3jb9

From Proteopedia

(Difference between revisions)

Revision as of 18:25, 10 April 2020

Cryo-EM structure of the yeast spliceosome at 3.6 angstrom resolution

3jb9, resolution 3.60Å

Structural highlights

3jb9 is a 43 chain structure with sequence from Schizosaccharomyces pombe and Schizosaccharomyces pombe 972h-. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
Activity:	Peptidylprolyl isomerase, with EC number 5.2.1.8
Experimental data:	Check to display Experimental Data
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[RU2B_SCHPO] Involved in pre-mRNA splicing. This protein is associated with snRNP U2. It binds stem loop IV of U2 snRNA (By similarity). [SLT11_SCHPO] Facilitates the cooperative formation of U2/U6 helix II in association with stem II in the spliceosome. Binds to RNA (By similarity). Involved in pre-mRNA splicing. [SMD2_SCHPO] Involved in pre-mRNA splicing. Binds snRNA U1, U2, U4 and U5 which contain a highly conserved structural motif called the Sm binding site (By similarity). [CWC15_SCHPO] Involved in pre-mRNA splicing. [SN114_SCHPO] Component of the U5 snRNP complex required for pre-mRNA splicing. Binds GTP. [SPP42_SCHPO] Involved in pre-mRNA splicing. May be involved in endoplasmic reticulum-associated protein degradation (ERAD) and required for growth at low and high temperatures (By similarity). Required for pre-spliceosome formation, which is the first step of pre-mRNA splicing. This protein is associated with snRNP U5. Has a role in branch site-3' splice site selection. Associates with the branch site-3' splice 3'-exon region.^[1] [PRP19_SCHPO] Probable ubiquitin-protein ligase involved in pre-mRNA splicing where it associates with cdc5 and the other cwf proteins as part of the spliceosome. May also function in DNA repair.[UniProtKB:P32523] [CWF11_SCHPO] Involved in mRNA splicing where it associates with cdc5 and the other cwf proteins as part of the spliceosome. [SPF27_SCHPO] Involved in mRNA splicing. [PRP17_SCHPO] Functions in the second step of pre-mRNA splicing. Involved in splicing intron which are longer than 200 nucleotides.^[2] [CWC2_SCHPO] Involved in the first step of pre-mRNA splicing. Required for cell growth and cell cycle control. Plays a role in the levels of the U1, U4, U5 and U6 snRNAs and the maintenance of the U4/U6 snRNA complex. May provide the link between the "nineteen complex" NTC spliceosome protein complex and the spliceosome through the U6 snRNA. Associates predominantly with U6 snRNAs in assembled active spliceosomes. Binds directly to the internal stem-loop (ISL) domain of the U6 snRNA and to the pre-mRNA intron near the 5' splice site during the activation and catalytic phases of the spliceosome cycle (By similarity). Involved in pre-mRNA splicing.^[3] [CWF14_SCHPO] Involved in mRNA splicing where it associates with cdc5 and the other cwf proteins as part of the spliceosome. [RUXG_SCHPO] Involved in pre-mRNA splicing. Binds snRNA U1, U2, U4 and U5 which contain a highly conserved structural motif called the Sm binding site (By similarity). [RU2A_SCHPO] Involved in pre-mRNA splicing. This protein is associated with sn-RNP U2. It helps the A' protein to bind stem loop IV of U2 snRNA (By similarity). [CWF19_SCHPO] Involved in mRNA splicing where it associates with cdc5 and the other cwf proteins as part of the spliceosome. Involved in mRNA splicing. [PRP45_SCHPO] Involved in pre-mRNA splicing. [PPIL1_SCHPO] PPIases accelerate the folding of proteins. It catalyzes the cis-trans isomerization of proline imidic peptide bonds in oligopeptides (By similarity). [SMD1_SCHPO] Involved in pre-mRNA splicing. Binds snRNA U1, U2, U4 and U5 which contain a highly conserved structural motif called the Sm binding site (By similarity). [RUXF_SCHPO] Involved in pre-mRNA splicing. Binds snRNA U1, U2, U4 and U5 which contain a highly conserved structural motif called the Sm binding site (By similarity). [CWF17_SCHPO] Involved in mRNA splicing where it associates with cdc5 and the other cwf proteins as part of the spliceosome. [RUXE_SCHPO] Involved in pre-mRNA splicing. Binds and is required for the stability of snRNA U1, U2, U4 and U5 which contain a highly conserved structural motif called the Sm binding site. Involved in cap modification (By similarity).[UniProtKB:Q12330] [SMD3_SCHPO] Involved in pre-mRNA splicing. Binds snRNA U1, U2, U4 and U5 which contain a highly conserved structural motif called the Sm binding site (By similarity). [CEF1_SCHPO] Involved in mRNA splicing and cell cycle control.^[4] ^[5] [RSMB_SCHPO] Involved in pre-mRNA splicing. Binds snRNA U1, U2, U4 and U5 which contain a highly conserved structural motif called the Sm binding site (By similarity).

