Structure of PDB 6j6n Chain C

Receptor sequence

>6j6nC (length=920) Species: 559292 (Saccharomyces cerevisiae S288C)

EHPYGKEVEVLMETKNTQSPQTPLVEPVTERTKLQEHTIFTQLKKNIPKT
RYNRDYMLSMANIPERIINVGVIGPLHSGKTSLMDLLVIDSHKRIPDMSK
NVELGWKPLRYLDNLKQEIDRGLSIKLNGSTLLCTDLESKSRMINFLDAP
GHVNFMDETAVALAASDLVLIVIDVVEGVTFVVEQLIKQSIKNNVAMCFV
INKLDRLILDLKLPPMDAYLKLNHIIANINSFTKGNVFSPIDNNIIFAST
KLGFTFTIKEFVSYYYAHSIPSSKIDDFTTRLWGSVYYHKGNFRTKPFEN
VEKYPTFVEFILIPLYKIFSYALSMEKDKLKNLLRSNFRVNLSQEALQYD
PQPFLKHVLQLIFRQQTGLVDAITRCYQPFELFDNKTAHLSIPGKSTPEG
TLWAHVLKTVDYGGAEWSLVRIYSGLLKRGDTVRILDTSQSESRQKRQLH
DEDDETPSCEVEEIGLLGGRYVYPVHEAHKGQIVLIKGISSAYIKSATLY
SVKSKEDMKQLKFFKPLDYITEAVFKIVLQPLLPRELPKLLDALNKISKY
YPGVIIKVEESGEHVILGNGELYMDCLLYDLRASYAKIEIKISDPLTVFS
ESCSNESSRLGEENLPGLSISVAAEPMDSKMIQDLSRNTLGKGQNCLDID
GIMDNPRKLSKILRTEYGWDSLASRNVWSFYNGNVLINDTLPDEISPELL
SKYKEQIIQGFYWAVKEGPLAEEPIYGVQYKLLSISVPSDVNIDVMKSQI
IPLMKKACYVGLLTAIPILLEPIYEVDITVHAPLLPIVEELMKKRRGSRI
YKTIKVAGTPLLEVRGQVPVIESAGFETDLRLSTNGLGMCQLYFWHKIWR
KVPGDVLDKDAFIPKLKPAPINSLSRDFVMKTRRRKGISTGGFMSNDGPT
LEKYISAELYAQLRENGLVP

3D structure

• PDB: 6j6n Structures of the Catalytically Activated Yeast Spliceosome Reveal the Mechanism of Branching.
• Chain: C
• Resolution: 3.86 Å

Interaction with ligand

Site #	Ligand	Ligand chain	Binding residues on receptor (original residue number in PDB)	Binding residues on receptor (residue number reindexed from 1)	Binding affinity
BS01	rna	C	R97 K99 L100 Q101 I105 F106 T107 Q108 L109 N112 R160 K173 H334 P337 S338 R405	R31 K33 L34 Q35 I39 F40 T41 Q42 L43 N46 R94 K107 H268 P271 S272 R339
BS02	GTP	C	L142 H143 G145 K146 T147 S148 P216 G217 K269 D271 S315 T316 K317	L76 H77 G79 K80 T81 S82 P150 G151 K203 D205 S249 T250 K251
BS03	MG	C	T147 S190	T81 S124

Gene Ontology

Molecular Function

• GO:0003924 GTPase activity
• GO:0005515 protein binding
• GO:0005525 GTP binding
• GO:0030623 U5 snRNA binding

Biological Process

• GO:0000244 spliceosomal tri-snRNP complex assembly
• GO:0000349 generation of catalytic spliceosome for first transesterification step
• GO:0000387 spliceosomal snRNP assembly
• GO:0000388 spliceosome conformational change to release U4 (or U4atac) and U1 (or U11)
• GO:0000398 mRNA splicing, via spliceosome
• GO:0006397 mRNA processing
• GO:0008380 RNA splicing

Cellular Component

• GO:0005634 nucleus
• GO:0005681 spliceosomal complex
• GO:0005682 U5 snRNP
• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0046540 U4/U6 x U5 tri-snRNP complex
• GO:0071007 U2-type catalytic step 2 spliceosome

External links

• PDB: RCSB:6j6n, PDBe:6j6n, PDBj:6j6n
• PDBsum: 6j6n
• PubMed: 30879786
• UniProt: P36048|SN114_YEAST Pre-mRNA-splicing factor SNU114 (Gene Name=SNU114)