Structure of PDB 8qpe Chain M

Receptor sequence

>8qpeM (length=124) Species: 9606 (Homo sapiens)

DVNPKAYPLADAHLTKKLLDLVQQSCNYKQLRKGANEATKTLNRGISEFI
VMAADAEPLEIILHLPLLCEDKNVPYVFVRSKQALGRACGVSRPVIACSV
TIKEGSQLKQQIQSIQQSIERLLV

3D structure

• PDB: 8qpe Structural insights into the cross-exon to cross-intron spliceosome switch
• Chain: M
• Resolution: 3.1 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	M	Y32 K37 G38 N40 E41 K44 E61 V95 R97 V99 I100 Q111	Y28 K33 G34 N36 E37 K40 E57 V91 R93 V95 I96 Q107
BS02	rna	M	Q28 Q111 Q114 Q115	Q24 Q107 Q110 Q111

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0005515 protein binding
• GO:0030515 snoRNA binding
• GO:0030621 U4 snRNA binding
• GO:0030622 U4atac snRNA binding
• GO:0034511 U3 snoRNA binding
• GO:0034512 box C/D sno(s)RNA binding
• GO:0051117 ATPase binding

Biological Process

• GO:0000398 mRNA splicing, via spliceosome
• GO:0000492 box C/D snoRNP assembly
• GO:0006397 mRNA processing
• GO:0007338 single fertilization
• GO:0008380 RNA splicing
• GO:0030490 maturation of SSU-rRNA
• GO:0042274 ribosomal small subunit biogenesis

Cellular Component

• GO:0001651 dense fibrillar component
• GO:0005634 nucleus
• GO:0005654 nucleoplasm
• GO:0005681 spliceosomal complex
• GO:0005690 U4atac snRNP
• GO:0005730 nucleolus
• GO:0031428 box C/D methylation guide snoRNP complex
• GO:0032040 small-subunit processome
• GO:0032991 protein-containing complex
• GO:0046540 U4/U6 x U5 tri-snRNP complex
• GO:0071005 U2-type precatalytic spliceosome
• GO:0071011 precatalytic spliceosome
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8qpe, PDBe:8qpe, PDBj:8qpe
• PDBsum: 8qpe
• PubMed: 38778104
• UniProt: P55769|NH2L1_HUMAN NHP2-like protein 1 (Gene Name=SNU13)