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- EMDB-6974: Cryo-EM structure of the yeast B complex at average resolution of... -

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Basic information

Entry
Database: EMDB / ID: EMD-6974
TitleCryo-EM structure of the yeast B complex at average resolution of 3.9 angstrom
Map data
Sampleyeast fully assembled spliceosomal B complex before activation
  • (Pre-mRNA-splicing factor ...) x 11
  • (U4/U6 small nuclear ribonucleoprotein ...) x 2
  • Pre-mRNA-processing factor 31
  • Spliceosomal protein DIB1Spliceosome
  • 13 kDa ribonucleoprotein-associated protein
  • (U6 snRNA-associated Sm-like protein ...) x 7
  • (nucleic-acidNucleic acid) x 5
  • 66 kDa U4/U6.U5 small nuclear ribonucleoprotein component
  • (Small nuclear ribonucleoprotein ...SnRNP) x 6
  • Small nuclear ribonucleoprotein-associated protein B
  • Pre-mRNA-splicing helicase BRR2
  • (U2 snRNP component ...) x 2
  • Cold sensitive U2 snRNA suppressor 1
  • Protein HSH49
  • RDS3 complex subunit 10
  • Pre-mRNA leakage protein 1
  • (U2 small nuclear ribonucleoprotein ...) x 2
  • 23 kDa U4/U6.U5 small nuclear ribonucleoprotein component
  • (ligand) x 2
Function / homology
Function and homology information


