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- EMDB-6416: Local map for Cwf10/Sm region of the yeast spliceosome at 3.30 an... -

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Basic information

Entry
Database: EMDB / ID: EMD-6416
TitleLocal map for Cwf10/Sm region of the yeast spliceosome at 3.30 angstrom resolution
Map dataReconstruction by applying local mask for Cwf10/Snu114 and Sm
Sample
  • Sample: Spliceosome from schizosaccharomyces pombe
  • Protein or peptide: Spliceosome
KeywordsLocal masking / Cwf10/Snu114 and Sm / 3.30 angstrom
Function / homology
Function and homology information


nucleolar peripheral inclusion body / mRNA Splicing - Major Pathway / Formation of TC-NER Pre-Incision Complex / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / spliceosomal conformational changes to generate catalytic conformation / siRNA-mediated pericentric heterochromatin formation / post-mRNA release spliceosomal complex / generation of catalytic spliceosome for first transesterification step / pICln-Sm protein complex ...nucleolar peripheral inclusion body / mRNA Splicing - Major Pathway / Formation of TC-NER Pre-Incision Complex / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / spliceosomal conformational changes to generate catalytic conformation / siRNA-mediated pericentric heterochromatin formation / post-mRNA release spliceosomal complex / generation of catalytic spliceosome for first transesterification step / pICln-Sm protein complex / U2-type catalytic step 1 spliceosome / pre-mRNA binding / snRNP binding / SMN-Sm protein complex / spliceosomal tri-snRNP complex / regulatory ncRNA-mediated gene silencing / commitment complex / mRNA cis splicing, via spliceosome / U2-type spliceosomal complex / U2-type catalytic step 2 spliceosome / U4 snRNP / U2 snRNP / U1 snRNP / U2-type prespliceosome / precatalytic spliceosome / spliceosomal complex assembly / mRNA 5'-splice site recognition / spliceosomal tri-snRNP complex assembly / Prp19 complex / U5 snRNA binding / protein K63-linked ubiquitination / U5 snRNP / U2 snRNA binding / U6 snRNA binding / pre-mRNA intronic binding / spliceosomal snRNP assembly / U1 snRNA binding / pericentric heterochromatin / U4/U6 x U5 tri-snRNP complex / catalytic step 2 spliceosome / peptidylprolyl isomerase / spliceosomal complex / peptidyl-prolyl cis-trans isomerase activity / mRNA splicing, via spliceosome / RING-type E3 ubiquitin transferase / metallopeptidase activity / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / nuclear envelope / protein folding / molecular adaptor activity / cysteine-type deubiquitinase activity / DNA repair / GTPase activity / mRNA binding / GTP binding / DNA binding / RNA binding / zinc ion binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Cwf19-like protein, C-terminal domain-2 / Cwf19-like, C-terminal domain-1 / Cwf19-like protein / Protein similar to CwfJ C-terminus 2 / Protein similar to CwfJ C-terminal / Slt11, RNA recognition motif / Pre-mRNA-splicing factor Cwc2, RNA recognition motif / Pre-mRNA-splicing factor SPF27 / Torus domain / Breast carcinoma amplified sequence 2 (BCAS2) ...Cwf19-like protein, C-terminal domain-2 / Cwf19-like, C-terminal domain-1 / Cwf19-like protein / Protein similar to CwfJ C-terminus 2 / Protein similar to CwfJ C-terminal / Slt11, RNA recognition motif / Pre-mRNA-splicing factor Cwc2, RNA recognition motif / Pre-mRNA-splicing factor SPF27 / Torus domain / Breast carcinoma amplified sequence 2 (BCAS2) / Torus domain / CWF11 family / Intron-binding protein aquarius, N-terminal / Intron-binding protein aquarius N-terminal / Pre-mRNA-processing factor 17 / Pre-mRNA-splicing factor 19 / Pre-mRNA-processing factor 19 / : / Prp19/Pso4-like / : / Pre-mRNA-splicing factor SYF1 middle HAT repeat / Cyclophilin-type peptidyl-prolyl cis-trans isomerase, cyclophilin A-like / : / : / STL11, N-terminal / : / Pre-mRNA-splicing factor Syf1/CRNKL1 C-terminal HAT repeat / SKI-interacting protein SKIP, SNW domain / SKI-interacting protein, SKIP / SKIP/SNW domain / : / Pre-mRNA-splicing factor Syf1/CNRKL1 N-terminal HAT repeat / Pre-mRNA-splicing factor Cwf15/Cwc15 / Cwf15/Cwc15 cell cycle control protein / WD repeat Prp46/PLRG1-like / Pre-mRNA-splicing factor Cwc2/Slt11 / : / G10 protein / Pre-mRNA-splicing factor BUD31 / Pre-mRNA splicing factor component Cdc5p/Cef1, C-terminal / : / : / pre-mRNA splicing factor component / Anaphase-promoting complex subunit 4, WD40 domain / DNA2/NAM7-like helicase / : / Myb-like DNA-binding domain / U2 small nuclear ribonucleoprotein A' / Anaphase-promoting complex subunit 4 WD40 domain / Small nuclear ribonucleoprotein D1 / U-box domain profile. / HIT-like superfamily / Zinc finger, CCCH-type superfamily / Modified RING finger domain / zinc finger / U-box domain / Leucine-rich repeat / 