4v98: Difference between revisions

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<StructureSection load='4v98' size='340' side='right'caption='[[4v98]], [[Resolution|resolution]] 3.10&Aring;' scene=''>
<StructureSection load='4v98' size='340' side='right'caption='[[4v98]], [[Resolution|resolution]] 3.10&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[4v98]] is a 160 chain structure with sequence from [http://en.wikipedia.org/wiki/Drome Drome] and [http://en.wikipedia.org/wiki/Human Human]. This structure supersedes the now removed PDB entries [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1vu2 1vu2], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1vu3 1vu3] and [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4f77 4f77]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4V98 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4V98 FirstGlance]. <br>
<table><tr><td colspan='2'>[[4v98]] is a 160 chain structure with sequence from [https://en.wikipedia.org/wiki/Drosophila_melanogaster Drosophila melanogaster] and [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. This structure supersedes the now removed PDB entries [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1vu2 1vu2], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1vu3 1vu3] and [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4f77 4f77]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4V98 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4V98 FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">SNRPD1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN]), SNRPD2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN]), SNRPE ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN]), SNRPF, PBSCF ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN]), Smn, CG16725, Dmel_CG16725 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=7227 DROME]), Gem2, CG10419, Dmel_CG10419 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=7227 DROME]), Dmel_CG4924, icln, icln-RA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=7227 DROME]), SNRPG, PBSCG ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4v98 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4v98 OCA], [https://pdbe.org/4v98 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4v98 RCSB], [https://www.ebi.ac.uk/pdbsum/4v98 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4v98 ProSAT]</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=4v98 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4v98 OCA], [http://pdbe.org/4v98 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4v98 RCSB], [http://www.ebi.ac.uk/pdbsum/4v98 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4v98 ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[http://www.uniprot.org/uniprot/GEMI2_DROME GEMI2_DROME]] The SMN complex plays an essential role in spliceosomal snRNP assembly in the cytoplasm, is required for pre-mRNA splicing in the nucleus and acts as a chaperone that discriminates target and non-target RNAs of Sm proteins.<ref>PMID:18621711</ref> <ref>PMID:23333303</ref>  [[http://www.uniprot.org/uniprot/RUXE_HUMAN RUXE_HUMAN]] Appears to function in the U7 snRNP complex that is involved in histone 3'-end processing. Associated with snRNP U1, U2, U4/U6 and U5. [[http://www.uniprot.org/uniprot/ICLN_DROME ICLN_DROME]] Chaperone that regulates the assembly of spliceosomal U1, U2, U4 and U5 small nuclear ribonucleoproteins (snRNPs), the building blocks of the spliceosome. Thereby, plays an important role in the splicing of cellular pre-mRNAs. Most spliceosomal snRNPs contain a common set of Sm proteins SNRPB, SNRPD1, SNRPD2, SNRPD3, SNRPE, SNRPF and SNRPG that assemble in a heptameric protein ring on the Sm site of the small nuclear RNA to form the core snRNP. In the cytosol, the Sm proteins SNRPD1, SNRPD2, SNRPE, SNRPF and SNRPG are trapped in an inactive 6S pICln-Sm complex by the chaperone CLNS1A that controls the assembly of the core snRNP. Dissociation by the SMN complex of CLNS1A from the trapped Sm proteins and their transfer to an SMN-Sm complex triggers the assembly of core snRNPs and their transport to the nucleus (By similarity). [[http://www.uniprot.org/uniprot/SMD2_HUMAN SMD2_HUMAN]] Required for pre-mRNA splicing. Required for snRNP biogenesis (By similarity). [[http://www.uniprot.org/uniprot/RUXG_HUMAN RUXG_HUMAN]] Appears to function in the U7 snRNP complex that is involved in histone 3'-end processing. Associated with snRNP U1, U2, U4/U6 and U5. [[http://www.uniprot.org/uniprot/SMD1_HUMAN SMD1_HUMAN]] May act as a charged protein scaffold to promote snRNP assembly or strengthen snRNP-snRNP interactions through nonspecific electrostatic contacts with RNA. [[http://www.uniprot.org/uniprot/RUXF_HUMAN RUXF_HUMAN]] Appears to function in the U7 snRNP complex that is involved in histone 3'-end processing. Associated with snRNP U1, U2, U4/U6 and U5. [[http://www.uniprot.org/uniprot/SMN_DROME SMN_DROME]] The SMN complex plays an essential role in spliceosomal snRNP assembly in the cytoplasm, is required for pre-mRNA splicing in the nucleus and acts as a chaperone that discriminates target and non-target RNAs of Sm proteins. Required for normal expression of spliceosomal snRNAs and for U12 intron splicing. Required in cholinergic neurons, but not in motor neurons, to ensure correct splicing and proper levels of stas mRNA and normal neurotransmitter release by motor neurons (PubMed:23063130 and PubMed:23063131). However, Smn is required in motor neurons, but not in cholinergic neurons, for normal motor behavior but plays no role in synaptic transmission according to PubMed:23103409. In both muscle and neurons, required for the formation of a normal neuromuscular junction (NMJ) structure. Plays a neuron-specific role in long-term homeostatic compensation at the larval NMJ. In the thorax of adult flies, required for Act88F, an indirect flight muscle (IFM)-specific actin, expression and for proper IFM myofibril formation. In nurse cells, oocytes and follicle cells, required to maintain normal organization of nuclear compartments including chromosomes, nucleoli, Cajal bodies, histone locus bodies and heterochromatin. Required for the functional integrity of the cytoplasmic U snRNP body (U body) and P body. Required in dividing postembryonic neuroblasts (pNBs) for the correct basal localization of mira. The tight regulation of its expression is critical for stem cell division, proliferation and differentiation in male germline and developing central nervous system (CNS). Required for tracheal terminal cell lumen formation.<ref>PMID:12783845</ref> <ref>PMID:17353360</ref> <ref>PMID:18621711</ref> <ref>PMID:18791638</ref> <ref>PMID:19464282</ref> <ref>PMID:21490958</ref> <ref>PMID:22813737</ref> <ref>PMID:23029159</ref> <ref>PMID:23063130</ref> <ref>PMID:23063131</ref> <ref>PMID:23103409</ref> <ref>PMID:23333303</ref> 
[https://www.uniprot.org/uniprot/SMD1_HUMAN SMD1_HUMAN] May act as a charged protein scaffold to promote snRNP assembly or strengthen snRNP-snRNP interactions through nonspecific electrostatic contacts with RNA.
<div style="background-color:#fffaf0;">
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
== Publication Abstract from PubMed ==
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</div>
</div>
<div class="pdbe-citations 4v98" style="background-color:#fffaf0;"></div>
<div class="pdbe-citations 4v98" style="background-color:#fffaf0;"></div>
==See Also==
*[[Nucleoprotein|Nucleoprotein]]
== References ==
== References ==
<references/>
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Drome]]
[[Category: Drosophila melanogaster]]
[[Category: Human]]
[[Category: Homo sapiens]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Diederichs, K]]
[[Category: Diederichs K]]
[[Category: Grimm, C]]
[[Category: Grimm C]]
[[Category: Kisker, C]]
[[Category: Kisker C]]
[[Category: Kuper, J]]
[[Category: Kuper J]]
[[Category: Pelz, J P]]
[[Category: Pelz JP]]
[[Category: Schindelin, H]]
[[Category: Schindelin H]]
[[Category: Assembly machinery]]
[[Category: Complex]]
[[Category: Splicing]]

