Structure of PDB 8y7e Chain 1

Receptor sequence

>8y7e1 (length=971) Species: 9606 (Homo sapiens)

YDPFAEHRPPKIADREDEYKKHRRTMIISPERLDPFADGGKTPDPKMNAR
TYMDVMREQHLTKEEREIRQQLAEKAERNRPLSDEELDAMFPEGYKVLPP
PAGYVPIMTGFHMQTEDRTMKSVNDQPSGNLPFLKPDDIQYFDKLLVDVD
ESTLSPEEQKERKIMKLLLKIKNGTPPMRKAALRQITDKAREFGAGPLFN
QILPLLMSPTLEDQERHLLVKVIDRILYKLDDLVRPYVHKILVVIEPLLI
DEDYYARVEGREIISNLAKAAGLATMISTMRPDIDNMDEYVRNTTARAFA
VVASALGIPSLLPFLKAVCKSKKSWQARHTGIKIVQQIAILMGCAILPHL
RSLVEIIEHGLVDEQQKVRTISALAIAALAEAATPYGIESFDSVLKPLWK
GIRQHRGKGLAAFLKAIGYLIPLMDAEYANYYTREVMLILIREFQSPDEE
MKKIVLKVVKQCCGTDGVEANYIKTEILPPFFKHFWQHRMALDRRNYRQL
VDTTVELANKVGAAEIISRIVDDLKDEAEQYRKMVMETIEKIMGNLGAAD
IDHKLEEQLIDGILYAFQEQTTEDSVMLNGFGTVVNALGKRVKPYLPQIC
GTVLWRLNNKSAKVRQQAADLISRTAVVMKTCQEEKLMGHLGVVLYEYLG
EEYPEVLGSILGALKAIVNVIGMHKMTPPIKDLLPRLTPILKNRHEKVQE
NCIDLVGRIADRGAEYVSAREWMRICFELLELLKAHKKAIRRATVNTFGY
IAKAIGPHDVLATLLNNLKVQERQNRVCTTVAIAIVAETCSPFTVLPALM
NEYRVPELNVQNGVLKSLSFLFEYIGEMGKDYIYAVTPLLEDALMDRDLV
HRQTASAVVQHMSLGVYGFGCEDSLNHLLNYVWPNVFETSPHVIQAVMGA
LEGLRVAIGPCRMLQYCLQGLFHPARKVRDVYWKIYNSIYIGSQDALIAH
YPRIYNDDKNTYIRYELDYIL

3D structure

• PDB: 8y7e Structural basis of U12-type intron engagement by the fully assembled human minor spliceosome
• Chain: 1
• Resolution: 4.66 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	1	Y119 I583 E585 Y587 R590 E622 N626 R630 I673 P780 H1069 K1071 R1075 Q1104 R1106 R1109 V1110 K1149 V1183 Q1186 H1225	Y19 I250 E252 Y254 R257 E289 N293 R297 I340 P447 H736 K738 R742 Q771 R773 R776 V777 K816 V850 Q853 H892
BS02	rna	1	R517 R558 H1069 S1223 P1224 P1257 A1258 R1259	R184 R225 H736 S890 P891 P924 A925 R926

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003729 mRNA binding
• GO:0005515 protein binding
• GO:1990935 splicing factor binding

Biological Process

• GO:0000245 spliceosomal complex assembly
• GO:0000375 RNA splicing, via transesterification reactions
• GO:0000398 mRNA splicing, via spliceosome
• GO:0006338 chromatin remodeling
• GO:0006397 mRNA processing
• GO:0008380 RNA splicing
• GO:0045943 positive regulation of transcription by RNA polymerase I
• GO:0045944 positive regulation of transcription by RNA polymerase II
• GO:0045945 positive regulation of transcription by RNA polymerase III
• GO:1903241 U2-type prespliceosome assembly

Cellular Component

• GO:0005634 nucleus
• GO:0005654 nucleoplasm
• GO:0005681 spliceosomal complex
• GO:0005684 U2-type spliceosomal complex
• GO:0005686 U2 snRNP
• GO:0005689 U12-type spliceosomal complex
• GO:0005730 nucleolus
• GO:0016607 nuclear speck
• GO:0034693 U11/U12 snRNP
• GO:0071004 U2-type prespliceosome
• GO:0071005 U2-type precatalytic spliceosome
• GO:0071013 catalytic step 2 spliceosome
• GO:0110016 B-WICH complex

External links

• PDB: RCSB:8y7e, PDBe:8y7e, PDBj:8y7e
• PDBsum: 8y7e
• PubMed: 38484052
• UniProt: O75533|SF3B1_HUMAN Splicing factor 3B subunit 1 (Gene Name=SF3B1)