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- EMDB-8012: The overall structure of the yeast spliceosomal U4/U6.U5 tri-snRN... -

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Basic information

Entry
Database: EMDB / ID: EMD-8012
TitleThe overall structure of the yeast spliceosomal U4/U6.U5 tri-snRNP at 3.7 Angstrom
Map data
SampleThe overall structure of the yeast spliceosomal U4/U6.U5 tri-snRNP
  • (nucleic-acidNucleic acid) x 3
  • (Pre-mRNA-splicing factor ...) x 3
  • (U4/U6 small nuclear ribonucleoprotein ...) x 2
  • Spliceosomal protein DIB1Spliceosome
  • Pre-mRNA-processing factor 31
  • Pre-mRNA-splicing helicase BRR2
  • Unknown protein
  • Small nuclear ribonucleoprotein-associated protein B
  • (Small nuclear ribonucleoprotein ...SnRNP) x 6
  • Snu66
  • 13 kDa ribonucleoprotein-associated protein
  • (U6 snRNA-associated Sm-like protein ...) x 7
  • ligand
Function / homology
Function and homology information


maturation of 5S rRNA / spliceosomal conformational changes to generate catalytic conformation / U4/U6 snRNP / snoRNA splicing / Lsm1-7-Pat1 complex / U6 snRNP / rRNA 2'-O-methylation / positive regulation of RNA binding / generation of catalytic spliceosome for first transesterification step / box C/D RNP complex ...maturation of 5S rRNA / spliceosomal conformational changes to generate catalytic conformation / U4/U6 snRNP / snoRNA splicing / Lsm1-7-Pat1 complex / U6 snRNP / rRNA 2'-O-methylation / positive regulation of RNA binding / generation of catalytic spliceosome for first transesterification step / box C/D RNP complex / spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) / splicing factor binding / P-body assembly / pICln-Sm protein complex / U4 snRNP / nuclear-transcribed mRNA catabolic process / small nuclear ribonucleoprotein complex / spliceosomal tri-snRNP complex / SMN-Sm protein complex / U4 snRNA binding / U2-type catalytic step 2 spliceosome / commitment complex / mRNA cis splicing, via spliceosome / U2 snRNP / U3 snoRNA binding / U12-type spliceosomal complex / generation of catalytic spliceosome for second transesterification step / U2-type prespliceosome / sno(s)RNA-containing ribonucleoprotein complex / spliceosomal snRNP assembly / U1 snRNP / mRNA 3'-splice site recognition / RNA metabolic process / mRNA 5'-splice site recognition / precatalytic spliceosome / tRNA processing / spliceosomal tri-snRNP complex assembly / rRNA methylation / U5 snRNP / poly(U) RNA binding / U5 snRNA binding / U2 snRNA binding / U6 snRNA binding / pre-mRNA intronic binding / maturation of SSU-rRNA / U4/U6 x U5 tri-snRNP complex / U1 snRNA binding / small-subunit processome / isopeptidase activity / catalytic step 2 spliceosome / maturation of LSU-rRNA / spliceosomal complex / P-body / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / rRNA processing / metallopeptidase activity / mRNA splicing, via spliceosome / ribonucleoprotein complex / RNA helicase / RNA helicase activity / GTPase activity / mRNA binding / GTP binding / nucleolus / mitochondrion / RNA binding / nucleoplasm / ATP binding / identical protein binding / nucleus / cytosol / cytoplasm
Translation protein, beta-barrel domain superfamily / PRP1 splicing factor, N-terminal / Ribosomal protein S5 domain 2-type fold, subgroup / Helicase superfamily 1/2, ATP-binding domain / Pre-mRNA-splicing factor 3 / Tetratricopeptide repeat-containing domain / PROCT domain / NOSIC / PROCN domain / PRO8NT domain ...Translation protein, beta-barrel domain superfamily / PRP1 splicing factor, N-terminal / Ribosomal protein S5 domain 2-type fold, subgroup / Helicase superfamily 1/2, ATP-binding domain / Pre-mRNA-splicing factor 3 / Tetratricopeptide repeat-containing domain / PROCT domain / NOSIC / PROCN domain / PRO8NT domain / Ribonuclease H-like superfamily / Tetratricopeptide-like helical domain superfamily / DEAD/DEAH box helicase domain / LSM domain superfamily / Domain of unknown function DUF1115 / Translation elongation factor EFG/EF2, domain IV / Pre-mRNA processing factor 4 (PRP4)-like / SNU66/SART1 family / Sec63 domain / Translation elongation factor EFTu-like, domain 2 / Dim1 family / 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 / LSM