Structure of PDB 8evq Chain V Binding Site BS01

Receptor Information

>8evq Chain V (length=189) Species: 4932 (Saccharomyces cerevisiae)

REKKAEYFAKLREYLEEYKSLFVVGVDNVSSQQMHEVRKELRGRAVVLMG
KNTMVRRAIRGFLSDLPDFEKLLPFVKGNVGFVFTNEPLTEIKNVIVSNR
VAAPARAGAVAPEDIWVRAVNTGMEPGKTSFFQALGVPTKIARGTIEIVS
DVKVVDAGNKVGQSEASLLNLLNISPFTFGLTVVQVYDN

Ligand information

>8evq Chain A1 (length=3198)

uugaccucaaaucagguaggaguacccgcugaacuuaagcauaucaauaa
gcggaggaaaagaaaccaaccgggauugccuuaguaacggcgagugaagc
ggcaaaagcucaaauuugaaaucugguaccuucggugcccgaguuguaau
uuggagagggcaacuuuggggccguuccuugucuauguuccuuggaacag
gacgucauagagggugagaaucccguguggcgaggagugcgguucuuugu
aaagugccuucgaagagucgaguuguuugggaaugcagcucuaagugggu
gguaaauuccaucuaaagcuaaauauuggcgagagaccgauagcgaacaa
guacagugauggaaagaugaaaagaacuuugaaaagagagugaaaaagua
cgugaaauuguugaaagggaagggcauuugaucagacaggccagcaucag
uuuugguggcaggauaaauccauaggaauguagcuugccucgguaaguau
uauagccugugggaauacugccagcugggacugaggacugcgacguaagu
caaggaugcuggcauaaugguuauaugccgcccgucuugaaacacggacc
aaggagucuaacgucuaugcgaguguuuggguguaaaacccauacgcgua
augaaagugaacguagguuggggccucgcaagaggugcacaaucgaccga
uccugaugucuucggauggauuugaguaagagcauagcuguugggacccg
aaagauggugaacuaugccugaauagggugaagccagaggaaacucuggu
ggaggcucguagcgguucugacgugcaaaucgaucgucgaauuuggguau
aggggcgaaagacuaaucgaaccaucuaguagcugguuccugccgaaguu
ucccucaggauagcagaagcucguaucaguuuuaugagguaaagcgaaug
auuagagguuccggggucaccuugaccuauucucaaacuuuaaauaugua
agaaguccuuguuacuuaauugaacguggacauuugaaugaagagcuuuu
agugggccauuuuugguaagcagaacuggcgaugcgggaugaaccgaacg
uagaguuaaggugccggaauacacgcucaucagacaccacaaaagguguu
aguucaucuagacagccggacgguggccauggaagucggaauccgcuaag
gaguguguaacaacucaccggccgaaugaacuagcccugaaaauggaugg
cgcucaagcguguuaccuauacucuaccgucaggguugauaugaugcccu
gacgaguaggcaggcguggaggucagugacgaagccuagaccguaagguc
gggucgaacggccucuagugcagaucuuggugguaguagcaaauauucaa
augagaacuuugaagacugaaguggggaaagguuccacgucaacagcagu
uggacguggguuagucgauccuaagagauggggaagcuccguuucaaagg
ccugauuuuaugcaggccaccaucgaaagggaauccgguuaagauuccgg
aaccuggauauggauucuucacgguaacguaacugaauguggagacgucg
gcgcgagcccugggaggaguuaucuuuucuucuuaacagcuuaucacccc
ggaauugguuuauccggagauggggucuuauggcuggaagaggccagcac
cuuugcuggcuccggugcgcuugugacggcccgugaaaauccacaggaag
gaauaguuuucaugccaggucguacugauaaccgcagcaggucuccaagg
ugaacagccucuaguugauagaauaauguagauaagggaagucggcaaaa
uagauccguaacuucgggauaaggauuggcucuaagggucggguacgauc
aacuuagaacugguacggacaaggggaaucugacugucuaauuaaaacau
agcauugcgauggucagaaagugauguugacgcaaugugauuucugccca
gugcucugaaugucaaagugaagaaauucaaccaagcgcggguaaacggc
gggaguaacuaugacucucuuaagguagccaaaugccucgucaucuaauu
agugacgcgcaugaauggauuaacgagauucccacugucccuaucuacua
ucuagcgaaaccacagccaagggaacgggcuuggcagaaucagcggggaa
agaagacccuguugagcuugacucuaguuugacauugugaagagacauag
aggguguagaauaagugggagcuucggcgccagugaaauaccacuaccuu
uauaguuucuuuacuuauucaaugaagcggagcuggaauucauuuuccac
guucuagcauucaaggucccauucggggcugauccggguugaagacauug
ucagguggggaguuuggcuggggcggcacaucuguuaaacgauaacgcag
auguccuaaggggggcucauggagaacagaaaucuccaguagaacaaaag
gguaaaagcccccuugauuuugauuuucagugugaauacaaaccaugaaa
guguggccuaucgauccuuuagucccucggaauuugaggcuagaggugcc
agaaaaguuaccacagggauaacuggcuuguggcagucaagcguucauag
cgacauugcuuuuugauucuucgaugucggcucuuccuaucauaccgaag
cagaauucgguaagcguuggauuguucacccacuaauagggaacgugagc
uggguuuagaccgucgugagacagguuaguuuuacccuacugaugaaugu
uaccgcaauaguaauugaacuuaguacgagaggaacaguucauucggaua
auugguuuuugcggcugucugaucaggcauugccgcgaagcuaccauccg
cuggauuauggcugaacgccucuaagucagaauccaugcuagaacgcggu
gauuucuuugcuccacacaauauagauggauacgaauaaggcguccuugu
ggcgucgcugaaccauagcaggcuagcaacggugcacuuggcggaaaggc
cuugggugcuugcuggcgaauugcaaugucauuuugcguggggauaaauc
auuuguauacgacuuagauguacaacgggguauuguaagcaguagaguag
ccuuguuguuacgaucugcugagauuaagccuuuguugucugauuugu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8evq Regulation of translation by ribosomal RNA pseudouridylation.
• Resolution: 2.72 Å
• Binding residue (original residue number in PDB): R5 K7 F12 D31 N32 S34 S35 Q36 M38 H39 R42 R46 L52 M53 K55 N56 T57 M58 R61 R64 K81 G82 R110
• Binding residue (residue number reindexed from 1): R1 K3 F8 D27 N28 S30 S31 Q32 M34 H35 R38 R42 L48 M49 K51 N52 T53 M54 R57 R60 K77 G78 R106

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome
• GO:0005515 protein binding
• GO:0070180 large ribosomal subunit rRNA binding

Biological Process

• GO:0000027 ribosomal large subunit assembly
• GO:0002181 cytoplasmic translation
• GO:0042254 ribosome biogenesis

Cellular Component

• GO:0005737 cytoplasm
• GO:0005840 ribosome
• GO:0022625 cytosolic large ribosomal subunit
• GO:0030686 90S preribosome
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8evq, PDBe:8evq, PDBj:8evq
• PDBsum: 8evq
• PubMed: 37595043
• UniProt: P05317|RLA0_YEAST Large ribosomal subunit protein uL10 (Gene Name=RPP0)