Structure of PDB 8xbs Chain B

Receptor sequence

>8xbsB (length=641) Species: 6239 (Caenorhabditis elegans)

SSVLVFEISSKMKMIEKKLEANTVHVLRLELDQSFILDLTKVAAEIVDSS
KYSKEDGVILEVTVSNGRDSFLLKLPTVYPNLKLYTDGKLLNPLVEQDFH
FHQNLIVTVQSRLNADIDYRLHVTHLDRAQYDFLKFKTGQTTKTLSNQKL
TFVKPIGFFLNCSEQNISQFHVTLYSEDDICANLITVPANESIYDRSVIS
DKTHNRRVLSFTKRADIFFTETEISMFKSFRIFVFIAPDDSGCSSFNEKK
KISFEFKKLENQSYAVPTALMMIFLTTPCLLFLPIVINIIKNSSLHGQML
QYPVAIILPVLMHTAIEFHKWTTSTMANRDEMCFHNHACARPLGELRAWN
NIITNIGYTLYGAIFIVLSICRRGSHVFGTYECTLLDVTIGVFMVLQSIA
SATYHICPSDVAFQFDTPCIQVICGLLMVRQWFVRHESPSPAYTNILLVG
VVSLNFLISAFSKTSYVRFIIAVIHVIVVGSICLAKERSLGSEKLKTRFF
IMAFSMGNFAAIVMYLTLSAFHLNQIATYCFIINCIMYLMYYGCMKVLHS
ERITSKAKLCGALSLLAWAVAGFFFFQDDTDWTRSAAASRALNKPCLLLG
FFGSHDLWHIFGALAGLFTFIFVSFVDDDLINTRKTSINIF

3D structure

• PDB: 8xbs Structural basis for double-stranded RNA recognition by SID1.
• Chain: B
• Resolution: 2.21 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	ZN	B	H540 D551 H740 H744	H405 D416 H605 H609
BS02	CLR	B	W703 A704 F708 F711	W568 A569 F573 F576
BS03	CLR	B	L674 C679 G696 S699 L700 F757	L539 C544 G561 S564 L565 F622
BS04	CLR	B	S313 T326	S263 T276

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003725 double-stranded RNA binding
• GO:0051033 RNA transmembrane transporter activity

Biological Process

• GO:0031047 regulatory ncRNA-mediated gene silencing
• GO:0033227 dsRNA transport
• GO:0035194 regulatory ncRNA-mediated post-transcriptional gene silencing
• GO:0050658 RNA transport

Cellular Component

• GO:0005764 lysosome
• GO:0005886 plasma membrane
• GO:0016020 membrane

External links

• PDB: RCSB:8xbs, PDBe:8xbs, PDBj:8xbs
• PDBsum: 8xbs
• PubMed: 38742627
• UniProt: Q9GZC8|SID1_CAEEL Systemic RNA interference defective protein 1 (Gene Name=sid-1)