Structure of PDB 7vg2 Chain A

Receptor sequence

>7vg2A (length=845) Species: 3702 (Arabidopsis thaliana)

SAAGSKKRKELHGTTCANALSGTWGENIDGATFQAYKFDFCCNISGEVYS
SFSLLLESTLAEDVGKVEMDLYLVRKLVKASVSPCGQIRLSQEELVKAKY
FQQFFFNGMFGKLFVGEFLLQTDTSSLWHPAFMFLLLPVETATIDWSAIN
SCASIVEFLKKNNLIHFANASSDKNSLEELVVIAIHTGRIYSIVEAVSDS
SAMSPFGYATYAEYFNKKYGIVLAHPNQPLMKLKQSHHAHNLLVDFNEEV
RKRKPNIHAHLPPELLARIDVPRAVLKSIYLLPSVMHRLESLMLASQLRE
EIDCSIDNFSISSTSILEAVTTLTCPESFSMERLELLGDSVLKYVASCHL
FLKYPDKDEGQLSRQRQSIISNSNLHRLTTSRKLQGYIRNGAFEPRRWTA
PGQFSLFPVPCKCGIDTREVPLDPKFFTENMTIKIGKSCDMGHRWVVSKS
VSDCAEALIGAYYVSGGLSASLHMMKWLGIDVDFDPNLVVEAINRVSLRC
YIPKEDELIELERKIQHEFSAKFLLKEAITHSSLRESYSYERLEFLGDSV
LDFLITRHLFNTYEQTGPGEMTDLRSACVNNENFAQVAVKNNLHTHLQRC
ATVLETQINDYLMSFQKPDETGRSIPSIQGPKALGDVVESIAGALLIDTR
LDLDQVWRVFEPLLSPLVTPDKLQLPPYRELNELCDSLGYFFRVKCSNDG
VKAQATIQLQLDDVLLTGDGSEQTNKLALGKAASHLLTQLEKRNVIPFIG
PINMKKGGPRGTLHEFCKKHLWPMPTFDTSEEKSRTPFEKRTSFSSFTST
ITLRIPNREAVMYAGEARPDKKSSFDSAVVELLYELERRKIVIIQ

3D structure

• PDB: 7vg2 Mechanism of siRNA production by a plant Dicer-RNA complex in dicing-competent conformation.
• Chain: A
• Resolution: 3.1 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 K626 K628 V693 K903 Q904 H906 H907 H909 N936 I937 L1003 E1039 G1040 S1043 R1044 R1076 F1087 D1228 S1256 V1259 N1260 N1261 E1319 P1356 Y1358 R1359 K1406 S1517 F1521 D1544 K1545	K6 K7 K9 V74 K234 Q235 H237 H238 H240 N256 I257 L323 E359 G360 S363 R364 R396 F407 D548 S576 V579 N580 N581 E639 P676 Y678 R679 K726 S793 F797 D820 K821
BS02	rna	A	F869 Y883 K887 Y888 F915 R931 K934 H940 P1006 L1016 D1019 Q1047 N1052 A1072 K1114 K1117 R1215 P1248 G1249 T1252 R1255 V1283 Q1287 R1359 D1366 Q1403 T1404 N1405 K1474 G1475 R1478 H1482 M1492 R1503 F1518 K1546	F206 Y214 K218 Y219 F246 R251 K254 H260 P326 L336 D339 Q367 N372 A392 K434 K437 R535 P568 G569 T572 R575 V603 Q607 R679 D686 Q723 T724 N725 K756 G757 R760 H764 M774 R785 F794 K822
BS03	CA	A	E1015 D1019 D1133 E1136	E335 D339 D453 E456
BS04	CA	A	N1261 D1316 E1319	N581 D636 E639
BS05	ZN	A	C1093 H1123	C413 H443

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:7vg2, PDBe:7vg2, PDBj:7vg2
• PDBsum: 7vg2
• PubMed: 34648373
• UniProt: Q9LXW7|DCL3_ARATH Endoribonuclease Dicer homolog 3 (Gene Name=DCL3)