maintenance of RNA location / maturation of 5S rRNA / response to xenobiotic stimulus / RES complex / spliceosomal conformational changes to generate catalytic conformation / U4/U6 snRNP / snoRNA splicing / Lsm1-7-Pat1 complex / U6 snRNP / rRNA 2'-O-methylation ...maintenance of RNA location / maturation of 5S rRNA / response to xenobiotic stimulus / RES complex / 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 / spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) / splicing factor binding / box C/D RNP complex / U2-type spliceosomal complex / P-body assembly / pICln-Sm protein complex / U4 snRNP / nuclear-transcribed mRNA catabolic process / small nuclear ribonucleoprotein complex / spliceosomal tri-snRNP complex / sno(s)RNA-containing ribonucleoprotein complex / SMN-Sm protein complex / mRNA cis splicing, via spliceosome / U4 snRNA binding / U2-type catalytic step 2 spliceosome / commitment complex / U2 snRNP / poly(A) binding / U12-type spliceosomal complex / U3 snoRNA binding / generation of catalytic spliceosome for second transesterification step / spliceosomal complex assembly / U2-type prespliceosome / spliceosomal snRNP assembly / U1 snRNP / mRNA 3'-splice site recognition / mRNA 5'-splice site recognition / precatalytic spliceosome / RNA metabolic process / 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 / mRNA export from nucleus / spliceosomal complex / mRNA 3'-UTR binding / P-body / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / metallopeptidase activity / rRNA processing / mRNA splicing, via spliceosome / ribonucleoprotein complex / RNA helicase / RNA helicase activity / GTPase activity / mRNA binding / GTP binding / nucleolus / mitochondrion / RNA binding / zinc ion binding / nucleoplasm / ATP binding / identical protein binding / metal ion binding / nucleus / cytosol / cytoplasm
Tetratricopeptide-like helical domain superfamily / PROCT domain / LSM domain superfamily / DEAD/DEAH box helicase domain / Armadillo-like helical / Ribonuclease H-like superfamily / PRO8NT domain / PROCN domain / Nucleotide-binding alpha-beta plait domain superfamily / NOSIC ...Tetratricopeptide-like helical domain superfamily / PROCT domain / LSM domain superfamily / DEAD/DEAH box helicase domain / Armadillo-like helical / Ribonuclease H-like superfamily / PRO8NT domain / PROCN domain / Nucleotide-binding alpha-beta plait domain superfamily / NOSIC / Tetratricopeptide repeat-containing domain / PRP1 splicing factor, N-terminal / Zinc finger C2H2-type / Pre-mRNA-splicing factor 3 / Helicase superfamily 1/2, ATP-binding domain / Ribosomal protein S5 domain 2-type fold, subgroup / Immunoglobulin E-set / Pre-mRNA processing factor 4 (PRP4)-like / WD40/YVTN repeat-like-containing domain superfamily / Armadillo-type fold / Domain of unknown function DUF1115 / Splicing factor 3B subunit 5/RDS3 complex subunit 10 / U6 snRNA-associated Sm-like protein LSm2 / Dim1 family / WD40 repeat / H/ACA ribonucleoprotein complex, subunit Nhp2, eukaryote / Nop domain / HAT (Half-A-TPR) repeat / U2A'/phosphoprotein 32 family A, C-terminal / Matrin/U1-C-like, C2H2-type zinc finger / Ribosomal protein L7Ae conserved site / Ribosomal protein L7Ae/L30e/S12e/Gadd45 / Translation elongation factor EFTu-like, domain 2 / Translation protein, beta-barrel domain superfamily / Sec63 domain / Cleavage/polyadenylation specificity factor, A subunit, C-terminal / SNU66/SART1 family / Pre-mRNA-splicing factor 38 / PHF5-like / Translation elongation factor EFG/EF2, domain IV / PSP, proline-rich / Domain of unknown function DUF382 / SMAD/FHA domain superfamily / Sm-like protein Lsm6/SmF / Sm-like protein Lsm7 / RNA-binding domain superfamily / Small nuclear ribonucleoprotein G / 50S ribosomal protein L30e-like / Pre-mRNA-splicing factor Prp9, N-terminal / SF3A3 domain / Splicing factor 3A subunit 3 / SF3A2 domain / 116kDa U5 small nuclear ribonucleoprotein component, N-terminal / Leucine-rich repeat domain superfamily / Sm-like protein LSm5 / Small nuclear ribonucleoprotein Sm D3 / P-loop containing nucleoside triphosphate hydrolase / Small nuclear ribonucleoprotein F / Sm-like protein Lsm4 / Sm-like protein Lsm8 / Sm-like protein Lsm3 / SF3B4, RNA recognition motif 1 / EF-G domain III/V-like / 116kDa U5 small nuclear ribonucleoprotein component, C-terminal / C2 domain superfamily / Pre-mRNA-processing-splicing factor 8 / Small nuclear ribonucleoprotein Sm D2 / WD40-repeat-containing domain / WD40 repeat, conserved site / Ribosomal protein L7Ae/L8/Nhp2 family / Bud13 / Cleavage/polyadenylation specificity factor, A subunit, N-terminal / Prp31 C-terminal / Pre-mRNA-processing-splicing factor 8, U6-snRNA-binding / Pre-mRNA-processing-splicing factor 8, U5-snRNA-binding / RNA recognition motif, spliceosomal PrP8 / Tetratricopeptide repeat / G-protein beta WD-40 repeat / Like-Sm (LSM) domain containing protein, LSm4/SmD1/SmD3 / Ribosomal protein S5 domain 2-type fold / PRP8 domain IV core / Splicing factor 3A subunit 1 / Zinc finger, double-stranded RNA binding / Splicing factor SF3a60 subunit C-terminal / Small nuclear ribonucleoprotein E / U4/U6 small nuclear ribonucleoprotein Prp3 / U4/U6 small nuclear ribonucleoprotein Prp31 / Pre-mRNA-processing factor 6/Prp1/STA1 / Helicase, C-terminal / Leucine-rich repeat / LSM domain, eukaryotic/archaea-type / U6 snRNA-associated Sm-like protein Lsm3 / Thioredoxin-like superfamily / Translational (tr)-type GTP-binding domain / WD40-repeat-containing domain superfamily / Winged helix DNA-binding domain superfamily / MPN domain / Splicing factor 3B subunit 1-like / U4/U6.U5 small nuclear ribonucleoprotein component Snu23 / Nop domain superfamily
