Structure of PDB 5t62 Chain I

Receptor sequence

>5t62I (length=222) Species: 559292 (Saccharomyces cerevisiae S288C)

AEQVAAERAARKAANKEKRAIILERNAAYQKEYETAERNIIQAKRDAKAA
GSYYVEAQHKLVFVVRIKGINKIPPKPRKVLQLLRLTRINSGTFVKVTKA
TLELLKLIEPYVAYGYPSYSTIRQLVYKRGFGKINKQRVPLSDNAIIEAN
LGKYGILSIDDLIHEIITVGPHFKQANNFLWPFKLSNPSGGWGVPRKFKH
FIQGGSFGNREEFINKLVKSMN

3D structure

• PDB: 5t62 Nmd3 is a structural mimic of eIF5A, and activates the cpGTPase Lsg1 during 60S ribosome biogenesis.
• Chain: I
• Resolution: 3.3 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	I	R30 R33 K34 R41 R67 K90 G91 N93 K94 P97 K98 K101 L105 I111 A122 E125 S142 R145 K150 K158 Q159 R160 K196 K206 L207 S208 N209 S211 W214 R218 K219 K241	R8 R11 K12 R19 R45 K68 G69 N71 K72 P75 K76 K79 L83 I89 A100 E103 S120 R123 K128 K136 Q137 R138 K174 K184 L185 S186 N187 S189 W192 R196 K197 K219
BS02	rna	I	K128 R218 H222 Q225	K106 R196 H200 Q203

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome

Biological Process

• GO:0000463 maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
• GO:0000470 maturation of LSU-rRNA
• GO:0002181 cytoplasmic translation
• GO:0042273 ribosomal large subunit biogenesis

Cellular Component

• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0022625 cytosolic large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:5t62, PDBe:5t62, PDBj:5t62
• PDBsum: 5t62
• PubMed: 28179369
• UniProt: P05737|RL7A_YEAST Large ribosomal subunit protein uL30A (Gene Name=RPL7A)