Structure of PDB 8hf1 Chain G Binding Site BS01

Receptor Information

>8hf1 Chain G (length=1561) Species: 7227 (Drosophila melanogaster)

EDVEIKPRGYQLRLVDHLTKSNGIVYLPTGSGKTFVAILVLKRFSQDFDK
PIESGGKRALFMCNTVELARQQAMAVRRCTNFKVGFYVGEQGVDDWTRGM
WSDEIKKNQVLVGTAQVFLDMVTQTYVALSSLSVVIIDECHHGTGHHPFR
EFMRLFTIANQTKLPRVVGLTGVLIKGNEITNVATKLKELEITYRGNIIT
VSDTKEMENVMLYATKPTEVMVSFPHQEQVLTVTRLISAEIEKFYVSLDL
MNIGVQPIRRSKSLQCLRDPSKKSFVKQLFNDFLYQMKEYGIYAASIAII
SLIVEFDIKRRQAETLSVKLMHRTALTLCEKIRHLLVQKLQDMTYDDDDD
NVNTEEVIMNFSTPKVQRFLMSLKVSFADKDPKDICCLVFVERRYTCKCI
YGLLLNYIQSTPELRNVLTPQFMVGRNNISPDFESVLERKWQKSAIQQFR
DGNANLMICSSVLEEGIDVQACNHVFILDPVKTFNMYVQSKGRARTTEAK
FVLFTADKEREKTIQQIYQYRKAHNDIAEYLKDRVLEKTEPELYEIKGHF
QDDIDPFTNENGAVLLPNNALAILHRYCQTIPTDAFGFVIPWFHVLQEDE
RDRIFGVSAKGKHVISINMPVNCMLRDTIYSDPMDNVKTAKISAAFKACK
VLYSLGELNERFVPKTLKERVASIADVHFEHWNKYGDSVTATVNKADKSK
DRTYKTECPLEFYDALPRVGEICYAYEIFLEPQFESCEYTEHMYLNLQTP
RNYAILLRNKLPRLAEMPLFSNQGKLHVRVANAPLEVIIQNSEQLELLHQ
FHGMVFRDILKIWHPFFVLDRRSKENSYLVVPLILGAGEQKCFDWELMTN
FRRLPQSHGSNVQQREQQPAPRPEDFEGKIVTQWYANYDKPMLVTKVHRE
LTPLSYMEKNQQDKTYYEFTMSKYGNRIGDVVHKDKFMIEVRDLTEQLTF
YVHNRGKFNAKSKAKMKVILIPELCFNFNFPGDLWLKLIFLPSILNRMYF
LLHAEALRKRFNTYLNLHLLPFNGTDYMPRPLEIDYSLKRNGKVKPLLIL
QKTVSKEHITPAEQGEFLAAITASSAADVFDMERLEILGNSFLKLSATLY
LASKYSDWNEGTLTEVKSKLVSNRNLLFCLIDADIPKTLNTIQFTPRYTW
LPPGISLPHNVLALWRENPEFAKIIGPHNLRDLALGDEESLVKGNCSDIN
YNRFVEGCRANGQSFYAGADFSSEVNFCVGLVTIPNKVIADTLEALLGVI
VKNYGLQHAFKMLEYFKICRADIDKPLTQLLNLELGGKKMRANVNTTEID
GFLINHYYLEKNLGYTFKDRRYLLQALTHPSYPTNRITGSYQELEFIGNA
ILDFLISAYIFENNTKMNPGALTDLRSALVNNTTLACICVRHRLHFFILA
ENAKLSEIISKFVNFQESQGHRVTNYVRILLEVPPKGEFNMSTNVDVPKA
LGDVLEALIAAVYLDCRDLQRTWEVIFNLFEPELQEFTRKVPINHIRQLV
EHKHAKPVFSSPIVEGETVMVSCQFTCMEKTIKVYGFGSNKDQAKLSAAK
HALQQLSKCDA

Ligand information

>8hf1 Chain L (length=9)

gagacuugg

.........

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8hf1 Structural mechanism of R2D2 and Loqs-PD synergistic modulation on DmDcr-2 oligomers.
• Resolution: 3.7 Å
• Binding residue (original residue number in PDB): H147 K177
• Binding residue (residue number reindexed from 1): H146 K176

Enzymatic activity

• Enzyme Commision number: 3.1.26.3: ribonuclease III.

Gene Ontology

Molecular Function

• GO:0003676 nucleic acid binding
• GO:0003723 RNA binding
• GO:0003730 mRNA 3'-UTR binding
• GO:0004386 helicase activity
• GO:0004518 nuclease activity
• GO:0004521 RNA endonuclease activity
• GO:0004525 ribonuclease III activity
• GO:0004530 deoxyribonuclease I activity
• GO:0005515 protein binding
• GO:0005524 ATP binding
• GO:0008186 ATP-dependent activity, acting on RNA
• GO:0016887 ATP hydrolysis activity
• GO:0016891 RNA endonuclease activity, producing 5'-phosphomonoesters
• GO:0035197 siRNA binding

Biological Process

• GO:0002230 positive regulation of defense response to virus by host
• GO:0006309 apoptotic DNA fragmentation
• GO:0006396 RNA processing
• GO:0007626 locomotory behavior
• GO:0009047 dosage compensation by hyperactivation of X chromosome
• GO:0009597 detection of virus
• GO:0009616 RNAi-mediated antiviral immune response
• GO:0030422 siRNA processing
• GO:0031047 regulatory ncRNA-mediated gene silencing
• GO:0031054 pre-miRNA processing
• GO:0031507 heterochromatin formation
• GO:0033227 dsRNA transport
• GO:0035194 regulatory ncRNA-mediated post-transcriptional gene silencing
• GO:0045089 positive regulation of innate immune response
• GO:0045752 positive regulation of Toll signaling pathway
• GO:0051607 defense response to virus
• GO:0070922 RISC complex assembly
• GO:0098586 cellular response to virus
• GO:0098795 global gene silencing by mRNA cleavage
• GO:0110064 lncRNA catabolic process

Cellular Component

• GO:0005634 nucleus
• GO:0005737 cytoplasm
• GO:0016442 RISC complex
• GO:0036464 cytoplasmic ribonucleoprotein granule
• GO:0048471 perinuclear region of cytoplasm
• GO:0070578 RISC-loading complex

External links

• PDB: RCSB:8hf1, PDBe:8hf1, PDBj:8hf1
• PDBsum: 8hf1
• PubMed: 37633971
• UniProt: A1ZAW0|DCR2_DROME Endoribonuclease Dcr-2 (Gene Name=Dcr-2)