Small nuclear ribonucleoprotein Sm D2 / Small nuclear ribonucleoprotein F / U6 snRNA-associated Sm-like protein LSm3 / Pre-mRNA-splicing factor 38 / Small nuclear ribonucleoprotein Sm D1 / Cold sensitive U2 snRNA suppressor 1 / U4/U6 small nuclear ribonucleoprotein PRP3 / Pre-mRNA-splicing factor RSE1 / Small nuclear ribonucleoprotein E / U6 snRNA-associated Sm-like protein LSm6 ...Small nuclear ribonucleoprotein Sm D2 / Small nuclear ribonucleoprotein F / U6 snRNA-associated Sm-like protein LSm3 / Pre-mRNA-splicing factor 38 / Small nuclear ribonucleoprotein Sm D1 / Cold sensitive U2 snRNA suppressor 1 / U4/U6 small nuclear ribonucleoprotein PRP3 / Pre-mRNA-splicing factor RSE1 / Small nuclear ribonucleoprotein E / U6 snRNA-associated Sm-like protein LSm6 / Spliceosomal protein DIB1 / Pre-mRNA-splicing factor RDS3 / Pre-mRNA-splicing factor PRP11 / Pre-mRNA leakage protein 1 / U2 small nuclear ribonucleoprotein A' / U2 snRNP component HSH155 / 23 kDa U4/U6.U5 small nuclear ribonucleoprotein component / 66 kDa U4/U6.U5 small nuclear ribonucleoprotein component / U6 snRNA-associated Sm-like protein LSm7 / U6 snRNA-associated Sm-like protein LSm5 / Pre-mRNA-processing factor 31 / U6 snRNA-associated Sm-like protein LSm2 / RDS3 complex subunit 10 / Pre-mRNA-splicing factor 6 / Pre-mRNA-splicing factor PRP9 / U4/U6 small nuclear ribonucleoprotein PRP4 / Pre-mRNA-splicing factor PRP21 / Pre-mRNA-splicing helicase BRR2 / Pre-mRNA-splicing factor 8 / Pre-mRNA-splicing factor SNU114 / Pre-mRNA-splicing factor SPP381 / U6 snRNA-associated Sm-like protein LSm8 / 13 kDa ribonucleoprotein-associated protein / Small nuclear ribonucleoprotein-associated protein B / U6 snRNA-associated Sm-like protein LSm4 / Small nuclear ribonucleoprotein G / U2 snRNP component IST3 / U2 small nuclear ribonucleoprotein B'' / Small nuclear ribonucleoprotein Sm D3 / Pre-mRNA-splicing factor CWC26 / Protein HSH49
Biological speciesSaccharomyces cerevisiae S288c (yeast) / Baker's yeast (baker's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsBai R / Wan R / Yan C / Shi Y
CitationJournal: Science / Year: 2018
Title: Structures of the fully assembled spliceosome before activation.
Authors: Rui Bai / Ruixue Wan / Chuangye Yan / Jianlin Lei / Yigong Shi /
Abstract: The precatalytic spliceosome (B complex) is preceded by the pre-B complex. Here we report the cryo-electron microscopy structures of the pre-B and B complexes at average resolutions of 3.3 to 4.6 ...The precatalytic spliceosome (B complex) is preceded by the pre-B complex. Here we report the cryo-electron microscopy structures of the pre-B and B complexes at average resolutions of 3.3 to 4.6 and 3.9 angstroms, respectively. In the pre-B complex, the duplex between the 5' splice site (5'SS) and U1 small nuclear RNA (snRNA) is recognized by Yhc1, Luc7, and the Sm ring. In the B complex, U1 small nuclear ribonucleoprotein is dissociated, the 5'-exon-5'SS sequences are translocated near U6 snRNA, and three B-specific proteins may orient the precursor messenger RNA. In both complexes, U6 snRNA is anchored to loop I of U5 snRNA, and the duplex between the branch point sequence and U2 snRNA is recognized by the SF3b complex. Structural analysis reveals the mechanism of assembly and activation for the yeast spliceosome.
Validation ReportSummary, Full report, XML, About validation report
History
DepositionMay 16, 2018-
Header (metadata) releaseAug 29, 2018-
Map releaseAug 29, 2018-
UpdateAug 29, 2018-
Current statusAug 29, 2018Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5zwo
  • Surface level: 0.03
  • 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_6974.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.34 Å/pix.
x 400 pix.
= 535.2 Å
1.34 Å/pix.
x 400 pix.
= 535.2 Å
1.34 Å/pix.
x 400 pix.
= 535.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.338 Å
Density
Contour LevelBy AUTHOR: 0.022 / Movie #1: 0.03
Minimum - Maximum-0.13556543 - 0.2485734
Average (Standard dev.)0.00055685086 (±0.005733394)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 535.2 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.3381.3381.338
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z535.200535.200535.200
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-0.1360.2490.001

