Structure of PDB 5lj3 Chain C

Receptor sequence

>5lj3C (length=882) Species: 4932 (Saccharomyces cerevisiae)

GKEVEVLMETKNTQSPQTPLVEPVTERTKLQEHTIFTQLKKNIPKTRYNR
DYMLSMANIPERIINVGVIGPLHSGKTSLMDLLVIDSHKRIPDMSKNVEL
GWKPLRYLDNLKQEIDRGLSIKLNGSTLLCTDLESKSRMINFLDAPGHVN
FMDETAVALAASDLVLIVIDVVEGVTFVVEQLIKQSIKNNVAMCFVINKL
DRLILDLKLPPMDAYLKLNHIIANINSFTKGNVFSPIDNNIIFASTKLGF
TFTIKEFVSYYYAHSIPSSKIDDFTTRLWGSVYYHKGNFRTKPFENVEKY
PTFVEFILIPLYKIFSYALSMEKDKLKNLLRSNFRVNLSQEALQYDPQPF
LKHVLQLIFRQQTGLVDAITRCYQPFELFDNKTAHLSIPGKSTPEGTLWA
HVLKTVDYGGAEWSLVRIYSGLLKRGDTVRILDTSQSESRQKRQLHDIED
DETPSCEVEEIGLLGGRYVYPVHEAHKGQIVLIKGISSAYIKSATLYSVK
SKEDMKQLKFFKPLDYITEAVFKIVLQPLLPRELPKLLDALNKISKYYPG
VIIKVEESGEHVILGNGELYMDCLLYDLRASYAKIEIKISDPLTVFSESC
SNESFASIPVSNISVAAEPMDSKMIQDLSRPRKLSKILRTEYGWDSLASR
NVWSFYNLINDTLPDEISPELLSKYKEQIIQGFYWAVKEGPLAEEPIYGV
QYKLLSISVPSDVNIDVMKSQIIPLMKKACYVGLLTAIPILLEPIYEVDI
TVHAPLLPIVEELMKKRRGSRIYKTIKVAGTPLLEVRGQVPVIESAGFET
DLRLSTNGLGMCQLYFWHKIWRKVPGDVLDKDAFIPKLKPAPINSLSRDF
VMKTRRRKGISTGGFMSNDGPTLEKYISAELY

3D structure

• PDB: 5lj3 Cryo-EM structure of the spliceosome immediately after branching.
• Chain: C
• Resolution: 3.8 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	L100 E102 H103 Q108 K110 N112 R160 P162 D163 R176 H334	L30 E32 H33 Q38 K40 N42 R90 P92 D93 R106 H264
BS02	GTP	C	L142 H143 G145 K146 T147 S148 L189 S190 G217 K269 S315 T316 K317	L72 H73 G75 K76 T77 S78 L119 S120 G147 K199 S245 T246 K247

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:5lj3, PDBe:5lj3, PDBj:5lj3
• PDBsum: 5lj3
• PubMed: 27459055
• UniProt: P36048|SN114_YEAST Pre-mRNA-splicing factor SNU114 (Gene Name=SNU114)