Structure of PDB 6xir Chain i Binding Site BS01

Receptor Information

>6xir Chain i (length=99) Species: 4932 (Saccharomyces cerevisiae)

TVKTGIAIGLNKGKKVTSMTPAPKISYKKGAASNRTKFVRSLVREIAGLS
PYERRLIDLIRNSGEKRARKVAKKRLGSFTRAKAKVEEMNNIIAASRRH

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

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

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): K4 G14 K15 I26 S27 Y28 K29 K30 G31 R36 R41 Y53 K67 R68 K74 R76 R82 K84 K86
• Binding residue (residue number reindexed from 1): K3 G13 K14 I25 S26 Y27 K28 K29 G30 R35 R40 Y52 K66 R67 K73 R75 R81 K83 K85

Gene Ontology

Molecular Function

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

Biological Process

• 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:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:6xir, PDBe:6xir, PDBj:6xir
• PDBsum: 6xir
• PubMed: 32855298
• UniProt: P05745|RL36A_YEAST Large ribosomal subunit protein eL36A (Gene Name=RPL36A)