Structure of PDB 5yzg Chain u

Receptor sequence

>5yzgu (length=390) Species: 9606 (Homo sapiens)

DMTKVEFETSEEVDVTPTFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQ
IIKGRDVIAQSQSGTGKTATFSISVLQCLDIQVRETQALILAPTRELAVQ
IQKGLLALGDYMNVQCHACIGGTNVGEDIRKLDYGQHVVAGTPGRVFDMI
RRRSLRTRAIKMLVLDEADEMLNKGFKEQIYDVYRYLPPATQVVLISATL
PHEILEMTNKFMTDPIRILVKRDELTLEGIKQFFVAVEREEWKFDTLCDL
YDTLTITQAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMK
EFRSGASRVLISTDVWARGLDVPQVSLIINYDLPNNRELYIHRIGRSGRY
GRKGVAINFVKNDDIRILRDIEQYYSTQIDEMPMNVADLI

3D structure

• PDB: 5yzg Structure of a human catalytic step I spliceosome
• Chain: u
• Resolution: 4.1 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	u	P114 T115 R116 G142 G143 T163 G165 R166 D169 R172 E191 F197 Q200 N285 T286 K287 H308 G309 R316 T334 D335 V336 N356	P93 T94 R95 G121 G122 T142 G144 R145 D148 R151 E170 F176 Q179 N264 T265 K266 H287 G288 R295 T313 D314 V315 N335
BS02	peptide	u	R260 E261 T286 R288 K289 W292 D353 P355 N356 N357 K382 I388 D391	R239 E240 T265 R267 K268 W271 D332 P334 N335 N336 K361 I367 D370
BS03	ATP	u	F58 Q65 G85 T86 G87 K88 T89 G340 D342 R367 R370 Y371	F37 Q44 G64 T65 G66 K67 T68 G319 D321 R346 R349 Y350

Gene Ontology

Molecular Function

• GO:0003676 nucleic acid binding
• GO:0003723 RNA binding
• GO:0003724 RNA helicase activity
• GO:0003729 mRNA binding
• GO:0004386 helicase activity
• GO:0005515 protein binding
• GO:0005524 ATP binding
• GO:0008143 poly(A) binding
• GO:0016787 hydrolase activity
• GO:0016887 ATP hydrolysis activity
• GO:0035368 selenocysteine insertion sequence binding
• GO:0035613 RNA stem-loop binding
• GO:0043021 ribonucleoprotein complex binding

Biological Process

• GO:0000184 nuclear-transcribed mRNA catabolic process, nonsense-mediated decay
• GO:0000398 mRNA splicing, via spliceosome
• GO:0006364 rRNA processing
• GO:0006397 mRNA processing
• GO:0006406 mRNA export from nucleus
• GO:0006417 regulation of translation
• GO:0008306 associative learning
• GO:0008380 RNA splicing
• GO:0010629 negative regulation of gene expression
• GO:0014070 response to organic cyclic compound
• GO:0017148 negative regulation of translation
• GO:0035640 exploration behavior
• GO:0045727 positive regulation of translation
• GO:0048701 embryonic cranial skeleton morphogenesis
• GO:0051028 mRNA transport
• GO:0072715 cellular response to selenite ion
• GO:0090394 negative regulation of excitatory postsynaptic potential
• GO:0099578 regulation of translation at postsynapse, modulating synaptic transmission
• GO:1904570 negative regulation of selenocysteine incorporation
• GO:1990416 cellular response to brain-derived neurotrophic factor stimulus
• GO:2000622 regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay

Cellular Component

• GO:0005634 nucleus
• GO:0005654 nucleoplasm
• GO:0005681 spliceosomal complex
• GO:0005730 nucleolus
• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0016020 membrane
• GO:0016607 nuclear speck
• GO:0030425 dendrite
• GO:0035145 exon-exon junction complex
• GO:0043025 neuronal cell body
• GO:0071006 U2-type catalytic step 1 spliceosome
• GO:0071013 catalytic step 2 spliceosome
• GO:0098794 postsynapse
• GO:0098978 glutamatergic synapse
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:5yzg, PDBe:5yzg, PDBj:5yzg
• PDBsum: 5yzg
• PubMed: 29301961
• UniProt: P38919|IF4A3_HUMAN Eukaryotic initiation factor 4A-III (Gene Name=EIF4A3)