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- EMDB-6420: Local map for Cwf17/Cwf8 region of the yeast spliceosome at 4.28 ... -

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Basic information

Entry
Database: EMDB / ID: EMD-6420
TitleLocal map for Cwf17/Cwf8 region of the yeast spliceosome at 4.28 angstrom resolution
Map dataReconstruction by applying local mask for Cwf17/Cwf8 region
Sample
  • Sample: Spliceosome
  • Protein or peptide: Spliceosome
KeywordsLocal masking / Cwf17/Cwf8 region / 4.28 angstrom
Function / homology
Function and homology information


: / : / : / : / protein modification by small protein conjugation or removal / regulation of siRNA-mediated facultative heterochromatin formation / Transport of Mature mRNA derived from an Intron-Containing Transcript / second spliceosomal transesterification activity / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER ...: / : / : / : / protein modification by small protein conjugation or removal / regulation of siRNA-mediated facultative heterochromatin formation / Transport of Mature mRNA derived from an Intron-Containing Transcript / second spliceosomal transesterification activity / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / : / spliceosomal conformational changes to generate catalytic conformation / post-mRNA release spliceosomal complex / generation of catalytic spliceosome for first transesterification step / U12-type spliceosomal complex / pre-mRNA binding / U2-type catalytic step 1 spliceosome / pICln-Sm protein complex / Prp19 complex / U4 snRNP / spliceosomal tri-snRNP complex / sno(s)RNA-containing ribonucleoprotein complex / SMN-Sm protein complex / Cul4-RING E3 ubiquitin ligase complex / U2-type spliceosomal complex / mRNA cis splicing, via spliceosome / commitment complex / U2-type catalytic step 2 spliceosome / U2 snRNP / U1 snRNP / spliceosomal complex assembly / U2-type prespliceosome / spliceosomal snRNP assembly / precatalytic spliceosome / protein K63-linked ubiquitination / mRNA 5'-splice site recognition / spliceosomal tri-snRNP complex assembly / U5 snRNA binding / U5 snRNP / U2 snRNA binding / U6 snRNA binding / pre-mRNA intronic binding / protein peptidyl-prolyl isomerization / U1 snRNA binding / U4/U6 x U5 tri-snRNP complex / spliceosomal complex / catalytic step 2 spliceosome / peptidylprolyl isomerase / mRNA splicing, via spliceosome / peptidyl-prolyl cis-trans isomerase activity / RING-type E3 ubiquitin transferase / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / metallopeptidase activity / protein folding / nuclear envelope / cysteine-type deubiquitinase activity / cell cycle / ribonucleoprotein complex / DNA repair / GTPase activity / mRNA binding / GTP binding / DNA binding / RNA binding / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Pre-mRNA-splicing factor Cwc2 / 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-terminus 1 / Suppressor of forked / Suppressor of forked protein (Suf) / Pre-mRNA-splicing factor SPF27 / Breast carcinoma amplified sequence 2 (BCAS2) ...Pre-mRNA-splicing factor Cwc2 / 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-terminus 1 / Suppressor of forked / Suppressor of forked protein (Suf) / Pre-mRNA-splicing factor SPF27 / Breast carcinoma amplified sequence 2 (BCAS2) / CWF11 family / Intron-binding protein aquarius, N-terminal / Intron-binding protein aquarius N-terminal / Torus domain / Pre-mRNA-splicing factor Cwc2, RNA recognition motif / Torus domain / Pre-mRNA-processing factor 17 / Pre-mRNA-splicing factor 19 / Pre-mRNA-processing factor 19 / Prp19/Pso4-like / : / SKI-interacting protein SKIP, SNW domain / SKI-interacting protein, SKIP / SKIP/SNW domain / Pre-mRNA-splicing factor Cwf15/Cwc15 / HAT (Half-A-TPR) repeat / Cwf15/Cwc15 cell cycle control protein / 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 / : / Small nuclear ribonucleoprotein D1 / U-box domain profile. / Modified RING finger domain / U-box domain / 116kDa U5 small nuclear ribonucleoprotein component, N-terminal / 116kDa U5 small nuclear ribonucleoprotein component, C-terminal / 116 kDa U5 small nuclear ribonucleoprotein component N-terminus / Zinc finger, CCCH-type superfamily / zinc finger / HIT-like superfamily / 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 Lsm6/SmF / Anaphase-promoting complex subunit 4, WD40 domain / Myb-type HTH DNA-binding domain profile. / Anaphase-promoting complex subunit 4 WD40 domain / Zinc finger, CCCH-type / LSM domain / Zinc finger C3H1-type profile. / 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 / Translation elongation factor EFG/EF2, domain IV / JAB1/Mov34/MPN/PAD-1 ubiquitin protease / Elongation factor G, domain IV / Elongation factor G, domain IV / LSM domain superfamily / Elongation factor G C-terminus / Elongation factor EFG, domain V-like / Elongation factor G C-terminus / Cyclophilin-type peptidyl-prolyl cis-trans isomerase, conserved site / Cyclophilin-type peptidyl-prolyl cis-trans isomerase signature. / EF-G domain III/V-like / 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 / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / SANT/Myb domain / 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 / Translation elongation factor EFTu-like, domain 2 / Elongation factor Tu domain 2 / JAB/MPN 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: 4.28 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-
UpdateSep 16, 2015-
Current statusSep 16, 2015Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0147
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.0147
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-3jb9
  • Surface level: 0.0147
  • 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_6420.map.gz / Format: CCP4 / Size: 173.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction by applying local mask for Cwf17/Cwf8 region
Voxel sizeX=Y=Z: 1.32 Å
Density
Contour LevelBy AUTHOR: 0.0147 / Movie #1: 0.0147
Minimum - Maximum-0.05515673 - 0.11499804
Average (Standard dev.)-0.00005559 (±0.00423111)
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
start NX/NY/NZ-800-4
NX/NY/NZ1611358
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS360360360
D min/max/mean-0.0550.115-0.000

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Supplemental data

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Sample components

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Entire : Spliceosome

EntireName: Spliceosome
Components
  • Sample: Spliceosome
  • Protein or peptide: Spliceosome

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Supramolecule #1000: Spliceosome

SupramoleculeName: Spliceosome / type: sample / ID: 1000 / 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
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
DateMar 29, 2015
Image recordingCategory: FILM / Film or detector model: GATAN K2 (4k x 4k) / Digitization - Scanner: TEMSCAN / Number real images: 2246
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: 4.28 Å / Resolution method: OTHER / Software - Name: RELION / Number images used: 112795

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