Structure of PDB 8cas Chain p Binding Site BS01

Receptor Information

>8cas Chain p (length=646) Species: 580240 (Saccharomyces cerevisiae W303)

EFNFDQYIVVNGAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATG
KTKGFLFVECGSMNDAKKIIKSFHGKRLDLKHRLFLYTMKDVERYNSPSS
SLKSWLMDDKVRDQFVLQDDVKTSVFWNSMFNEEDSLVESRENWSTNYVR
FSPKGTYLFSYHQQGVTAWGGPNFDRLRRFYHPDVRNSSVSPNEKYLVTF
STEPIIVEEDNEFSPFTKKNEGHQLCIWDIASGLLMATFPVIKSPYLKWP
LVRWSYNDKYCARMVGDSLIVHDATKNFMPLEAKALKPSGIRDFSFAPEG
VKLQPFRNGDEPSVLLAYWTPETNNSACTATIAEVPRGRVLKTVNLVQVS
NVTLHWQNQAEFLCFNVERHTKSGKTQFSNLQICRLTERDIPVEKVELKD
SVFEFGWEPHGNRFVTISVHEVADMNYAIPANTIRFYAPETKEKTDVIKR
WSLVKEIPKTFANTVSWSPAGRFVVVGALVGPNMRRSDLQFYDMDYPGEK
NINDNNDVSASLKDVAHPTYSAATNITWDPSGRYVTAWSSSLKHKVEHGY
KIFNIAGNLVKEDIIAGFKNFAWRPRPSILSNAERKKVRKNLREWSAQFE
EQDAMEADTDLILHQRELLKQWTEYREKIGQEMEKSMNFKIFDVQP

Ligand information

>8cas Chain 2 (length=1763)

uaucugguugauccugccaguagucauaugcuugucucaaagauuaagcc
augcaugucuaaguauaagcaauuuauacagugaaacugcgaauggcuca
uuaaaucaguuaucguuuauuugauaguuacaugguauaacugugguaau
ucuagagcuaauacaugcuuaaaaucucgacccuuuggaagagauguauu
uauuagauaaaaaaucaaugucuucggacucuuugaugauucauaauaac
uuuucgaaucgcauggccuugugcuggcgaugguucauucaaauuucugc
ccuaucaacuuucgaugguaggauaguggccuaccaugguuucaacgggu
aacggggaauaaggguucgauuccggagagggagccugagaaacggcuac
cacauccaaggaaggcagcaggcgcgcaaauuacccaauccuaauucagg
gagguagugacaauaaauaacgauacagggcccauucgggucuuguaauu
ggaaugaguacaauguaaauaccuuaacgaggaacaauuggagggcaagu
cuggugccagcagccgcgguaauuccagcuccaauagcguauauuaaagu
uguugcaguuaaaaagcucguaguugaacuuugggcccgguuggccgguc
ggauuuccaacggggccuuuccuucuggcuaaccuugagcuuggcgaacc
aggacuuuuacuuugaaaaaauuagaguguucaaagcaggcguauugcuc
gaauauauuagcauggaauaauagaauaggacguuugguucuauuuuguu
gguuucuaggaccaucguaaugauuaauagggacggucgggggcaucagu
auucaauugucagaggugaaauucuuggauuuauugaagacuaacuacug
cgaaagcauuugccaaggacguuuucauuaaucaagaacgaaaguuaggg
gaucgaagaugaucagauaccgucguagucuuaaccauaaacuaugccga
cuagggaucgggugguguuuuuuuaaugacccacucggcaccuuacgaga
aaucaaagucuuuggguucuggggggaguauggucgcaaggcugaaacuu
aaaggaauugacggaagggcaccaccaggaguggagccugcggcuuaauu
ugacucaacacggggaaacucaccagguccagacacaauaaggauugaca
gauugagagcucuuucuugauuuugugggugguggugcauggccguucuu
aguugguggagugauuugucugcuuaauugcgauaacgaacgagaccuua
accuacuaaauaguggugcuagcauuugcugguuauccacuucuuagagg
gacuaucgguuucaagccgauggaaguuugaggcaauaacaggucuguga
ugcccuuagacguucugggccgcacgcgcgcuacacugacggagccagcg
agucuaaccuuggccgagaggucuugguaaucuugugaaacuccgucgug
cuggggauagagcauuguaauuauugcucuucaacgaggaauuccuagua
agcgcaagucaucagcuugcguugauuacgucccugcccuuuguacacac
cgcccgucgcuaguaccgauugaauggcuuagugaggccucaggaucugc
uuagagaagggggcaacuccaucucagagcggagaauuuggacaaacuug
gucauuuagaggaacuaaaagucguaacaagguuuccguaggugaaccug
cggaaggaucauu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8cas Molecular basis for recognition and deubiquitination of 40S ribosomes by Otu2.
• Resolution: 3.3 Å
• Binding residue (original residue number in PDB): K459 S460 K462
• Binding residue (residue number reindexed from 1): K372 S373 K375

Gene Ontology

Molecular Function

• GO:0003676 nucleic acid binding
• GO:0003723 RNA binding
• GO:0003743 translation initiation factor activity
• GO:0005515 protein binding
• GO:0031369 translation initiation factor binding
• GO:0042802 identical protein binding

Biological Process

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

Cellular Component

• 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

External links

• PDB: RCSB:8cas, PDBe:8cas, PDBj:8cas
• PDBsum: 8cas
• PubMed: 37169754
• UniProt: P06103|EIF3B_YEAST Eukaryotic translation initiation factor 3 subunit B (Gene Name=PRT1)