- EMDB-6581: 3D structure determination of the human *U4/U6.U5* tri-snRNP complex -
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Basic information
Entry
Database: EMDB / ID: EMD-6581
Title
3D structure determination of the human *U4/U6.U5* tri-snRNP complex
Map data
Reconstruction of human tri-snRNP
Sample
Sample: human U4/U6.U5 tri-snRNP
Protein or peptide: U4/U6.U5 tri-snRNP
Keywords
snRNP / splicing / spliceosome / human
Function / homology
Function and homology information
Lsm2-8 complex / U6 snRNA 3'-end binding / spliceosomal snRNP complex / ribonucleoprotein complex localization / snRNP binding / U4atac snRNP / RNA localization / R-loop processing / U4atac snRNA binding / mRNA decay by 5' to 3' exoribonuclease ...Lsm2-8 complex / U6 snRNA 3'-end binding / spliceosomal snRNP complex / ribonucleoprotein complex localization / snRNP binding / U4atac snRNP / RNA localization / R-loop processing / U4atac snRNA binding / mRNA decay by 5' to 3' exoribonuclease / Lsm1-7-Pat1 complex / U6 snRNP / box C/D sno(s)RNA binding / positive regulation of primary miRNA processing / PH domain binding / U2 snRNP binding / U7 snRNA binding / histone pre-mRNA DCP binding / U7 snRNP / dense fibrillar component / histone pre-mRNA 3'end processing complex / cis assembly of pre-catalytic spliceosome / SLBP independent Processing of Histone Pre-mRNAs / SLBP Dependent Processing of Replication-Dependent Histone Pre-mRNAs / spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) / protein methylation / U12-type spliceosomal complex / methylosome / P-body assembly / U4/U6 snRNP / 7-methylguanosine cap hypermethylation / U1 snRNP binding / pICln-Sm protein complex / U2-type catalytic step 1 spliceosome / RNA splicing, via transesterification reactions / small nuclear ribonucleoprotein complex / sno(s)RNA-containing ribonucleoprotein complex / SMN-Sm protein complex / spliceosomal tri-snRNP complex / P granule / U4 snRNA binding / telomerase holoenzyme complex / box C/D methylation guide snoRNP complex / U2-type spliceosomal complex / U2-type precatalytic spliceosome / commitment complex / telomerase RNA binding / U2-type prespliceosome assembly / U2-type catalytic step 2 spliceosome / U4 snRNP / box C/D snoRNP assembly / U2 snRNP / rRNA modification in the nucleus and cytosol / RNA Polymerase II Transcription Termination / tRNA processing / U1 snRNP / U3 snoRNA binding / nuclear-transcribed mRNA catabolic process / U2-type prespliceosome / K63-linked polyubiquitin modification-dependent protein binding / positive regulation of miRNA metabolic process / precatalytic spliceosome / spliceosomal complex assembly / mRNA Splicing - Minor Pathway / mRNA catabolic process / MLL1 complex / spliceosomal tri-snRNP complex assembly / single fertilization / Major pathway of rRNA processing in the nucleolus and cytosol / U5 snRNA binding / U5 snRNP / RNA processing / U2 snRNA binding / U6 snRNA binding / spliceosomal snRNP assembly / Cajal body / ribonucleoprotein complex binding / pre-mRNA intronic binding / U1 snRNA binding / U4/U6 x U5 tri-snRNP complex / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / RNA splicing / helicase activity / response to cocaine / maturation of LSU-rRNA / maturation of SSU-rRNA / small-subunit processome / response to bacterium / spliceosomal complex / P-body / mRNA processing / small GTPase binding / mRNA splicing, via spliceosome / osteoblast differentiation / cellular response to xenobiotic stimulus / protein-macromolecule adaptor activity / cellular response to tumor necrosis factor / ribosomal small subunit biogenesis / snRNP Assembly Similarity search - Function
USP39 / PRP4-like superfamily / pre-mRNA processing factor 4 (PRP4) like / PWI domain superfamily / PWI domain / PWI domain profile. / 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 ...USP39 / PRP4-like superfamily / pre-mRNA processing factor 4 (PRP4) like / PWI domain superfamily / PWI domain / PWI domain profile. / 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 / PWI domain / PWI, domain in splicing factors / Dim1 family / Mitosis protein DIM1 / Mitosis protein DIM1 / PRP1 splicing factor, N-terminal / PRP1 splicing factor, N-terminal / : / Small ribonucleoprotein associated, SmB/SmN / Small nuclear ribonucleoprotein D1 / Brr2, N-terminal helicase PWI domain / : / N-terminal helicase PWI domain / Pre-mRNA-splicing helicase BRR2 plug domain / H/ACA ribonucleoprotein complex, subunit Nhp2-like / Ubiquitin Carboxyl-terminal Hydrolase-like zinc finger / Zinc finger, UBP-type / NOSIC / Pre-mRNA-splicing factor Syf1-like / Zn-finger in ubiquitin-hydrolases and other protein / Zinc finger UBP-type profile. / NOSIC (NUC001) domain / Nop domain / Nop domain superfamily / Nop, C-terminal domain / snoRNA binding domain, fibrillarin / Nop domain profile. / Sec63 Brl domain / Snu114, GTP-binding 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 / Tetratricopeptide repeat / Small nuclear ribonucleoprotein Sm D3 / Small nuclear ribonucleoprotein Sm D2 / Small nuclear ribonucleoprotein E / Small nuclear ribonucleoprotein G / Small nuclear ribonucleoprotein F / Sec63 domain / Sec63 Brl domain / Sm-like protein Lsm7/SmG / Like-Sm (LSM) domain containing protein, LSm4/SmD1/SmD3 / 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 / Tetratricopeptide repeat / Peptidase C19, ubiquitin carboxyl-terminal hydrolase / Ubiquitin carboxyl-terminal hydrolase / : / Ubiquitin specific protease domain / Ubiquitin specific protease (USP) domain profile. / Sm domain profile. / DEAD-box subfamily ATP-dependent helicases signature. / ATP-dependent RNA helicase DEAD-box, conserved site / RNA helicase, DEAD-box type, Q motif / Elongation Factor G, domain II / Elongation Factor G, domain III / DEAD-box RNA helicase Q motif 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 / 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 Similarity search - Domain/homology
U4/U6 small nuclear ribonucleoprotein Prp4 / U4/U6 small nuclear ribonucleoprotein Prp3 / U5 small nuclear ribonucleoprotein 200 kDa helicase / Pre-mRNA-processing factor 6 / U6 snRNA-associated Sm-like protein LSm8 / Small nuclear ribonucleoprotein-associated proteins B and B' / NHP2-like protein 1 / Small nuclear ribonucleoprotein E / Small nuclear ribonucleoprotein F / Small nuclear ribonucleoprotein G ...U4/U6 small nuclear ribonucleoprotein Prp4 / U4/U6 small nuclear ribonucleoprotein Prp3 / U5 small nuclear ribonucleoprotein 200 kDa helicase / Pre-mRNA-processing factor 6 / U6 snRNA-associated Sm-like protein LSm8 / Small nuclear ribonucleoprotein-associated proteins B and B' / NHP2-like protein 1 / Small nuclear ribonucleoprotein E / Small nuclear ribonucleoprotein F / Small nuclear ribonucleoprotein G / U6 snRNA-associated Sm-like protein LSm3 / U6 snRNA-associated Sm-like protein LSm6 / Small nuclear ribonucleoprotein Sm D1 / Small nuclear ribonucleoprotein Sm D2 / Small nuclear ribonucleoprotein Sm D3 / Thioredoxin-like protein 4A / 116 kDa U5 small nuclear ribonucleoprotein component / Ubiquitin carboxyl-terminal hydrolase 39 / 60 kDa U4/U6 snRNP-specific spliceosomal protein / Pre-mRNA-processing-splicing factor 8 / U4/U6 small nuclear ribonucleoprotein Prp31 / U5 small nuclear ribonucleoprotein 40 kDa protein / Probable ATP-dependent RNA helicase DDX23 / U6 snRNA-associated Sm-like protein LSm7 / U6 snRNA-associated Sm-like protein LSm2 / U6 snRNA-associated Sm-like protein LSm5 / U6 snRNA-associated Sm-like protein LSm4 Similarity search - Component
Biological species
Homo sapiens (human)
Method
single particle reconstruction / cryo EM / Resolution: 7.0 Å
Journal: Science / Year: 2016 Title: Molecular architecture of the human U4/U6.U5 tri-snRNP. Authors: Dmitry E Agafonov / Berthold Kastner / Olexandr Dybkov / Romina V Hofele / Wen-Ti Liu / Henning Urlaub / Reinhard Lührmann / Holger Stark / Abstract: The U4/U6.U5 triple small nuclear ribonucleoprotein (tri-snRNP) is a major spliceosome building block. We obtained a three-dimensional structure of the 1.8-megadalton human tri-snRNP at a resolution ...The U4/U6.U5 triple small nuclear ribonucleoprotein (tri-snRNP) is a major spliceosome building block. We obtained a three-dimensional structure of the 1.8-megadalton human tri-snRNP at a resolution of 7 angstroms using single-particle cryo-electron microscopy (cryo-EM). We fit all known high-resolution structures of tri-snRNP components into the EM density map and validated them by protein cross-linking. Our model reveals how the spatial organization of Brr2 RNA helicase prevents premature U4/U6 RNA unwinding in isolated human tri-snRNPs and how the ubiquitin C-terminal hydrolase-like protein Sad1 likely tethers the helicase Brr2 to its preactivation position. Comparison of our model with cryo-EM three-dimensional structures of the Saccharomyces cerevisiae tri-snRNP and Schizosaccharomyces pombe spliceosome indicates that Brr2 undergoes a marked conformational change during spliceosome activation, and that the scaffolding protein Prp8 is also rearranged to accommodate the spliceosome's catalytic RNA network.
History
Deposition
Jan 15, 2016
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Header (metadata) release
Mar 9, 2016
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Map release
Mar 9, 2016
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Update
Apr 27, 2016
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Current status
Apr 27, 2016
Processing site: RCSB / Status: Released
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Structure visualization
Movie
Surface view with section colored by density value
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