Structure of PDB 5gmk Chain C

Receptor sequence

>5gmkC (length=878) Species: 559292 (Saccharomyces cerevisiae S288C)

EHPYGKEVEVLMETKNTQSPQTPLVEPVTERTKLQEHTIFTQLKKNIPKT
RYNRDYMLSMANIPERIINVGVIGPLHSGKTSLMDLLVIDSHKRIPDMSK
NVELGWKPLRYLDNLKQEIDRGLSIKLNGSTLLCTDLESKSRMINFLDAP
GHVNFMDETAVALAASDLVLIVIDVVEGVTFVVEQLIKQSIKNNVAMCFV
INKLDRLILDLKLPPMDAYLKLNHIIANINSFTKGNVFSPIDNNIIFAST
KLGFTFTIKEFVSYYYAHSIPSSKIDDFTTRLWGSVYYHKGNFRTKPFEN
VEKYPTFVEFILIPLYKIFSYALSMEKDKLKNLLRSNFRVNLSQEALQYD
PQPFLKHVLQLIFRQQTGLVDAITRCYQPFELFDNKTAHLSIPGKSTPEG
TLWAHVLKTVDYGGAEWSLVRIYSGLLKRGDTVRILDTSQSESREDDETP
SCEVEEIGLLGGRYVYPVHEAHKGQIVLIKGISSAYIKSATLYSVKSKED
MKQLKFFKPLDYITEAVFKIVLQPLLPRELPKLLDALNKISKYYPGVIIK
VEESGEHVILGNGELYMDCLLYDLRASYAKIEIKISDPLTVFSESCSNSR
LGEENLPGLSISVAAEPMDSKMIQDLSRNTLGKGQNCLDIDGIMDNPRKL
SKILRTEYGWDSLASRNVWSFYNGNVLINDTLPDEISPELLSKYKEQIIQ
GFYWAVKEGPLAEEPIYGVQYKLLSISVPSDVNIDVMKSQIIPLMKKACY
VGLLTAIPILLEPIYEVDITVHAPLLPIVEELMKKRRGSRIYKTIKVAGT
PLLEVRGQVPVIESAGFETDLRLSTNGLGMCQLYFWHKIWRKVPGDVLDK
DAFIPKLKPAPINSLSRDFVMKTRRRKG

3D structure

• PDB: 5gmk Structure of a yeast catalytic step I spliceosome at 3.4 angstrom resolution
• Chain: C
• Resolution: 3.4 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 Q101 I105 L109 K173	R31 K33 Q35 I39 L43 K107
BS02	GTP	C	H143 G145 K146 T147 S148 S190 G217 K269 D271 S315 T316 K317	H77 G79 K80 T81 S82 S124 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:5gmk, PDBe:5gmk, PDBj:5gmk
• PDBsum: 5gmk
• PubMed: 27445308
• UniProt: P36048|SN114_YEAST Pre-mRNA-splicing factor SNU114 (Gene Name=SNU114)