Structure of PDB 8agt Chain u Binding Site BS01

Receptor Information

>8agt Chain u (length=136) Species: 4932 (Saccharomyces cerevisiae)

TDSIVKASNWRLVEVGRVVLIKKGQSAGKLAAIVEIIDQKKVLIDGPKAG
VPRQAINLGQVVLTPLTFALPRGARTATVSKKWAAAAVCEKWAASSWAKK
IAQRERRAALTDFERFQVMVLRKQKRYTVKKALAKA

Ligand information

>8agt Chain f (length=3216)

uugaccucaaaucagguaggaguacccgcugaacuuaagcauaucaauaa
gcggaggaaaagaaaccaaccgggauugccuuaguaacggcgagugaagc
ggcaaaagcucaaauuugaaaucugguaccuucggugcccgaguuguaau
uuggagagggcaacuuuggggccguuccuugucuauguuccuuggaacag
gacgucauagagggugagaaucccguguggcgaggagugcgguucuuugu
aaagugccuucgaagagucgaguuguuugggaaugcagcucuaagugggu
gguaaauuccaucuaaagcuaaauauuggcgagagaccgauagcgaacaa
guacagugauggaaagaugaaaagaacuuugaaaagagagugaaaaagua
cgugaaauuguugaaagggaagggcauuugaucagacaugguguuuugua
uuucacuggccagcaucaguuuugguggcaggauaaauccauaggaaugu
agcuugccucgguaaguauuauagccugugggaauacugccagcugggac
ugaggacugcgacguaagucaaggaugcuggcauaaugguuauaugccgc
ccgucuugaaacacggaccaaggagucuaacgucuaugcgaguguuuggg
uguaaaacccauacgcguaaugaaagugaacguagguuggggccucgcaa
gaggugcacaaucgaccgauccugaugucuucggauggauuugaguaaga
gcauagcuguugggacccgaaagauggugaacuaugccugaauaggguga
agccagaggaaacucugguggaggcucguagcgguucugacgugcaaauc
gaucgucgaauuuggguauaggggcgaaagacuaaucgaaccaucuagua
gcugguuccugccgaaguuucccucaggauagcagaagcucguaucaguu
uuaugagguaaagcgaaugauuagagguuccggggucgaaaugaccuuga
ccuauucucaaacuuuaaauauguaagaaguccuuguuacuuaauugaac
guggacauuugaaugaagagcuuuuagugggccauuuuugguaagcagaa
cuggcgaugcgggaugaaccgaacguagaguuaaggugccggaauacacg
cucaucagacaccacaaaagguguuaguucaucuagacagccggacggug
gccauggaagucggaauccgcuaaggaguguguaacaacucaccggccga
augaacuagcccugaaaauggauggcgcucaagcguguuaccuauacucu
accgucaggguugauaugaugcccugacgaguaggcaggcguggagguca
gugacgaagccuagaccguaaggucgggucgaacggccucuagugcagau
cuuggugguaguagcaaauauucaaaugagaacuuugaagacugaagugg
ggaaagguuccacgucaacagcaguuggacguggguuagucgauccuaag
agauggggaagcuccguuucaaaggccugauuuuaugcaggccaccaucg
aaagggaauccgguuaagauuccggaaccuggauauggauucuucacggu
aacguaacugaauguggagacgucggcgcgagcccugggaggaguuaucu
uuucuucuuaacagcuuaucaccccggaauugguuuauccggagaugggg
ucuuauggcuggaagaggccagcaccuuugcuggcuccggugcgcuugug
acggcccgugaaaauccacaggaaggaauaguuuucaugccaggucguac
ugauaaccgcagcaggucuccaaggugaacagccucuaguugauagaaua
auguagauaagggaagucggcaaaauagauccguaacuucgggauaagga
uuggcucuaagggucggguacgaucaacuuagaacugguacggacaaggg
gaaucugacugucuaauuaaaacauagcauugcgauggucagaaagugau
guugacgcaaugugauuucugcccagugcucugaaugucaaagugaagaa
auucaaccaagcgcggguaaacggcgggaguacucucuuaagguagccaa
augccucgucaucuaauuagugacgcgcaugaauggauuaacgagauucc
cacugucccuaucuacuaucuagcgaaaccacagccaagggaacgggcuu
ggcagaaucagcggggaaagaagacccuguugagcuugacucuaguuuga
cauugugaagagacauagaggguguagaauaagugggagcuucggcgcca
gugaaauaccacuaccuuuauaguuucuuuacuuauucaaugaagcggag
cuggaauucauuuuccacguucuagcauucaaggucccauucggggcuga
uccggguugaagacauugucagguggggaguuuggcuggggcggcacauc
uguuaaacgauaacgcagauguccuaaggggggcucauggagaacagaaa
ucuccaguagaacaaaaggguaaaagcccccuugauuuugauuuucagug
ugaauacaaaccaugaaaguguggccuaucgauccuuuagucccucggaa
uuugaggcuagaggugccagaaaaguuaccacagggauaacuggcuugug
gcagucaagcguucauagcgacauugcuuuuugauucuucgaugucggcu
cuuccuaucauaccgaagcagaauucgguaagcguuggauuguucaccca
cuaauagggaacgugagcuggguuuagaccgucgugagacagguuaguuu
uacccuacugaugaauguuaccgcaauaguaauugaacuuaguacgagag
gaacaguucauucggauaauugguuuuugcggcugucugaucaggcauug
ccgcgaagcuaccauccgcuggauuauggcugaacgccucuaagucagaa
uccaugcuagaacgcggugauuucuuugcuccacacaauauagauggaua
cgaauaaggcguccuuguggcgucgcugaaccauagcaggcuagcaacgg
ugcacuuggcggaaaggccuugggugcuugcuggcgaauugcaaugucau
uuugcguggggauaaaucauuuguauacgacuuagauguacaacggggua
uuguaagcaguagaguagccuuguuguuacgaucugcugagauuaagccu
uuguugucugauuugu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8agt Molecular basis of eIF5A-dependent CAT tailing in eukaryotic ribosome-associated quality control.
• Resolution: 2.6 Å
• Binding residue (original residue number in PDB): K8 R13 K42 N59 P73 R74 G75 R77 T78 T80 K84 S98 W99 R106 R109 M121 R124 K125 Q126 R128 Y129 K132 K133 A136
• Binding residue (residue number reindexed from 1): K6 R11 K40 N57 P71 R72 G73 R75 T76 T78 K82 S96 W97 R104 R107 M119 R122 K123 Q124 R126 Y127 K130 K131 A134

Gene Ontology

Molecular Function

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

Biological Process

• GO:0000027 ribosomal large subunit assembly
• GO:0000470 maturation of LSU-rRNA
• GO:0002181 cytoplasmic translation
• GO:0006412 translation
• GO:0016236 macroautophagy
• GO:0042273 ribosomal large subunit biogenesis

Cellular Component

• GO:0005730 nucleolus
• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0022625 cytosolic large ribosomal subunit
• GO:0032991 protein-containing complex
• GO:0043232 intracellular non-membrane-bounded organelle
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8agt, PDBe:8agt, PDBj:8agt
• PDBsum: 8agt
• PubMed: 36804914
• UniProt: P36105|RL14A_YEAST Large ribosomal subunit protein eL14A (Gene Name=RPL14A)