Publication Abstract from PubMed

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.

Structure of a yeast spliceosome at 3.6-angstrom resolution.,Yan C, Hang J, Wan R, Huang M, Wong CC, Shi Y Science. 2015 Sep 11;349(6253):1182-91. doi: 10.1126/science.aac7629. Epub 2015, Aug 20. PMID:26292707^[6]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Bottner CA, Schmidt H, Vogel S, Michele M, Kaufer NF. Multiple genetic and biochemical interactions of Brr2, Prp8, Prp31, Prp1 and Prp4 kinase suggest a function in the control of the activation of spliceosomes in Schizosaccharomyces pombe. Curr Genet. 2005 Sep;48(3):151-61. Epub 2005 Oct 12. PMID:16133344 doi:http://dx.doi.org/10.1007/s00294-005-0013-6
↑ Sapra AK, Arava Y, Khandelia P, Vijayraghavan U. Genome-wide analysis of pre-mRNA splicing: intron features govern the requirement for the second-step factor, Prp17 in Saccharomyces cerevisiae and Schizosaccharomyces pombe. J Biol Chem. 2004 Dec 10;279(50):52437-46. Epub 2004 Sep 27. PMID:15452114 doi:http://dx.doi.org/10.1074/jbc.M408815200
↑ Potashkin J, Li R, Frendewey D. Pre-mRNA splicing mutants of Schizosaccharomyces pombe. EMBO J. 1989 Feb;8(2):551-9. PMID:2721492
↑ McDonald WH, Ohi R, Smelkova N, Frendewey D, Gould KL. Myb-related fission yeast cdc5p is a component of a 40S snRNP-containing complex and is essential for pre-mRNA splicing. Mol Cell Biol. 1999 Aug;19(8):5352-62. PMID:10409726
↑ Ohi R, McCollum D, Hirani B, Den Haese GJ, Zhang X, Burke JD, Turner K, Gould KL. The Schizosaccharomyces pombe cdc5+ gene encodes an essential protein with homology to c-Myb. EMBO J. 1994 Jan 15;13(2):471-83. PMID:8313892
↑ Yan C, Hang J, Wan R, Huang M, Wong CC, Shi Y. Structure of a yeast spliceosome at 3.6-angstrom resolution. Science. 2015 Sep 11;349(6253):1182-91. doi: 10.1126/science.aac7629. Epub 2015, Aug 20. PMID:26292707 doi:http://dx.doi.org/10.1126/science.aac7629

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 See Also
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3jb9"

@@ Line 3: / Line 3: @@
 <SX load='3jb9' size='340' side='right' viewer='molstar' caption='[[3jb9]], [[Resolution|resolution]] 3.60&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3jb9]] is a 43 chain structure with sequence from [http://en.wikipedia.org/wiki/Schizosaccharomyces_pombe Schizosaccharomyces pombe] and [http://en.wikipedia.org/wiki/Schizosaccharomyces_pombe_972h- Schizosaccharomyces pombe 972h-]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3JB9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3JB9 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3jb9]] is a 43 chain structure with sequence from [http://en.wikipedia.org/wiki/Schizosaccharomyces_pombe Schizosaccharomyces pombe] and [http://en.wikipedia.org/wiki/Schizosaccharomyces_pombe_972h- Schizosaccharomyces pombe 972h-]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3JB9 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=3JB9 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=GDP:GUANOSINE-5-DIPHOSPHATE'>GDP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=GDP:GUANOSINE-5-DIPHOSPHATE'>GDP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
 <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=UNK:UNKNOWN'>UNK</scene></td></tr>
 <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Peptidylprolyl_isomerase Peptidylprolyl isomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.2.1.8 5.2.1.8] </span></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3jb9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3jb9 OCA], [http://pdbe.org/3jb9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3jb9 RCSB], [http://www.ebi.ac.uk/pdbsum/3jb9 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3jb9 ProSAT]</span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=3jb9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3jb9 OCA], [http://pdbe.org/3jb9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3jb9 RCSB], [http://www.ebi.ac.uk/pdbsum/3jb9 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3jb9 ProSAT]</span></td></tr>
 </table>
 == Function ==

3jb9

From Proteopedia

Revision as of 18:25, 10 April 2020

Cryo-EM structure of the yeast spliceosome at 3.6 angstrom resolution

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

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