Structure of PDB 8agv Chain e Binding Site BS01

Receptor Information

>8agv Chain e (length=1527) Species: 4932 (Saccharomyces cerevisiae)

SFGGINTFQQYNTDLGLGHNGVRISLNYFDGLPDPSLLNSLYSNELKLIF
KSLLKRDETTKEKALMDLSNLISDFNQNEYFFNDIFLLCWSQIYAKLIIS
DYKVIRLQSHQITIMLVKSLRKKISKFLKDFIPLILLGTCELDYSVSKPS
LNELTECFNKDPAKINALWAVFQEQLLNLVKEIVVNENEDTISDERYSSK
EESEFRYHRVIASAVLLLIKLFVHNKDVSERNSSSLKVILSDESIWKLLN
LKNGQNTNAYETVLRLIDVLYTRGYMPSHKNIMKLAVKKLLKSLTHITSK
NILKVCPVLPSILNLLATLDDYEDGTIWSYDKSSKEKVLKFLSVSRTSPS
PGFFNAVFALYSSTKRHSFLDYYLEWLPFWQKSVQRLNEKGFSARNSAEV
LNEFWTNFLKFAEDSSEERVKKMVESEIFNSLSCGKSLSEYTKLNQTLSG
VFPPDKWEREIEDYFTSDEDIRKIKVSFEKNLFALLVTSPNNESAISRLF
DFFVQLIETDPSNVFNKYDGVYDALNYFLDSDMIFLNGKIGKFINEIPTL
VQESTYQNFAGIMAQYSNSKFFKMNTDAITSLEDFFIVALSFNLPKTIIL
ATMNELDNDIYQQLMKSDSLELELYIEDFMKNYKFDDSGEIFKGNNKFLN
QRTITTLYRSAVANGQVEQFCAVLSKLDETFFSTLLLNTDFLSCALYEVS
EDTNEKLFKLSLQLAKGNSEIANKLAQVILQHAQVYFSPGAKEKYVTHAV
ELINGCNDTSQIFFPANAIEVFARYMPAIDYRSSLVSSLSTNTHLLLTDD
KPINLKNMQKLIRYALFLDALLDALPERVNNHIVAFITVVSELVTDYNCL
SEEPNDLYYDFGHTFFKHGKVNLNFSDIVGNVIQPANGGDAMLTFDIAES
NSVYFFYYSRVLYKVLLNSIDTVSSTTLNGLLASVESFVTKTVRDQKSTD
KDYLLCAILLLMFNRSNSKDEITKLRTLLASQLIGIREVELVDQEFKSLA
LLNNLLDIPQADKQFVPIAPQRLNMIFRSILKWLDSDLAYEPSFSTVRLL
LLDFFTKLMRFEGVRDMGITAFELSERLLADSLSMCQIDDTLYLLELRSS
CLNLYETLSQEYGDEIQENLIELMFLNFNQERNNQVSTLFYQKLYKVISS
MELKKLESQYKRIFEVVLNDKDIGSNINQSRLLTTLLGSLVVKTQQDIII
EYELRINSKFKLPQKLLQKVTDEVPKEYLEYENKNSFIKYLWYWHLILMY
FKDTSYNMRQIFIEQLKEAGLINRMFDFITDQIDLRDTEFWKQVDTKEIS
EYNIVGNNFSPYKEDIFEECKKLLGHTLYQLFNNVGCLTSIWWLNIKDRT
LQNDIEKFVSEFISPILIKNEFDDINSKMDRLTALTIKLNNITNEVKASY
LIDDQKLEISFKLPKNYPLTNIQVNGVSRVGISEQKWKQWIMSTQHVITG
MNGSVLDSLELFTKNVHLQFSGFEECAICYSILHAVDRKLPSKTCPTCKN
KFHGACLYKWFRSSGNNTCPLCRSEIP

Ligand information

>8agv 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: 8agv Molecular basis of eIF5A-dependent CAT tailing in eukaryotic ribosome-associated quality control.
• Resolution: 2.6 Å
• Binding residue (original residue number in PDB): K56 D58 T61 K64 Y198 K1375 D1376 R1377 P1559
• Binding residue (residue number reindexed from 1): K55 D57 T60 K63 Y197 K1347 D1348 R1349 P1527

Enzymatic activity

• Enzyme Commision number: 2.3.2.27: RING-type E3 ubiquitin transferase.

Gene Ontology

Molecular Function

• GO:0004842 ubiquitin-protein transferase activity
• GO:0008270 zinc ion binding
• GO:0016740 transferase activity
• GO:0043023 ribosomal large subunit binding
• GO:0046872 metal ion binding
• GO:0061630 ubiquitin protein ligase activity

Biological Process

• GO:0006325 chromatin organization
• GO:0006511 ubiquitin-dependent protein catabolic process
• GO:0010498 proteasomal protein catabolic process
• GO:0016567 protein ubiquitination
• GO:0030163 protein catabolic process
• GO:0031509 subtelomeric heterochromatin formation
• GO:0072344 rescue of stalled ribosome
• GO:1990116 ribosome-associated ubiquitin-dependent protein catabolic process

Cellular Component

• GO:0000781 chromosome, telomeric region
• GO:0005634 nucleus
• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0022626 cytosolic ribosome
• GO:1990112 RQC complex

External links

• PDB: RCSB:8agv, PDBe:8agv, PDBj:8agv
• PDBsum: 8agv
• PubMed: 36804914
• UniProt: Q04781|LTN1_YEAST E3 ubiquitin-protein ligase listerin (Gene Name=RKR1)