Structure of PDB 7vg3 Chain A

Receptor sequence

>7vg3A (length=860) Species: 3702 (Arabidopsis thaliana)

AAGSKKRKELHGTTCANALSGTWGENIDGATFQAYKFDFCCNISGEVYSS
FSLLLESTLAEDVGKVEMDLYLVRKLVKASVSPCGQIRLSQEELVKAKYF
QQFFFNGMFGKLFVGSKSQGTKREFLLQTDTSSLWHPAFMFLLLPVETND
LASSATIDWSAINSCASIVEFLKKNNLIHFANASSDKNSLEELVVIAIHT
GRIYSIVEAVSDSSAMSPFEGYATYAEYFNKKYGIVLAHPNQPLMKLKQS
HHAHNLLVDFNEEMVRKRKPNIHAHLPPELLARIDVPRAVLKSIYLLPSV
MHRLESLMLASQLREEIDCSIDNFSISSTSILEAVTTLTCPESFSMERLE
LLGDSVLKYVASCHLFLKYPDKDEGQLSRQRQSIISNSNLHRLTTSRKLQ
GYIRNGAFEPRRWTAPGQFSLFPVPCKCGIDTREVPLDPKFFTENMTIKI
GKSCDMGHRWVVSKSVSDCAEALIGAYYVSGGLSASLHMMKWLGIDVDFD
PNLVVEAINRVSLRCYDELIELERKIQHEFSAKFLLKEAITHSSLRESYS
YERLEFLGDSVLDFLITRHLFNTYEQTGPGEMTDLRSACVNNENFAQVAV
KNNLHTHLQRCATVLETQINDYLMSFQKPGRSIPSIQGPKALGDVVESIA
GALLIDTRLDLDQVWRVFEPLLSPLVTPDKLQLPPYRELNELCDSLGYFF
RVKCSNDGVKAQATIQLQLDDVLLTGDGSEQTNKLALGKAASHLLTQLEK
RNISEIQSIVIPFIGPINMKKGGPRGTLHEFCKKHLWPMPTFDTSEEKSR
TPFEFIDGGEKRTSFSSFTSTITLRIPNREAVMYAGEARPDKKSSFDSAV
VELLYELERR

3D structure

• PDB: 7vg3 Mechanism of siRNA production by a plant Dicer-RNA complex in dicing-competent conformation.
• Chain: A
• Resolution: 3.73 Å

Enzymatic activity

• Enzyme Commision number: 3.1.26.-

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	K625 Q904 H906 R931 L1003 E1039 R1044 F1087 E1224 D1228 S1256 N1261 R1359 K1406 D1544 K1545	K5 Q249 H251 R266 L338 E374 R379 F422 E555 D559 S587 N592 R687 K734 D841 K842
BS02	rna	A	F733 G735 K737 H849 K887 Y888 F915 N916 H940 E1015 D1019 Q1047 N1052 T1252 E1363 D1366 N1378 Q1403 T1404 K1474 R1478 H1482 R1503 F1518 K1546	F113 G115 K117 H199 K232 Y233 F260 N261 H275 E350 D354 Q382 N387 T583 E691 D694 N706 Q731 T732 K771 R775 H779 R800 F815 K843
BS03	CA	A	E1224 D1316 E1319	E555 D644 E647
BS04	ZN	A	C1093 C1119 H1123	C428 C454 H458

Gene Ontology

Molecular Function

• GO:0003676 nucleic acid binding
• GO:0003723 RNA binding
• GO:0003725 double-stranded RNA binding
• GO:0004386 helicase activity
• GO:0004519 endonuclease activity
• GO:0004525 ribonuclease III activity
• GO:0005515 protein binding
• GO:0005524 ATP binding
• GO:0046872 metal ion binding

Biological Process

• GO:0006396 RNA processing
• GO:0006952 defense response
• GO:0010267 ta-siRNA processing
• GO:0030422 siRNA processing
• GO:0031047 regulatory ncRNA-mediated gene silencing
• GO:0051214 RNAi-mediated antiviral immunity against RNA virus
• GO:0051607 defense response to virus

Cellular Component

• GO:0005634 nucleus
• GO:0005730 nucleolus

External links

• PDB: RCSB:7vg3, PDBe:7vg3, PDBj:7vg3
• PDBsum: 7vg3
• PubMed: 34648373
• UniProt: Q9LXW7|DCL3_ARATH Endoribonuclease Dicer homolog 3 (Gene Name=DCL3)