Structure of PDB 1yvp Chain A

Receptor sequence

>1yvpA (length=529) Species: 8355 (Xenopus laevis)

MDQTQPLNEKQVPNSEGCYVWQVSDMNRLRRFLCFGSEGGTYYIEEKKLG
QENAEALLRLIEDGKGCEVVQEIKTFSQEGRAAKQEPTLFALAVCSQCSD
IKTKQAAFRAVPEVCRIPTHLFTFIQFKKDLKEGMKCGMWGRALRKAVSD
WYNTKDALNLAMAVTKYKQRNGWSHKDLLRLSHIKPANEGLTMVAKYVSK
GWKEVQEAYKEKELSPETEKVLKYLEATERVKRTKDELEIIHLIDEYRLV
REHLLTIHLKSKEIWKSLLQDMPLTALLRNLGKMTADSVLAPASSEVSSV
CERLTNEKLLKKARIHPFHILVALETYKKGHGLRWIPDTSIVEALDNAFY
KSFKLVEPTGKRFLLAIDVSASMNQRVLGSILNASVVAAAMCMLVARTEK
DSHMVAFSDEMLPCPITVNMLLHEVVEKMSDITMGSTDCALPMLWAQKTN
TAADIFIVFTDCETNVEDVHPATALKQYREKMGIPAKLIVCAMTSNGFSI
ADPDDRGMLDICGFDSGALDVIRNFTLDL

3D structure

• PDB: 1yvp Structural Insights into RNA Quality Control: The Ro Autoantigen Binds Misfolded RNAs via Its Central Cavity
• Chain: A
• Resolution: 2.2 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	A	K108 Q109 K133 G142 W144 G145 R146 A147 R149 W177 D181 R184 L185 H187	K104 Q105 K129 G138 W140 G141 R142 A143 R145 W173 D177 R180 L181 H183	PDBbind-CN: Kd=5.2nM
BS02	rna	A	R146 R149 H187 I188 K189 P190 A199 K200 S203 K204	R142 R145 H183 I184 K185 P186 A195 K196 S199 K200	PDBbind-CN: Kd=5.2nM
BS03	rna	A	R120 I121 T123 K170 Y171 R174 R252 V254 R255 E256 P277 T279 A280 R283 L313 K316 R318	R116 I117 T119 K166 Y167 R170 R248 V250 R251 E252 P273 T275 A276 R279 L309 K312 R314	PDBbind-CN: Kd=5.2nM
BS04	MG	A	S378 S380 T445	S370 S372 T437

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0034336 misfolded RNA binding
• GO:0046872 metal ion binding

Biological Process

• GO:0030030 cell projection organization

Cellular Component

• GO:0005737 cytoplasm
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:1yvp, PDBe:1yvp, PDBj:1yvp
• PDBsum: 1yvp
• PubMed: 15907467
• UniProt: P42700|RO60_XENLA RNA-binding protein RO60 (Gene Name=ro60)