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Supplemental data

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Sample components

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Entire yeast fully assembled spliceosomal B complex before activation

EntireName: yeast fully assembled spliceosomal B complex before activation
Number of components: 49

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Component #1: cellular-component, yeast fully assembled spliceosomal B complex ...

Cellular-componentName: yeast fully assembled spliceosomal B complex before activation
Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae S288c (yeast)

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Component #2: 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: S288c

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Component #3: 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: S288c

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Component #4: 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: S288c

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Component #5: 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: S288c

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Component #6: 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: S288c

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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: S288c

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Component #8: 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: S288c

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Component #9: protein, Pre-mRNA-splicing factor SNU114

ProteinName: Pre-mRNA-splicing factor SNU114 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 114.174008 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: S288c

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Component #10: 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: S288c

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Component #11: 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: S288c

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Component #12: 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: S288c

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Component #13: 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: S288c

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Component #14: 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: S288c

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Component #15: 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: S288c

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Component #16: 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: S288c

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Component #17: nucleic-acid, U6 snRNA

nucleic acidName: U6 snRNAU6 spliceosomal RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
GUUCGCGAAA UUUUACUUCG UGGACAUUUG GUCAAUUUGA AACAAUACAG AGAUGAUCAG CAGUUCCCCU GCAUAAGGAU GAACCGUUUU ACAAAGAGAU UUAUUUCGUU UU
MassTheoretical: 35.846105 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: S288c

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Component #18: 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: S288c

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Component #19: protein, 66 kDa U4/U6.U5 small nuclear ribonucleoprotein component

ProteinName: 66 kDa U4/U6.U5 small nuclear ribonucleoprotein component
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 66.544047 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: S288c

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Component #20: protein, Small nuclear ribonucleoprotein Sm D3

ProteinName: Small nuclear ribonucleoprotein Sm D3 / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 11.240139 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: S288c

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Component #21: protein, Small nuclear ribonucleoprotein-associated protein B

ProteinName: Small nuclear ribonucleoprotein-associated protein B / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 22.42699 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: S288c

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Component #22: protein, Small nuclear ribonucleoprotein Sm D1

ProteinName: Small nuclear ribonucleoprotein Sm D1 / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 16.296798 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: S288c

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Component #23: protein, Small nuclear ribonucleoprotein Sm D2

ProteinName: Small nuclear ribonucleoprotein Sm D2 / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 12.876066 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: S288c

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Component #24: protein, Small nuclear ribonucleoprotein E

ProteinName: Small nuclear ribonucleoprotein E / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 10.385098 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: S288c

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Component #25: protein, Small nuclear ribonucleoprotein F

ProteinName: Small nuclear ribonucleoprotein F / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 9.669945 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: S288c

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Component #26: protein, Small nuclear ribonucleoprotein G

ProteinName: Small nuclear ribonucleoprotein G / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 8.490809 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: S288c

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Component #27: 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 GAAUUACCUU U
MassTheoretical: 51.492188 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: S288c

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Component #28: 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: S288c

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Component #29: nucleic-acid, Pre-mRNA

nucleic acidName: Pre-mRNAPrimary transcript / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
AAAAAAAAUU UUUUUUAAAA AAAAAAAACU AGAUACUAAC ACAUUUAAUU UUUUUUUGUU
MassTheoretical: 19.067297 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: S288c

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Component #30: protein, U2 snRNP component HSH155

ProteinName: U2 snRNP component HSH155 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 110.166672 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: S288c

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Component #31: protein, Cold sensitive U2 snRNA suppressor 1

ProteinName: Cold sensitive U2 snRNA suppressor 1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 50.339879 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: S288c

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Component #32: protein, Pre-mRNA-splicing factor RSE1

ProteinName: Pre-mRNA-splicing factor RSE1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 153.956781 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: S288c

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Component #33: protein, Protein HSH49

ProteinName: Protein HSH49 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 24.534152 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: S288c

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Component #34: protein, Pre-mRNA-splicing factor RDS3

ProteinName: Pre-mRNA-splicing factor RDS3 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 12.283573 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: S288c

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Component #35: protein, RDS3 complex subunit 10

ProteinName: RDS3 complex subunit 10 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 10.045401 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: S288c

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Component #36: protein, U2 snRNP component IST3

ProteinName: U2 snRNP component IST3 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 17.121127 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: S288c

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Component #37: protein, Pre-mRNA-splicing factor CWC26

ProteinName: Pre-mRNA-splicing factor CWC26 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 30.529141 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: S288c

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Component #38: protein, Pre-mRNA leakage protein 1

ProteinName: Pre-mRNA leakage protein 1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 23.685682 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: S288c

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Component #39: nucleic-acid, U2 snRNA