domain, eukaryotic/archaea-type / Translational (tr)-type GTP-binding domain / Elongation factor EFG, domain V-like / Immunoglobulin E-set / WD40/YVTN repeat-like-containing domain superfamily / 116kDa U5 small nuclear ribonucleoprotein component, C-terminal / U4/U6 small nuclear ribonucleoprotein Prp31 / Sm-like protein Lsm3 / Sm-like protein Lsm8 / Sm-like protein Lsm4 / Small nuclear ribonucleoprotein F / Small nuclear ribonucleoprotein Sm D3 / Small nuclear ribonucleoprotein G / Sm-like protein LSm5 / 116kDa U5 small nuclear ribonucleoprotein component, N-terminal / 50S ribosomal protein L30e-like / 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 / Pre-mRNA-processing factor 6/Prp1/STA1 / U4/U6 small nuclear ribonucleoprotein Prp3 / Sm-like protein Lsm6/SmF / Small nuclear ribonucleoprotein E / PRP8 domain IV core / Ribosomal protein S5 domain 2-type fold / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Tetratricopeptide repeat / 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 / Sm-like protein Lsm7 / U6 snRNA-associated Sm-like protein LSm2 / JAB1/MPN/MOV34 metalloenzyme domain / EF-G domain III/V-like / Nop domain superfamily / Brr2, N-terminal helicase PWI domain / WD40-repeat-containing domain superfamily / Winged helix DNA-binding domain superfamily / C2 domain superfamily / MPN domain / U6 snRNA-associated Sm-like protein Lsm3 / Nop, C-terminal domain / Pre-mRNA-processing-splicing factor 8, U5-snRNA-binding domain superfamily / Prp8 RNase domain IV, palm region / Prp8 RNase domain IV, fingers region / Snu114, GTP-binding domain / Thioredoxin-like superfamily
U6 snRNA-associated Sm-like protein LSm8 / Small nuclear ribonucleoprotein E / Spliceosomal protein DIB1 / U6 snRNA-associated Sm-like protein LSm6 / Small nuclear ribonucleoprotein Sm D2 / U4/U6 small nuclear ribonucleoprotein PRP3 / Small nuclear ribonucleoprotein Sm D1 / U6 snRNA-associated Sm-like protein LSm3 / Small nuclear ribonucleoprotein F / U6 snRNA-associated Sm-like protein LSm7 ...U6 snRNA-associated Sm-like protein LSm8 / Small nuclear ribonucleoprotein E / Spliceosomal protein DIB1 / U6 snRNA-associated Sm-like protein LSm6 / Small nuclear ribonucleoprotein Sm D2 / U4/U6 small nuclear ribonucleoprotein PRP3 / Small nuclear ribonucleoprotein Sm D1 / U6 snRNA-associated Sm-like protein LSm3 / Small nuclear ribonucleoprotein F / U6 snRNA-associated Sm-like protein LSm7 / Pre-mRNA-processing factor 31 / U6 snRNA-associated Sm-like protein LSm2 / Small nuclear ribonucleoprotein Sm D3 / Small nuclear ribonucleoprotein G / U6 snRNA-associated Sm-like protein LSm5 / U6 snRNA-associated Sm-like protein LSm4 / Small nuclear ribonucleoprotein-associated protein B / 13 kDa ribonucleoprotein-associated protein / Pre-mRNA-splicing factor SNU114 / Pre-mRNA-splicing factor 8 / Pre-mRNA-splicing helicase BRR2 / U4/U6 small nuclear ribonucleoprotein PRP4 / Pre-mRNA-splicing factor 6 / U6 snRNA-associated Sm-like protein LSm6 / 66 kDa U4/U6.U5 small nuclear ribonucleoprotein component
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) releaseJan 27, 2016-
Map releaseJan 27, 2016-
UpdateDec 11, 2019-
Current statusDec 11, 2019Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.036
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.036
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5gan
  • Surface level: 0.036
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_8012.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: 0.036 / Movie #1: 0.036
Minimum - Maximum-0.121906534 - 0.2434729
Average (Standard dev.)0.00001066356 (±0.007296074)
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-0.1220.2430.000

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Supplemental data

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Sample components

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Entire The overall structure of the yeast spliceosomal U4/U6.U5 tri-snRNP

EntireName: The overall structure of the yeast spliceosomal U4/U6.U5 tri-snRNP
Details: 30 proteins and 3 snRNAs / Number of components: 30

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Component #1: protein, The overall structure of the yeast spliceosomal U4/U6.U5...

