Structure of PDB 9fmd Chain p

Receptor sequence

>9fmdp (length=92) Species: 9606 (Homo sapiens)

IRPNHTIYINNMNDKIKKEELKRSLYALFSQFGHVVDIVALKTMKMRGQA
FVIFKELGSSTNALRQLQGFPFYGKPMRIQYAKTDSDIISKM

3D structure

• PDB: 9fmd Mechanism for the initiation of spliceosome disassembly.
• Chain: p
• Resolution: 3.3 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	p	Y10 N13 D16 K17 K20 K24 V41 L43 K44 T45 K47 M48 R49 Q51 F53 A84 K85 T86 D87 S88 D89	Y8 N11 D14 K15 K18 K22 V39 L41 K42 T43 K45 M46 R47 Q49 F51 A82 K83 T84 D85 S86 D87

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0005515 protein binding
• GO:0030619 U1 snRNA binding

Biological Process

• GO:0000398 mRNA splicing, via spliceosome
• GO:0006397 mRNA processing
• GO:0008380 RNA splicing
• GO:1903241 U2-type prespliceosome assembly

Cellular Component

• GO:0001650 fibrillar center
• GO:0005634 nucleus
• GO:0005654 nucleoplasm
• GO:0005681 spliceosomal complex
• GO:0005684 U2-type spliceosomal complex
• GO:0005685 U1 snRNP
• GO:0005686 U2 snRNP
• GO:0016607 nuclear speck
• GO:0036464 cytoplasmic ribonucleoprotein granule
• GO:0071005 U2-type precatalytic spliceosome
• GO:0071007 U2-type catalytic step 2 spliceosome
• GO:0071013 catalytic step 2 spliceosome

External links

• PDB: RCSB:9fmd, PDBe:9fmd, PDBj:9fmd
• PDBsum: 9fmd
• PubMed: 38925148
• UniProt: P08579|RU2B_HUMAN U2 small nuclear ribonucleoprotein B'' (Gene Name=SNRPB2)