Structure of PDB 6xir Chain j Binding Site BS01

Receptor Information

>6xir Chain j (length=87) Species: 4932 (Saccharomyces cerevisiae)

GKGTPSFGKRHNKSHTLCNRCGRRSFHVQKKTCSSCGYPAAKTRSYNWGA
KAKRRHTTGTGRMRYLKHVSRRFKNGFQTGSASKASA

Ligand information

>6xir Chain 1 (length=3113)

uugaccucaaaucagguaggaguacccgcugaacuuaagcauaucaauaa
gcggaggaaaagaaaccaaccgggauugccuuaguaacggcgagugaagc
ggcaaaagcucaaauuugaaaucugguaccuucggugcccgaguuguaau
uuggagagggcaacuuuggggccguuccuugucuauguuccuuggaacag
gacgucauagagggugagaaucccguguggcgaggagugcgguucuuugu
aaagugccuucgaagagucgaguuguuugggaaugcagcucuaagugggu
gguaaauuccaucuaaagcuaaauauuggcgagagaccgauagcgaacaa
guacagugauggaaagaugaaaagaacuuugaaaagagagugaaaaagua
cgugaaauuguugaaagggaagggcauuugaucagacaugguguuuugua
uuucacuggccagcaucaguuuugguggcaggauaaauccauaggaaugu
agcuugccucgguaaguauuauagccugugggaauacugccagcugggac
ugaggacugcgacguaagucaaggaugcuggcauaaugguuauaugccgc
ccgucuugaaacacggaccaaggagucuaacgucuaugcgaguguuuggg
uguaaaacccauacgcguaaugaaagugaacguagguuggggccucgcaa
gaggugcacaaucgaccgauccugaugucuucggauggauuugaguaaga
gcauagcuguugggacccgaaagauggugaacuaugccugaauaggguga
agccagaggaaacucugguggaggcucguagcgguucugacgugcaaauc
gaucgucgaauuuggguauaggggcgaaagacuaaucgaaccaucuagua
gcugguuccugccgaaguuucccucaggauagcagaagcucguaucaguu
uuaugagguaaagcgaaugauuagagguuccggggucgaaaugaccuuga
ccuauucucaaacuuuaaauauguaagaaguccuuguuacuuaauugaac
guggacauuugaaugaagagcuuuuagugggccauuuuugguaagcagaa
cuggcgaugcgggaugaaccgaacguagaguuaaggugccggaauacacg
cucaucagacaccacaaaagguguuaguucaucuagacagcccaccggcc
gaaugaacuagcccugaaaauggauggcgcucaagcguguuaccuauacu
cuaccgucaggguugauaugaugcccugacgaguaggcaggcguggaggu
cagugacgaagccuagaccguaaggucgggucgaacggccucuagugcag
aucuuggugguaguagcaaauauucaaaugagaacuuugaagacugaagu
ggggaaagguuccacgucaacagcaguuggacguggguuagucgauccua
agagauggggaagcuccguuucaaaggccugauuuuaugcaggccaccau
cgaaagggaauccgguuaagauuccggaaccuggauauggauucuucacg
guaacguaacugaauguggagacgucggcgcgagcccugggaggaguuau
cuuuucuucuuaacagcuuaucaccccggaauugguuuauccggagaugg
ggucuuauggcuggaagaggccagcaccuuugcuggcuccggugcgcuug
ugacggcccgugaaaauccacaggaaggaauaguuuucaugccaggucgu
acugauaaccgcagcaggucuccaaggugaacagccucuaguugauagaa
uaauguagauaagggaagucggcaaaauagauccguaacuucgggauaag
gauuggcucuaagggucggguacgaucaacuuagaacugguacggacaag
gggaaucugacugucuaauuaaaacauagcauugcgauggucagaaagug
auguugacgcaaugugauuucugcccagugcucugaaugucaaagugaag
aaauucaaccaagcgcggguaaacggcgggaguaacuaugacucucuuaa
gguagccaaaugccucgucaucuaauuagugacgcgcaugaauggauuaa
cgagauucccacugucccuaucuacuaucuagcgaaaccacagccaaggg
aacgggcuuggcagaaucagcggggaaagaagacccuguugagcuugacu
cuaguuugacauugugaagagaucuuuacuuauucaaugaagcggagcug
gaauucauuuuccacguucuagcauucaaggucccauucggggcugaucc
ggguugaagacauugucagguggggaguuuggcuggggcggcacaucugu
uaaacgauaacgcagauguccuaaggggggcucauggagaacagaaaucu
ccaguagaacaaaaggguaaaagcccccuugauuuugauuuucaguguga
auacaaaccaugaaaguguggccuaucgauccuuuagucccucggaauuu
gaggcuagaggugccagaaaaguuaccacagggauaacuggcuuguggca
gucaagcguucauagcgacauugcuuuuugauucuucgaugucggcucuu
ccuaucauaccgaagcagaauucgguaagcguuggauuguucacccacua
auagggaacgugagcuggguuuagaccgucgugagacagguuaguuuuac
ccuacugaugaauguuaccgcaauaguaauugaacuuaguacgagaggaa
caguucauucggauaauugguuuuugcggcugucugaucaggcauugccg
cgaagcuaccauccgcuggauuauggcugaacgccucuaagucagaaucc
augcuagaacgcggugauuucuuugcuccacacaauauagauggauacga
auaaggcguccuuguggcgucgcugaaccauagcaggcuagcaacggugc
acuuggcggaaaggccuugggugcuugcuggcgaauugcaaugucauuuu
gcguggggauaaaucauuuguauacgacuuagauguacaacgggguauug
uaagcaguagaguagccuuguuguuacgaucugcugagauuaagccuuug
uugucugauuugu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6xir Structural impact of K63 ubiquitin on yeast translocating ribosomes under oxidative stress.
• Resolution: 3.2 Å
• Binding residue (original residue number in PDB): G2 K3 G4 T5 P6 F8 G9 K10 R11 H12 N13 S15 H16 R24 R25 H28 Q30 K31 S35 K43 T44 R45 Y47 N48 W49 K52 R55 R56
• Binding residue (residue number reindexed from 1): G1 K2 G3 T4 P5 F7 G8 K9 R10 H11 N12 S14 H15 R23 R24 H27 Q29 K30 S34 K42 T43 R44 Y46 N47 W48 K51 R54 R55

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0008270 zinc ion binding
• GO:0019843 rRNA binding
• GO:0046872 metal ion binding

Biological Process

• GO:0000448 cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
• GO:0002181 cytoplasmic translation
• GO:0006412 translation

Cellular Component

• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0022625 cytosolic large ribosomal subunit
• GO:0030687 preribosome, large subunit precursor
• GO:0044391 ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:6xir, PDBe:6xir, PDBj:6xir
• PDBsum: 6xir
• PubMed: 32855298
• UniProt: P49166|RL37A_YEAST Large ribosomal subunit protein eL37A (Gene Name=RPL37A)