Revision as of 11:14, 29 March 2023

The 8S snRNP Assembly IntermediateThe 8S snRNP Assembly Intermediate

Structural highlights

4v98 is a 160 chain structure with sequence from Drosophila melanogaster and Homo sapiens. This structure supersedes the now removed PDB entries 1vu2, 1vu3 and 4f77. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

SMD1_HUMAN May act as a charged protein scaffold to promote snRNP assembly or strengthen snRNP-snRNP interactions through nonspecific electrostatic contacts with RNA.

Publication Abstract from PubMed

Small nuclear ribonucleoproteins (snRNPs) represent key constituents of major and minor spliceosomes. snRNPs contain a common core, composed of seven Sm proteins bound to snRNA, which forms in a step-wise and factor-mediated reaction. The assembly chaperone pICln initially mediates the formation of an otherwise unstable pentameric Sm protein unit. This so-called 6S complex docks subsequently onto the SMN complex, which removes pICln and enables the transfer of pre-assembled Sm proteins onto snRNA. X-ray crystallography and electron microscopy was used to investigate the structural basis of snRNP assembly. The 6S complex structure identifies pICln as an Sm protein mimic, which enables the topological organization of the Sm pentamer in a closed ring. A second structure of 6S bound to the SMN complex components SMN and Gemin2 uncovers a plausible mechanism of pICln elimination and Sm protein activation for snRNA binding. Our studies reveal how assembly factors facilitate formation of RNA-protein complexes in vivo.

Structural Basis of Assembly Chaperone- Mediated snRNP Formation.,Grimm C, Chari A, Pelz JP, Kuper J, Kisker C, Diederichs K, Stark H, Schindelin H, Fischer U Mol Cell. 2013 Jan 15. pii: S1097-2765(12)01018-0. doi:, 10.1016/j.molcel.2012.12.009. PMID:23333303[1]

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

References

  1. ↑ Grimm C, Chari A, Pelz JP, Kuper J, Kisker C, Diederichs K, Stark H, Schindelin H, Fischer U. Structural Basis of Assembly Chaperone- Mediated snRNP Formation. Mol Cell. 2013 Jan 15. pii: S1097-2765(12)01018-0. doi:, 10.1016/j.molcel.2012.12.009. PMID:23333303 doi:http://dx.doi.org/10.1016/j.molcel.2012.12.009

4v98, resolution 3.10Å

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