Structure of PDB 6fyx Chain o Binding Site BS01

Receptor Information

>6fyx Chain o (length=529) Species: 559292 (Saccharomyces cerevisiae S288C)

FRPENAIKRADELISVGEKQAALQSLHDFITARRIRWATPSTVEPVVFKF
LEIGVELKKGKLLKDGLHQYKKLIQGSTEGLVSVGAVARKFIDLVESKIA
SEQTRADELQKQEIDAITSWLRFTWESYRAVLDLLRNNALLEITYSGVVK
KTMHFCLKYQRKNEFKRLAEMLRQHLDAANYQQSDADTLQRYLDQRFQQV
DVSVKLELWHEAYRSIEDVFHLMKISKRAPKPSTLANYYENLVKVFFVSG
DPLLHTTAWKKFYKLYSTNPRATEEEFKTYSSTIFLSAISTQLDEIPSIG
YDPHLRMYRLLNLDAKPTRKEMLQSIIEDESIYGKVDEELKELYDIIEVN
FDVDTVKQQLENLLVKLSSKTYFSQYIAPLRDVIMRRVFVAASQKFTTVS
QSELYKLATLPAPLDLSAWDIEKSLLQAAVEDYVSITIDHESAKVTFAKD
PAAKKARIEEVRKRRYEEAIARRKEEIANAERQKRAQELAEATRKQREIE
EAAAKKSAGRTAGGSSPATPATPATPATP

Ligand information

>6fyx Chain 2 (length=1780)

uaucugguugauccugccaguagucauaugcuugucucaaagauuaagcc
augcaugucuaaguauaagcaauuuauacagugaaacugcgaauggcuca
uuaaaucaguuaucguuuauuugauaguuccuuuacuacauggauaucug
ugguaauucuagagcuaauacaugcuuaaaaucucgacccuuuggaagag
auguauuuauuagauaaaaaaucaaugucuucggacuccuugaugauuca
uaauaacuuuucgaaucgcauggccuugugcuggcgaugguucauucaaa
uuucugcccuaucaacuuucgaugguaggauaguggccuaccaugguuuc
aacggguaacggggaauaaggguucgauuccggagagggagccugagaaa
cggcuaccacauccaaggaaggcagcaggcgcgcaaauuacccaauccua
auucagggagguagugacaauaaauaacgauacagggcccauucgggucu
uguaauuggaaugaguacaauguaaauaccuuaacgaggaacaacuggag
ggcaagucuggugccagcagccgcgguaauuccagcuccaguagcguaua
uuaaaguuguugcaguuaaaaagcucguaguugaacuuugggucugguug
uccggucgguuuuucaaccggaucuuuccuucuggcuaaccuguacuccu
ugugggugcaggcgaaccaggacuuuuacuuugaaaaaauuagaguguuc
aaagcaggcgaaagcucgaauauauuagcauggaauaauggaauaggacg
uuugguucuauuuuguugguuucuaggaccaucguaaugauuaauaggga
cggucgggggcaucaguauucaauugucagaggugaaauucuuggauuua
uugaagacuaacuacugcgaaagcauuugccaaggacguuuucauuaauc
aagaacgaaaguuaggggaucgaagaugaucagauaccgucguagucuua
accauaaacuaugccgacuagggaucgggugguguuuuucuuaugaccca
cucggcaccuuacgagaaaucaaagucuuuggguucuggggggaguaugg
ucgcaaggcugaaacuuaaaggaauugacggaagggcaccaccaggagug
gagccugcggcuuaauuugacucaacacggggaaacucaccagguccaga
cacaauaaggauugacagauugagagcucuuucuugauuuuguggguggu
ggugcauggccguucuuaguugguggagugauuugucugcuuaauugcga
uaacgaacgagaccuuaaccuacuaaauaggguugcuggcacuugccggu
ugacucuucuuagagggacuaucgguuucaagccgauggaaguuugaggc
aauaacaggucugugaugcccuuagacguucugggccgcacgcgcgcuac
acugacggagccagcgaguacaaccuuggccgagaggucuggguaaucuu
gugaaacuccgucgugcuggggauagagcauuguaauuauugcucuucaa
cgaggaauuccuaguaagcgcaagucaucagcuugcguugauuacguccc
ugcccuuuguacacaccgcccgucgcuaguaccgauugaauggcuuagug
aggccucaggauuugcuuagagaagggggcaacuccaucucagagcgaag
aaucuggucaaacuuggucauuuagaggaacuaaaagucguaacaagguu
uccguaggugaaccugcggaaggaucauua

