dim1 family / Domain of unknown function DUF1115 / PROCT domain / NOSIC / PROCN domain / PRO8NT domain / Ribonuclease H-like superfamily / Tetratricopeptide-like helical domain superfamily / DEAD/DEAH box helicase domain / PRP1 splicing factor, N-terminal / Pre-mRNA-splicing factor 3 / Sec63 domain / Ribosomal protein L7Ae/L30e/S12e/Gadd45 / Ribosomal protein L7Ae conserved site / HAT (Half-A-TPR) repeat / Nop domain / H/ACA ribonucleoprotein complex, subunit Nhp2, eukaryote / WD40 repeat / Helicase, C-terminal / Tetratricopeptide repeat-containing domain / Helicase superfamily 1/2, ATP-binding domain / Nop domain superfamily / WD40 repeat, conserved site / 50S ribosomal protein L30e-like / Pre-mRNA-processing-splicing factor 8 / P-loop containing nucleoside triphosphate hydrolase / Pre-mRNA-processing factor 6/Prp1/STA1 / U4/U6 small nuclear ribonucleoprotein Prp31 / U4/U6 small nuclear ribonucleoprotein Prp3 / PRP8 domain IV core / G-protein beta WD-40 repeat / Tetratricopeptide repeat / Immunoglobulin E-set / RNA recognition motif, spliceosomal PrP8 / Pre-mRNA-processing-splicing factor 8, U5-snRNA-binding / Pre-mRNA-processing-splicing factor 8, U6-snRNA-binding / Prp31 C-terminal / Ribosomal protein L7Ae/L8/Nhp2 family / WD40-repeat-containing domain / WD40/YVTN repeat-like-containing domain superfamily / Pre-mRNA processing factor 4 (PRP4)-like / JAB1/MPN/MOV34 metalloenzyme domain / C2 domain superfamily / WD40-repeat-containing domain superfamily / Winged helix DNA-binding domain superfamily / Prp8 RNase domain IV, fingers region / Prp8 RNase domain IV, palm region / Thioredoxin-like superfamily / Pre-mRNA-processing-splicing factor 8, U5-snRNA-binding domain superfamily / Nop, C-terminal domain / Brr2, N-terminal helicase PWI domain / MPN domain
Pre-mRNA-splicing factor 6 / U4/U6 small nuclear ribonucleoprotein PRP4 / Pre-mRNA-splicing helicase BRR2 / Pre-mRNA-splicing factor 8 / 13 kDa ribonucleoprotein-associated protein / Pre-mRNA-processing factor 31 / U4/U6 small nuclear ribonucleoprotein PRP3 / Spliceosomal protein DIB1
Biological speciesSaccharomyces cerevisiae (baker's yeast) / Baker's yeast (baker's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsNguyen THD / Galej WP / Oubridge C / Bai XC / Newman A / Scheres S / Nagai K
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom) United Kingdom
CitationJournal: 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.
Validation ReportSummary, Full report, XML, About validation report
History
DepositionDec 15, 2015-
Header (metadata) releaseJan 27, 2016-
Map releaseJan 27, 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: 0.06
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.06
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-5gap
  • Surface level: 0.06
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

-
Map

FileDownload / File: emd_8014.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 AUTHOR: 0.02 / Movie #1: 0.06
Minimum - Maximum-0.2323884 - 0.32634056
Average (Standard dev.)-0.0001666498 (±0.0078094634)
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-0.2320.326-0.000

-
Supplemental data

-
Sample components

+
Entire Body region of the U4/U6.U5 tri-snRNP complex

EntireName: Body region of the U4/U6.U5 tri-snRNP complex / Number of components: 13

+
Component #1: protein, Body region of the U4/U6.U5 tri-snRNP complex

ProteinName: Body region of the U4/U6.U5 tri-snRNP complex / Recombinant expression: No
MassTheoretical: 500 kDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)

+
Component #2: nucleic-acid, U4 snRNA, 5' region, nucleotides 1-67

nucleic acidName: U4 snRNA, 5' region, nucleotides 1-67U4 spliceosomal RNA
Class: RNA / Details: U4 snRNA 5' region, nucleotides 1-67. / Structure: OTHER / Synthetic: No
Sequence:
AUCCUUAUGC ACGGGAAAUA CGCAUAUCAG UGAGGAUUCG UCCGAGAUUG UGUUUUUGCU GGUUGAA
MassTheoretical: 21.528688 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #3: nucleic-acid, U6 snRNA

nucleic acidName: U6 snRNAU6 spliceosomal RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
GUUCGCGAAG UAACCCUUCG UGGACAUUUG GUCAAUUUGA AACAAUACAG AGAUGAUCAG CAGUUCCCCU GCAUAAGGAU GAACCGUUUU ACAAAGAGAU UUAUUUCGUU UU
MassTheoretical: 35.883176 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #4: nucleic-acid, U5 snRNA

nucleic acidName: U5 snRNAU5 spliceosomal RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence: AAGCAGCUUU ACAGAUCAAU GGCGGAGGGA GGUCAACAUC AAGAACUGUG GGCCUUUUAU UGCCUAUAGA ACUUAUAACG AACAUGGUUC UUGCCUUUUA CCAGAACCAU CCGGGUGUUG UCUCCAUAGA AACAGGUAAA GCUGUCCGUU ACUGUGGGCU UGCCAUAUUU ...Sequence:
AAGCAGCUUU ACAGAUCAAU GGCGGAGGGA GGUCAACAUC AAGAACUGUG GGCCUUUUAU UGCCUAUAGA ACUUAUAACG AACAUGGUUC UUGCCUUUUA CCAGAACCAU CCGGGUGUUG UCUCCAUAGA AACAGGUAAA GCUGUCCGUU ACUGUGGGCU UGCCAUAUUU UUUGGAACUU UUCUGCCCUU UUUCUCAAUG AGUAAGGAGG GCGU
MassTheoretical: 68.643344 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #5: protein, unknown protein

ProteinName: unknown protein
Details: Clear helical regions were built as poly(Ala) but could not be assigned to a specific protein.
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.996616 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #6: protein, Pre-mRNA-splicing factor 8

ProteinName: Pre-mRNA-splicing factor 8 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 279.867469 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #7: protein, U4/U6 small nuclear ribonucleoprotein PRP4

ProteinName: U4/U6 small nuclear ribonucleoprotein PRP4 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 52.506984 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #8: protein, Pre-mRNA-splicing factor 6

ProteinName: Pre-mRNA-splicing factor 6 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 104.370133 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #9: protein, Spliceosomal protein DIB1

ProteinName: Spliceosomal protein DIB1Spliceosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 16.798387 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #10: protein, Pre-mRNA-processing factor 31

ProteinName: Pre-mRNA-processing factor 31 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 56.382516 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #11: protein, U4/U6 small nuclear ribonucleoprotein PRP3

ProteinName: U4/U6 small nuclear ribonucleoprotein PRP3 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 55.97432 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #12: protein, 13 kDa ribonucleoprotein-associated protein

ProteinName: 13 kDa ribonucleoprotein-associated protein / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.582855 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #13: protein, Pre-mRNA-splicing helicase BRR2

ProteinName: Pre-mRNA-splicing helicase BRR2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 246.470266 kDa
SourceSpecies: Baker's yeast (baker's yeast)

-
Experimental details

-
Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionSpecimen conc.: 0.2 mg/mL / pH: 7.9
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Temperature: 277 K / Humidity: 100 %
Details: Grids were blotted at 4 deg C for 2 seconds before plunging..

-
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: 3.6 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