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- EMDB-6566: The cryo-EM structure of yeast spliceosomal U4/U6.U5 tri-snRNP (i... -

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Basic information

Entry
Database: EMDB / ID: EMD-6566
TitleThe cryo-EM structure of yeast spliceosomal U4/U6.U5 tri-snRNP (improved map for Prp3 region at 3.46 A)
Map dataReconstruction of tri-snRNP
Sample
  • Sample: U4/U6.U5 tri-snRNP from Saccharomyces cerevisiae
  • Organelle or cellular component: U4/U6.U5 tri-snRNP
Keywordstri-snRNP / pre-mRNA splicing
Function / homology
Function and homology information


spliceosomal conformational changes to generate catalytic conformation / mRNA decay by 5' to 3' exoribonuclease / snoRNA splicing / snoRNA guided rRNA 2'-O-methylation / Lsm1-7-Pat1 complex / U6 snRNP / box C/D sno(s)RNA 3'-end processing / deadenylation-dependent decapping of nuclear-transcribed mRNA / generation of catalytic spliceosome for first transesterification step / box C/D methylation guide snoRNP complex ...spliceosomal conformational changes to generate catalytic conformation / mRNA decay by 5' to 3' exoribonuclease / snoRNA splicing / snoRNA guided rRNA 2'-O-methylation / Lsm1-7-Pat1 complex / U6 snRNP / box C/D sno(s)RNA 3'-end processing / deadenylation-dependent decapping of nuclear-transcribed mRNA / generation of catalytic spliceosome for first transesterification step / box C/D methylation guide snoRNP complex / splicing factor binding / U4/U6 snRNP / spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) / 7-methylguanosine cap hypermethylation / pICln-Sm protein complex / P-body assembly / sno(s)RNA-containing ribonucleoprotein complex / snRNP binding / small nuclear ribonucleoprotein complex / U4 snRNA binding / SMN-Sm protein complex / spliceosomal tri-snRNP complex / poly(U) RNA binding / U3 snoRNA binding / commitment complex / U2-type prespliceosome assembly / U2-type catalytic step 2 spliceosome / U4 snRNP / U2 snRNP / U1 snRNP / U2-type prespliceosome / tRNA processing / precatalytic spliceosome / Major pathway of rRNA processing in the nucleolus and cytosol / generation of catalytic spliceosome for second transesterification step / spliceosomal complex assembly / mRNA 5'-splice site recognition / nuclear-transcribed mRNA catabolic process / mRNA 3'-splice site recognition / spliceosomal tri-snRNP complex assembly / U5 snRNA binding / U5 snRNP / U2 snRNA binding / U6 snRNA binding / spliceosomal snRNP assembly / cellular response to glucose starvation / pre-mRNA intronic binding / U1 snRNA binding / U4/U6 x U5 tri-snRNP complex / catalytic step 2 spliceosome / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / small-subunit processome / spliceosomal complex / P-body / mRNA splicing, via spliceosome / rRNA processing / metallopeptidase activity / nucleic acid binding / RNA helicase activity / RNA helicase / GTPase activity / mRNA binding / GTP binding / nucleolus / ATP hydrolysis activity / mitochondrion / RNA binding / nucleoplasm / ATP binding / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Sm-like protein Lsm8 / U6 snRNA-associated Sm-like protein Lsm1/8 / Pre-mRNA processing factor 4 (PRP4)-like / U6 snRNA-associated Sm-like protein LSm2 / Sm-like protein Lsm4 / Splicing Factor Motif, present in Prp18 and Pr04 / Sm-like protein Lsm7 / Sm-like protein LSm5 / Sm-like protein Lsm3 / U6 snRNA-associated Sm-like protein Lsm3 ...Sm-like protein Lsm8 / U6 snRNA-associated Sm-like protein Lsm1/8 / Pre-mRNA processing factor 4 (PRP4)-like / U6 snRNA-associated Sm-like protein LSm2 / Sm-like protein Lsm4 / Splicing Factor Motif, present in Prp18 and Pr04 / Sm-like protein Lsm7 / Sm-like protein LSm5 / Sm-like protein Lsm3 / U6 snRNA-associated Sm-like protein Lsm3 / Pre-mRNA-splicing factor 3 / U4/U6 small nuclear ribonucleoprotein Prp3 / pre-mRNA processing factor 3 domain / Prp31 C-terminal / U4/U6 small nuclear ribonucleoprotein Prp31 / Prp31 C terminal domain / Small nuclear ribonucleoprotein Prp3, C-terminal domain / Small nuclear ribonucleoprotein Prp3, C-terminal domain / Dim1 family / Mitosis protein DIM1 / Mitosis protein DIM1 / PRP1 splicing factor, N-terminal / PRP1 splicing factor, N-terminal / H/ACA ribonucleoprotein complex, subunit Nhp2-like / NOSIC / NOSIC (NUC001) domain / Nop domain / Nop domain superfamily / Nop, C-terminal domain / snoRNA binding domain, fibrillarin / Nop domain profile. / Brr2, N-terminal helicase PWI domain / : / N-terminal helicase PWI domain / Pre-mRNA-splicing helicase BRR2 plug domain / Sec63 Brl domain / : / Pre-mRNA-splicing factor Syf1-like / 116kDa U5 small nuclear ribonucleoprotein component, N-terminal / 116kDa U5 small nuclear ribonucleoprotein component, C-terminal / Snu114, GTP-binding domain / 116 kDa U5 small nuclear ribonucleoprotein component N-terminus / Sec63 domain / : / Sec63 Brl domain / Small nuclear ribonucleoprotein Sm D3 / Small nuclear ribonucleoprotein Sm D2 / Small nuclear ribonucleoprotein E / Small nuclear ribonucleoprotein G / Small nuclear ribonucleoprotein F / Like-Sm (LSM) domain containing protein, LSm4/SmD1/SmD3 / Sm-like protein Lsm7/SmG / Sm-like protein Lsm6/SmF / LSM domain / LSM domain, eukaryotic/archaea-type / snRNP Sm proteins / HAT (Half-A-TPR) repeat / HAT (Half-A-TPR) repeats / : / Sm domain profile. / LSM domain superfamily / Translation elongation factor EFG/EF2, domain IV / Elongation factor G, domain IV / Elongation factor G, domain IV / Elongation factor G C-terminus / Elongation factor EFG, domain V-like / Elongation factor G C-terminus / EF-G domain III/V-like / PROCT domain / Prp8 RNase domain IV, fingers region / PROCT (NUC072) domain / PRO8NT domain / PROCN domain / Pre-mRNA-processing-splicing factor 8, U6-snRNA-binding / Pre-mRNA-processing-splicing factor 8, U5-snRNA-binding / RNA recognition motif, spliceosomal PrP8 / PRP8 domain IV core / Pre-mRNA-processing-splicing factor 8, U5-snRNA-binding domain superfamily / Prp8 RNase domain IV, palm region / PRO8NT (NUC069), PrP8 N-terminal domain / PROCN (NUC071) domain / U6-snRNA interacting domain of PrP8 / U5-snRNA binding site 2 of PrP8 / RNA recognition motif of the spliceosomal PrP8 / PRP8 domain IV core / Pre-mRNA-processing-splicing factor 8 / JAB/MPN domain / JAB1/MPN/MOV34 metalloenzyme domain / MPN domain / MPN domain profile. / Ribosomal protein L7Ae conserved site / Ribosomal protein L7Ae signature. / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / Tetratricopeptide repeats / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / C2 domain superfamily / :
Similarity search - Domain/homology
Pre-mRNA-splicing factor 6 / U4/U6 small nuclear ribonucleoprotein PRP4 / Pre-mRNA-splicing helicase BRR2 / Pre-mRNA-splicing factor 8 / Pre-mRNA-splicing factor SNU114 / U6 snRNA-associated Sm-like protein LSm2 / 13 kDa ribonucleoprotein-associated protein / Small nuclear ribonucleoprotein-associated protein B / U6 snRNA-associated Sm-like protein LSm4 / U6 snRNA-associated Sm-like protein LSm5 ...Pre-mRNA-splicing factor 6 / U4/U6 small nuclear ribonucleoprotein PRP4 / Pre-mRNA-splicing helicase BRR2 / Pre-mRNA-splicing factor 8 / Pre-mRNA-splicing factor SNU114 / U6 snRNA-associated Sm-like protein LSm2 / 13 kDa ribonucleoprotein-associated protein / Small nuclear ribonucleoprotein-associated protein B / U6 snRNA-associated Sm-like protein LSm4 / U6 snRNA-associated Sm-like protein LSm5 / Small nuclear ribonucleoprotein G / Small nuclear ribonucleoprotein Sm D3 / U6 snRNA-associated Sm-like protein LSm8 / Pre-mRNA-processing factor 31 / U6 snRNA-associated Sm-like protein LSm7 / Small nuclear ribonucleoprotein F / U6 snRNA-associated Sm-like protein LSm3 / Small nuclear ribonucleoprotein Sm D1 / U4/U6 small nuclear ribonucleoprotein PRP3 / Small nuclear ribonucleoprotein Sm D2 / U6 snRNA-associated Sm-like protein LSm6 / Spliceosomal protein DIB1 / Small nuclear ribonucleoprotein E
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.46 Å
AuthorsWan R / Yan C / Bai R / Wang L / Huang M / Wong C / Shi Y
CitationJournal: Science / Year: 2016
Title: The 3.8 Å structure of the U4/U6.U5 tri-snRNP: Insights into spliceosome assembly and catalysis.
Authors: Ruixue Wan / Chuangye Yan / Rui Bai / Lin Wang / Min Huang / Catherine C L Wong / Yigong Shi /
Abstract: Splicing of precursor messenger RNA is accomplished by a dynamic megacomplex known as the spliceosome. Assembly of a functional spliceosome requires a preassembled U4/U6.U5 tri-snRNP complex, which ...Splicing of precursor messenger RNA is accomplished by a dynamic megacomplex known as the spliceosome. Assembly of a functional spliceosome requires a preassembled U4/U6.U5 tri-snRNP complex, which comprises the U5 small nuclear ribonucleoprotein (snRNP), the U4 and U6 small nuclear RNA (snRNA) duplex, and a number of protein factors. Here we report the three-dimensional structure of a Saccharomyces cerevisiae U4/U6.U5 tri-snRNP at an overall resolution of 3.8 angstroms by single-particle electron cryomicroscopy. The local resolution for the core regions of the tri-snRNP reaches 3.0 to 3.5 angstroms, allowing construction of a refined atomic model. Our structure contains U5 snRNA, the extensively base-paired U4/U6 snRNA, and 30 proteins including Prp8 and Snu114, which amount to 8495 amino acids and 263 nucleotides with a combined molecular mass of ~1 megadalton. The catalytic nucleotide U80 from U6 snRNA exists in an inactive conformation, stabilized by its base-pairing interactions with U4 snRNA and protected by Prp3. Pre-messenger RNA is bound in the tri-snRNP through base-pairing interactions with U6 snRNA and loop I of U5 snRNA. This structure, together with that of the spliceosome, reveals the molecular choreography of the snRNAs in the activation process of the spliceosomal ribozyme.
History
DepositionDec 23, 2015-
Header (metadata) releaseFeb 10, 2016-
Map releaseFeb 10, 2016-
UpdateFeb 10, 2016-
Current statusFeb 10, 2016Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0233
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.0233
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-3jcm
  • Surface level: 0.0233
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