ProteinName: The overall structure of the yeast spliceosomal U4/U6.U5 tri-snRNP
Details: 30 proteins and 3 snRNAs / Recombinant expression: No
MassTheoretical: 1.5 MDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast) / Strain: BCY123

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Component #2: nucleic-acid, U4 snRNA

nucleic acidName: U4 snRNAU4 spliceosomal RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
AUCCUUAUGC ACGGGAAAUA CGCAUAUCAG UGAGGAUUCG UCCGAGAUUG UGUUUUUGCU GGUUGAAAUU UAAUUAUAAA CCAGACCGUC UCCUCAUGGU CAAUUCGGUG UUCGCUUUUG AAUACUUCAA GACUAUGUAG GGAAUUUUUG GAAUACCUUU
MassTheoretical: 51.186023 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: BCY123

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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) / Strain: BCY123

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Component #4: 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) / Strain: BCY123

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Component #5: 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) / Strain: BCY123

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Component #6: 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) / Strain: BCY123

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Component #7: 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) / Strain: BCY123

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Component #8: 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) / Strain: BCY123

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Component #9: 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) / Strain: BCY123

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Component #10: 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) / Strain: BCY123

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Component #11: protein, Unknown protein

ProteinName: Unknown protein / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 8.528504 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: BCY123

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Component #12: protein, Small nuclear ribonucleoprotein-associated protein B

ProteinName: Small nuclear ribonucleoprotein-associated protein B / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 22.42699 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: BCY123

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Component #13: protein, Small nuclear ribonucleoprotein Sm D1

ProteinName: Small nuclear ribonucleoprotein Sm D1 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 16.296798 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: BCY123

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Component #14: protein, Small nuclear ribonucleoprotein Sm D2

ProteinName: Small nuclear ribonucleoprotein Sm D2 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 12.876066 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: BCY123

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Component #15: protein, Small nuclear ribonucleoprotein Sm D3

ProteinName: Small nuclear ribonucleoprotein Sm D3 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 11.240139 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: BCY123

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Component #16: protein, Small nuclear ribonucleoprotein E

ProteinName: Small nuclear ribonucleoprotein E / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 10.385098 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: BCY123

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Component #17: protein, Small nuclear ribonucleoprotein F

ProteinName: Small nuclear ribonucleoprotein F / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 9.669945 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: BCY123

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Component #18: protein, Small nuclear ribonucleoprotein G

ProteinName: Small nuclear ribonucleoprotein G / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 8.490809 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: BCY123

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Component #19: protein, Snu66

ProteinName: Snu66
Details: Snu66 is mostly fitted as polyAla into helices and extended polypeptides within the EM map. The authors do not believe that the sequence number is correct.
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 28.660018 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: BCY123

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Component #20: 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) / Strain: BCY123

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Component #21: 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) / Strain: BCY123

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Component #22: protein, U6 snRNA-associated Sm-like protein LSm2

ProteinName: U6 snRNA-associated Sm-like protein LSm2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.177888 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: BCY123

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Component #23: protein, U6 snRNA-associated Sm-like protein LSm3

ProteinName: U6 snRNA-associated Sm-like protein LSm3 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 10.039262 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: BCY123

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Component #24: protein, U6 snRNA-associated Sm-like protein LSm4

ProteinName: U6 snRNA-associated Sm-like protein LSm4 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 21.29807 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: BCY123

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Component #25: protein, U6 snRNA-associated Sm-like protein LSm5

ProteinName: U6 snRNA-associated Sm-like protein LSm5 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 10.432954 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: BCY123

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Component #26: protein, U6 snRNA-associated Sm-like protein LSm6

ProteinName: U6 snRNA-associated Sm-like protein LSm6 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 9.406579 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: BCY123

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Component #27: protein, U6 snRNA-associated Sm-like protein LSm7

ProteinName: U6 snRNA-associated Sm-like protein LSm7 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.027045 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: BCY123

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Component #28: protein, U6 snRNA-associated Sm-like protein LSm8

ProteinName: U6 snRNA-associated Sm-like protein LSm8 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 12.403378 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: BCY123

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Component #29: protein, Pre-mRNA-splicing factor SNU114

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

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Component #30: ligand, GUANOSINE-5'-TRIPHOSPHATE

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

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Experimental details

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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

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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)

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Image acquisition

Image acquisitionNumber of digital images: 2477

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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)

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Atomic model buiding

Modeling #1Refinement space: RECIPROCAL
Output model

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