nucleic acidName: U2 snRNAU2 spliceosomal RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence: ACGAAUCUCU UUGCCUUUUG GCUUAGAUCA AGUGUAGUAU CUGUUCUUUU CAGUGUAACA ACUGAAAUGA CCUCAAUGAG GCUCAUUACC UUUUAAUUUG UUACAAUACA CAUUUUUUGG CACCCAAAAU AAUAAAAUGG ACGGGAAGAG ACUUUUUAAG CAAGACGUUU ...Sequence:
ACGAAUCUCU UUGCCUUUUG GCUUAGAUCA AGUGUAGUAU CUGUUCUUUU CAGUGUAACA ACUGAAAUGA CCUCAAUGAG GCUCAUUACC UUUUAAUUUG UUACAAUACA CAUUUUUUGG CACCCAAAAU AAUAAAAUGG ACGGGAAGAG ACUUUUUAAG CAAGACGUUU UCCGCUAAUG ACACCUCGCA CGAGUCGUUC UUGCUAUCUU UGGUCGCUUG AUGUUUCUUC UUAACCCGUU CUUAUGAUGG UUUUUCGAAA UUGGUUUUUG AGACGACGGU UGCUCAAGGU UAUUGUUUUU GUUUUCUUCU GGUUGUUUUC UAUUUUCUUU UUUUUAGCUU UCUGUUUCUC CCUUAGUUUG GCUUUUUGCU UCAUACUCUU CCCUGUCUUU CCGAGCCGUU UAUGUCCAAC GCGGGAUUUG GUUUUUCUUU AUCGAUGGGA AGAAAUGGUG CUAUAGUAGG UUGGGAGAUA AUAUUUAUGG UAUGGGGUGC UAGUGCGGAU GGGGCGCUCU UAUUGUUGAU UUCUUCGCUC GUCUUCUUUU UCUGGUGGCG CUGCAAGAGG AAGUUUUUCG ACUUUGUUAU GAUUUUUGGU UUGCAAGGAA AGGUGUCUUA CGAUUCUUUU UUUGAUGUAA UAGGAUAAGC UUGCUUAUCC CCCAAGUAUC GGCCAAAGUU GUUGAUUUUC CUUUUGAAGU GUCCUCGGUU UGAGGGGGUG UAGGGUGGGG UUGGUCUACA AUAAGAGUGU UCCAUUGUUA ACGUGCUGGC GUCUUUUACU AUAUUUUUUU UCCCAGUUUA UUUUGUGCUU AUUUUCUCAU UGAGGAGAAG GAGCUCUUCU CGCAGGAUAU AAAUGGAGGU UUGCUAAAGG GGAGGAGAUG UGUUUGUGAG AAUACUGCUG AGAGAGUUCU GGAAGAGAAA AAAAGGAGGC AAUGGAAGGC GUUUGCUGGG AAAAGAGAAG AGCCAUGACU GCAUCUGUUG UUUCAAGGCC AGUUUUAUUA ACCGCCUAUG UCAUAGAGGC GUUUUUUUUG GAGGGAUUUG AAGAAUGCCG GCGGCAUCAA GAAACGGACU UGAUGGUUGA CGCCUGUUUU UAAAGUUAGA GACGUCGCGA CCCUCGCACU UGUGGAGUCG UUCUUGACUU UUACUUUGGU CGCUUGAUGU UUCUCUCGUC UUCCCGUUCG CUCUU
MassTheoretical: 376.324562 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: S288c

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Component #40: protein, U2 small nuclear ribonucleoprotein A'

ProteinName: U2 small nuclear ribonucleoprotein A' / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 27.232252 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: S288c

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Component #41: protein, U2 small nuclear ribonucleoprotein B''

ProteinName: U2 small nuclear ribonucleoprotein B'' / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 12.850944 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: S288c

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Component #42: protein, Pre-mRNA-splicing factor PRP9

ProteinName: Pre-mRNA-splicing factor PRP9 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 63.126445 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: S288c

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Component #43: protein, Pre-mRNA-splicing factor PRP21

ProteinName: Pre-mRNA-splicing factor PRP21 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 33.111512 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: S288c

+
Component #44: protein, Pre-mRNA-splicing factor PRP11

ProteinName: Pre-mRNA-splicing factor PRP11 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 29.962809 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: S288c

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Component #45: protein, 23 kDa U4/U6.U5 small nuclear ribonucleoprotein component

ProteinName: 23 kDa U4/U6.U5 small nuclear ribonucleoprotein component
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 22.717799 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: S288c

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Component #46: protein, Pre-mRNA-splicing factor 38

ProteinName: Pre-mRNA-splicing factor 38 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 27.995619 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: S288c

+
Component #47: protein, Pre-mRNA-splicing factor SPP381

ProteinName: Pre-mRNA-splicing factor SPP381 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 33.830926 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: S288c

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Component #48: ligand, GUANOSINE-5'-TRIPHOSPHATE

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

+
Component #49: ligand, MAGNESIUM ION

LigandName: MAGNESIUM ION / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 2.430505 MDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: Cell / Method: cryo EM
Sample solutionpH: 7.9
VitrificationCryogen name: ETHANE

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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: 50 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 342588
3D reconstructionResolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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