Structure of PDB 8v87 Chain 3

Receptor sequence

>8v873 (length=656) Species: 1247190 (Saccharomyces cerevisiae BY4741)

GSFPSFGLSKIVLNNIKRKGFRQPTPIQRKTIPLILQSRDIVGMARTGSG
KTAAFILPMVEKLKSHSGKIGARAVILSPSRELAMQTFNVFKDFARGTEL
RSVLLTGGDSLEEQFGMMMTNPDVIIATPGRFLHLKVEMNLDLKSVEYVV
FDEADRLFEMGFQEQLNELLASLPTTRQTLLFSATLPNSLVDFVKAGLVN
PVLVRLDAETKVSENLEMLFLSSKNADREANLLYILQEIIKIPLATSEQL
QKLQNSNLPSEKATILFVPTRHHVEYISQLLRDCGYLISYIYGTLDQHAR
KRQLYNFRAGLTSILVVTDVAARGVDIPMLANVINYTLPGSSKIFVHRVG
RTARAGNKGWAYSIVAENELPYLLDLELFLGKKILLTPMYDSLVDVMKKR
WIDEGKPEYQFQPPKLSYTKRLVLGSCPRLDVEGLGDLYKNLMSSNFDLQ
LAKKTAMKAEKLYYRTRTSASPESLKRSKEIISSGWDAQNAFFGKNEEKE
KLDFLAKLQNRRNKETVFEFTRNPDDEMAVFMKRRRKQLAPIQRKATERR
ELLEKERMKSFKDPTFFLSHYAPANGFANDAAQAAYDLNSDDKVQVHKQT
AIIGESGQKIAASFRSGRFDDWSKARNFKHKQMKAPKMPDKHRDNYYSQK
KKVEKA

3D structure

• PDB: 8v87 The DEAD-box ATPase Dbp10/DDX54 initiates peptidyl transferase center formation during 60S ribosome biogenesis.
• Chain: 3
• Resolution: 2.66 Å

Enzymatic activity

• Enzyme Commision number: 3.6.4.13: RNA helicase.

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	3	G244 D245 L247 H270 K280 R683 N694 D697 K704 I713 Q714 Q828 H830 T833 I858 E860 S861 Q863 I865 F869 S871 R873 F918 K919 H920 Q922 K924 P926 K927 R933 Y937 Q939 K942	G108 D109 L111 H134 K144 R512 N523 D526 K533 I542 Q543 Q595 H597 T600 I603 E605 S606 Q608 I610 F614 S616 R618 F628 K629 H630 Q632 K634 P636 K637 R643 Y647 Q649 K652
BS02	ADP	3	F157 T183 G184 S185 G186 K187 T188	F21 T47 G48 S49 G50 K51 T52

Gene Ontology

Molecular Function

• GO:0003676 nucleic acid binding
• GO:0003723 RNA binding
• GO:0003724 RNA helicase activity
• GO:0004386 helicase activity
• GO:0005515 protein binding
• GO:0005524 ATP binding
• GO:0016787 hydrolase activity
• GO:0016887 ATP hydrolysis activity
• GO:0042802 identical protein binding

Biological Process

• GO:0000463 maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
• GO:0000466 maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
• GO:0006364 rRNA processing
• GO:0042254 ribosome biogenesis
• GO:1902626 assembly of large subunit precursor of preribosome

Cellular Component

• GO:0005634 nucleus
• GO:0005730 nucleolus
• GO:0030687 preribosome, large subunit precursor

External links

• PDB: RCSB:8v87, PDBe:8v87, PDBj:8v87
• PDBsum: 8v87
• PubMed: 38632236
• UniProt: Q12389|DBP10_YEAST ATP-dependent RNA helicase DBP10 (Gene Name=DBP10)