Structure of PDB 6j6q Chain C

Receptor sequence

>6j6qC (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: 6j6q Structures of the Catalytically Activated Yeast Spliceosome Reveal the Mechanism of Branching.
• Chain: C
• Resolution: 3.7 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 F106 T107 Q108 L109 N112 R160 D163 K173	R31 K33 L34 Q35 F40 T41 Q42 L43 N46 R94 D97 K107
BS02	GTP	C	H143 G145 K146 T147 S148 S190 G217 K269 D271 R272 S315 T316 K317	H77 G79 K80 T81 S82 S124 G151 K203 D205 R206 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:6j6q, PDBe:6j6q, PDBj:6j6q
• PDBsum: 6j6q
• PubMed: 30879786
• UniProt: P36048|SN114_YEAST Pre-mRNA-splicing factor SNU114 (Gene Name=SNU114)