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 / Pre-mRNA-splicing factor Syf1-like / Small nuclear ribonucleoprotein Sm D3 / Small nuclear ribonucleoprotein Sm D2 / Small nuclear ribonucleoprotein E / Small nuclear ribonucleoprotein G / Small nuclear ribonucleoprotein F / Sm-like protein Lsm7/SmG / Like-Sm (LSM) domain containing protein, LSm4/SmD1/SmD3 / Sm-like protein Lsm6/SmF / Myb-type HTH DNA-binding domain profile. / Zinc finger, CCCH-type / Zinc finger C3H1-type profile. / LSM domain / LSM domain, eukaryotic/archaea-type / snRNP Sm proteins / HAT (Half-A-TPR) repeat / HAT (Half-A-TPR) repeats / Myb domain / Cyclophilin-type peptidyl-prolyl cis-trans isomerase / : / Sm domain profile. / LSM domain superfamily / JAB1/Mov34/MPN/PAD-1 ubiquitin protease / Translation elongation factor EFG/EF2, domain IV / Elongation factor G, domain IV / Elongation factor G, domain IV / Elongation factor G C-terminus / Cyclophilin-type peptidyl-prolyl cis-trans isomerase, conserved site / Cyclophilin-type peptidyl-prolyl cis-trans isomerase signature. / Elongation factor EFG, domain V-like / Elongation factor G C-terminus / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain profile. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain / Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD / Cyclophilin-like domain superfamily / EF-G domain III/V-like / PROCT domain / Prp8 RNase domain IV, fingers region / PROCT (NUC072) domain
Similarity search - Domain/homology
Pre-mRNA-splicing factor prp5 / Pre-mRNA-processing factor 19 / Small nuclear ribonucleoprotein Sm D2 / Pre-mRNA-splicing factor spp42 / Small nuclear ribonucleoprotein Sm D1 / Pre-mRNA-processing factor 17 / Small nuclear ribonucleoprotein F / Pre-mRNA-splicing factor cwf5 / Pre-mRNA-splicing factor cwf14 / Small nuclear ribonucleoprotein G ...Pre-mRNA-splicing factor prp5 / Pre-mRNA-processing factor 19 / Small nuclear ribonucleoprotein Sm D2 / Pre-mRNA-splicing factor spp42 / Small nuclear ribonucleoprotein Sm D1 / Pre-mRNA-processing factor 17 / Small nuclear ribonucleoprotein F / Pre-mRNA-splicing factor cwf5 / Pre-mRNA-splicing factor cwf14 / Small nuclear ribonucleoprotein G / Pre-mRNA-splicing factor cwf10 / Pre-mRNA-splicing factor cwf11 / Pre-mRNA-splicing factor cwf17 / Pre-mRNA-splicing factor cdc5 / Pre-mRNA-splicing factor cwf15 / Peptidyl-prolyl cis-trans isomerase ppi1 / Pre-mRNA-splicing factor cwf2 / Pre-mRNA-splicing factor cwf4 / Pre-mRNA-processing protein 45 / Pre-mRNA-splicing factor cwf19 / Small nuclear ribonucleoprotein-associated protein B / Probable U2 small nuclear ribonucleoprotein B'' / Pre-mRNA-splicing factor cwf3 / Pre-mRNA-splicing factor cwf7 / U2 small nuclear ribonucleoprotein A' / Small nuclear ribonucleoprotein E / Small nuclear ribonucleoprotein Sm D3
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsYan C / Hang J / Wan R / Huang M / Wong C / Shi Y
CitationJournal: Science / Year: 2015
Title: Structure of a yeast spliceosome at 3.6-angstrom resolution.
Authors: Chuangye Yan / Jing Hang / Ruixue Wan / Min Huang / Catherine C L Wong / Yigong Shi /
Abstract: Splicing of precursor messenger RNA (pre-mRNA) in yeast is executed by the spliceosome, which consists of five small nuclear ribonucleoproteins (snRNPs), NTC (nineteen complex), NTC-related proteins ...Splicing of precursor messenger RNA (pre-mRNA) in yeast is executed by the spliceosome, which consists of five small nuclear ribonucleoproteins (snRNPs), NTC (nineteen complex), NTC-related proteins (NTR), and a number of associated enzymes and cofactors. Here, we report the three-dimensional structure of a Schizosaccharomyces pombe spliceosome at 3.6-angstrom resolution, revealed by means of single-particle cryogenic electron microscopy. This spliceosome contains U2 and U5 snRNPs, NTC, NTR, U6 small nuclear RNA, and an RNA intron lariat. The atomic model includes 10,574 amino acids from 37 proteins and four RNA molecules, with a combined molecular mass of approximately 1.3 megadaltons. Spp42 (Prp8 in Saccharomyces cerevisiae), the key protein component of the U5 snRNP, forms a central scaffold and anchors the catalytic center. Both the morphology and the placement of protein components appear to have evolved to facilitate the dynamic process of pre-mRNA splicing. Our near-atomic-resolution structure of a central spliceosome provides a molecular framework for mechanistic understanding of pre-mRNA splicing.
History
DepositionAug 9, 2015-
Header (metadata) releaseSep 16, 2015-
Map releaseSep 16, 2015-
UpdateJun 8, 2016-
Current statusJun 8, 2016Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0139
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.0139
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-3jb9
  • Surface level: 0.0139
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

