Structure of PDB 8s9v Chain D

Receptor sequence

>8s9vD (length=518) Species: 1148 (Synechocystis sp. PCC 6803)

ARKVTTRWKITGTLIAETPLHIGGVGGDADTDLALAVNGAGEYYVPGTSL
AGALRGWMTQLLNNDESQIKDLWGDHLDAKRGASFVIVDDAVIHIPNNAD
VEIREGVGIDRHFGTAANGFKYSRAVIPKGSKFKLPLTFDSQDDGLPNAL
IQLLCALEAGDIRLGAAKTRGLGRIKLDDLKLKSFALDKPEGIFSALLDQ
GKKLDWNQLKANVTYQSPPYLGISITWNPKDPVMVKAEGDGLAIDILPLV
SQVGSDVRFVIPGSSIKGILRTQAERIIRTICQSNGSEKNFLEQLRINLV
NELFGSASLSQKQNGKDIDLGKIGALAVNDCFSSLSMTPDQWKAVENATE
MTGNLQPALKQATGYPNNISQAYKVLQPAMHVAVDRWTGGAAEGMLYSVL
EPIGVTWEPIQVHLDIARLKNYYHGKEEKLKPAIALLLLVLRDLANKKIP
VGYGTNRGMGTITVSQITLNGKALPTELEPLNKTMTCPNLTDLDEAFRQD
LSTAWKEWIADPIDLCQQ

3D structure

• PDB: 8s9v RNA targeting and cleavage by the type III-Dv CRISPR effector complex.
• Chain: D
• Resolution: 3.0 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	D	G24 T49 S50 R56 D76 H77 G83 S85 E106 G107 V108 I110 R112 K122 Y123 A167 A168 K169 T170 R171 K237 S265 S266 K268 G269 R272 G306 S307 A308 S309 K323 G325 M381 H382 V383 V385 R387 G391 L397 Y398 G453 Y454 G455 N457 R458	G23 T48 S49 R55 D75 H76 G82 S84 E105 G106 V107 I109 R111 K121 Y122 A166 A167 K168 T169 R170 K236 S264 S265 K267 G268 R271 G305 S306 A307 S308 K322 G324 M380 H381 V382 V384 R386 G390 L396 Y397 G452 Y453 G454 N456 R457
BS02	rna	D	D33 H77 N119 G120 F121 K122 Y123 D246 L293 S309 L310 S311 E394 G395 L397 Y398	D32 H76 N118 G119 F120 K121 Y122 D245 L292 S308 L309 S310 E393 G394 L396 Y397
BS03	MG	D	D246 L397	D245 L396

Gene Ontology

Molecular Function

• GO:0003723 RNA binding

Biological Process

• GO:0051607 defense response to virus

External links

• PDB: RCSB:8s9v, PDBe:8s9v, PDBj:8s9v
• PDBsum: 8s9v
• PubMed: 38637512
• UniProt: Q6ZED3