...<<<<<...[[[[>>>>>[[[[.((((((................[[[
.[[[..<<....<<....<<..........>>...>>.>>......{{..
......[[[......{{....[[[[...............<<.....<<.
<<.......>>.>>......>>........<<<<<..<<....>>..>>>
>>[..[.(((((......<<<<<<<.<<<....>>>....<<......>>
)))))].....]...<<<<..<<<.....>>>.>>>>..].]]]...}}.
...]]].<<<....<<<....<<<<<<<<.......>>>>>>>>>>>...
...>>>...<<<.<<<<....>>>>....>>>.}}.<<.<<<........
..>>>.>>.<.<<....>>.>...]]]]]].........<<<....<<<.
....>>>..>>>...............<<<<<<<<<<..........>>>
>>>>.>>>......<<..<...........>..>>.........<<<<<(
(......<<<<.....<<..))>>.......>>>>.>>>>>..))))))]
]]].........[[[<........{{...[[[.{{....<<<<<<<<<<<
.....<<>>.....>>>>>>>>>>>.....<<<<<......<<..<<...
....>>..>>......>>>>>....<<<<<.<<.......<<...<....
...>..<<<....>>>....>>......>>.>>..>>>.........[[[
..(((((((......>>>>>>>..))))))).]]].....}}....<<<<
<<.<<...<<<<..<<..<<<<<<.<...<<<......>>>......>.>
>>>>>..>>......<<<....>>>..>>>>..>.>>>>.>>>...]]].
..}}......<<<<<<<...<...<<<<.<.....>.>>>>...>>>>>>
>>..........<<<.<<.<<<..<<<<<<<<.<<.<.......>>>>>>
>>>>>..>>>...<<..>.>>...>>.....>>>.]]].<<<......<<
<<....>>>>....>>>..]]]]..<<<<<.<<<<<<<..<<.<<<<<<.
.<<<.<<<<<<......<<........>>..........<<<<<......
<<<<<........<<.<<<........>>>.>>......>>>>>...<<.
<<<..<<<<<<<<<....<<<.<<<<......>>...<<<......>>>.
..>>.>>>....<<<<<.<<..<<<<..<<<<<<<<<<<<....>>>>>>
.>>>>>>..>>>>.>>....<<<<<<.....>>>>>>.......>>>>>.
...>>>.>>>...>.>>>>>>>.......>>>>>...>>.>>>>.>>>..
...<<<<<<<......<<.....<<<.<<<<....>>>>.>>>....>>.
......>>>>>>>...........<<<<<<..........>>>>>>....
......>>>>>>....<<<<<<<<.......>>>>>>>>......>>...
>>>>>>>>>>.>>....<..<<.<..<<<<.<<....<<<<<<<<.<<<.
.<<<<..<...<<<<<<..........................>>>>>>.
..>..>>>>..>>>.>>>>>>>>...>>.>>>>...>.>>...>.....<
<<<<<<<<<..>>>>>>>>>>.........

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6fyx Translational initiation factor eIF5 replaces eIF1 on the 40S ribosomal subunit to promote start-codon recognition.
• Resolution: 3.5 Å
• Binding residue (original residue number in PDB): Q25 K64
• Binding residue (residue number reindexed from 1): Q20 K59

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003729 mRNA binding
• GO:0003743 translation initiation factor activity
• GO:0005515 protein binding

Biological Process

• GO:0001732 formation of cytoplasmic translation initiation complex
• GO:0002183 cytoplasmic translational initiation
• GO:0002188 translation reinitiation
• GO:0006412 translation
• GO:0006413 translational initiation

Cellular Component

• GO:0000131 incipient cellular bud site
• GO:0005737 cytoplasm
• GO:0005852 eukaryotic translation initiation factor 3 complex
• GO:0010494 cytoplasmic stress granule
• GO:0016282 eukaryotic 43S preinitiation complex
• GO:0033290 eukaryotic 48S preinitiation complex
• GO:0043614 multi-eIF complex
• GO:0071540 eukaryotic translation initiation factor 3 complex, eIF3e
• GO:0071541 eukaryotic translation initiation factor 3 complex, eIF3m

External links

• PDB: RCSB:6fyx, PDBe:6fyx, PDBj:6fyx
• PDBsum: 6fyx
• PubMed: 30475211
• UniProt: P38249|EIF3A_YEAST Eukaryotic translation initiation factor 3 subunit A (Gene Name=RPG1)