400_6416.gif

Downloads & links

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Map

FileDownload / File: emd_6416.map.gz / Format: CCP4 / Size: 173.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction by applying local mask for Cwf10/Snu114 and Sm
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.32 Å/pix.
x 360 pix.
= 475.2 Å		1.32 Å/pix.
x 360 pix.
= 475.2 Å		1.32 Å/pix.
x 360 pix.
= 475.2 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: 0.0139 / Movie #1: 0.0139
Minimum - Maximum-0.08244001 - 0.20157485
Average (Standard dev.)-0.00005255 (±0.00457164)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 475.2 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.321.321.32
M x/y/z360360360
origin x/y/z0.0000.0000.000
length x/y/z475.200475.200475.200
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS360360360
D min/max/mean-0.0820.202-0.000

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Supplemental data

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Sample components

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Entire : Spliceosome from schizosaccharomyces pombe

EntireName: Spliceosome from schizosaccharomyces pombe
Components
  • Sample: Spliceosome from schizosaccharomyces pombe
  • Protein or peptide: Spliceosome

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Supramolecule #1000: Spliceosome from schizosaccharomyces pombe

SupramoleculeName: Spliceosome from schizosaccharomyces pombe / type: sample / ID: 1000 / Details: The sample was monodisperse / Number unique components: 1

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Macromolecule #1: Spliceosome

MacromoleculeName: Spliceosome / type: protein_or_peptide / ID: 1 / Recombinant expression: No / Database: NCBI
Source (natural)Organism: Schizosaccharomyces pombe (fission 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 / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
DateMar 29, 2015
Image recordingCategory: FILM / Film or detector model: GATAN K2 (4k x 4k) / Digitization - Scanner: TEMSCAN / Number real images: 2246
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: DARK 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

CTF correctionDetails: Each particle
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: OTHER / Software - Name: RELION / Number images used: 112795

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