400_6566.gif

Downloads & links

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Map

FileDownload / File: emd_6566.map.gz / Format: CCP4 / Size: 122.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of tri-snRNP
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.32 Å/pix.
x 320 pix.
= 422.4 Å		1.32 Å/pix.
x 320 pix.
= 422.4 Å		1.32 Å/pix.
x 320 pix.
= 422.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.32 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0233 / Movie #1: 0.0233
Minimum - Maximum-0.1576885 - 0.26797166
Average (Standard dev.)-0.00005958 (±0.00512167)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 422.40002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.321.321.32
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z422.400422.400422.400
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-0.1580.268-0.000

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Supplemental data

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Sample components

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Entire : U4/U6.U5 tri-snRNP from Saccharomyces cerevisiae

EntireName: U4/U6.U5 tri-snRNP from Saccharomyces cerevisiae
Components
  • Sample: U4/U6.U5 tri-snRNP from Saccharomyces cerevisiae
  • Organelle or cellular component: U4/U6.U5 tri-snRNP

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Supramolecule #1000: U4/U6.U5 tri-snRNP from Saccharomyces cerevisiae

SupramoleculeName: U4/U6.U5 tri-snRNP from Saccharomyces cerevisiae / type: sample / ID: 1000 / Number unique components: 34

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Supramolecule #1: U4/U6.U5 tri-snRNP

SupramoleculeName: U4/U6.U5 tri-snRNP / type: organelle_or_cellular_component / ID: 1 / Recombinant expression: No / Database: NCBI
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
DateAug 8, 2015
Image recordingCategory: FILM / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Digitization - Scanner: TEMSCAN / Number real images: 3141
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.46 Å / Resolution method: OTHER / Software - Name: RELION / Number images used: 172134

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