Structure of PDB 8y0u Chain Lg Binding Site BS01

Receptor Information

>8y0u Chain Lg (length=112) Species: 4932 (Saccharomyces cerevisiae)

AQRVTFRRRNPYNTRSNKIKVVKTPGGILRAQHVKKLATRPKCGDCGSAL
QGISTLRPRQYATVSKTHKTVSRAYGGSRCANCVKERIIRAFLIEEQKIV
KKVVKEQTEAAK

Ligand information

>8y0u Chain C1 (length=3221)

uugaccucaaaucagguaggaguacccgcugaacuuaagcauaucaauaa
gcggaggaaaagaaaccaaccgggauugccuuaguaacggcgagugaagc
ggcaaaagcucaaauuugaaaucugguaccuucggugcccgaguuguaau
uuggagagggcaacuuuggggccguuccuugucuauguuccuuggaacag
gacgucauagagggugagaaucccguguggcgaggagugcgguucuuugu
aaagugccuucgaagagucgaguuguuugggaaugcagcucuaagugggu
gguaaauuccaucuaaagcuaaauauuggcgagagaccgauagcgaacaa
guacagugauggaaagaugaaaagaacuuugaaaagagagugaaaaagua
cgugaaauuguugaaagggaagggcauuugaucagacaugguguuuugua
uuucacgccagcaucaguuuugguggcaggauaaauccauaggaauguag
cuugccucgguaaguauuauagccugugggaauacugccagcugggacug
aggacugcgacguaagucaaggaugcuggcauaaugguuauaugccgccc
gucuugaaacacggaccaaggagucuaacgucuaugcgaguguuugggug
uaaaacccauacgcguaaugaaagugaacguagguuggggccucgcaaga
ggugcacaaucgaccgauccugaugucuucggauggauuugaguaagagc
auagcuguugggacccgaaagauggugaacuaugccugaauagggugaag
ccagaggaaacucugguggaggcucguagcgguucugacgugcaaaucga
ucgucgaauuuggguauaggggcgaaagacuaaucgaaccaucuaguagc
ugguuccugccgaaguuucccucaggauagcagaagcucguaucaguuuu
augagguaaagcgaaugauuagagguuccggggucgaaaugaccuugacc
uauucucaaacuuuaaauauguaagaaguccuuguuacuuaauugaacgu
ggacauuugaaugaagagcuuuuagugggccauuuuugguaagcagaacu
ggcgaugcgggaugaaccgaacguagaguuaaggugccggaauacacgcu
caucagacaccacaaaagguguuaguucaucuagacagccggacgguggc
cauggaagucggaauccgcuaaggaguguguaacaacucaccggccgaau
gaacuagcccugaaaauggauggcgcucaagcguguuaccuauacucuac
cgucaggguugauaugaugcccugacgaguaggcaggcguggaggucagu
gacgaagccuagaccguaaggucgggucgaacggccucuagugcagaucu
uggugguaguagcaaauauucaaaugagaacuuugaagacugaagugggg
aaagguuccacgucaacagcaguuggacguggguuagucgauccuaagag
auggggaagcuccguuucaaaggccugauuuuaugcaggccaccaucgaa
agggaauccgguuaagauuccggaaccuggauauggauucuucacgguaa
cguaacugaauguggagacgucggcgcgagcccugggaggaguuaucuuu
ucuucuuaacagcuuaucaccccggaauugguuuauccggagaugggguc
uuauggcuggaagaggccagcaccuuugcuggcuccggugcgcuugugac
ggcccgugaaaauccacaggaaggaauaguuuucaugccaggucguacug
auaaccgcagcaggucuccaaggugaacagccucuaguugauagaauaau
guagauaagggaagucggcaaaauagauccguaacuucgggauaaggauu
ggcucuaagggucggguacgaucaacuuagaacugguacggacaagggga
aucugacugucuaauuaaaacauagcauugcgauggucagaaagugaugu
ugacgcaaugugauuucugcccagugcucugaaugucaaagugaagaaau
ucaaccaagcgcggguaaacggcgggaguaacuaugacucucuuaaggua
gccaaaugccucgucaucuaauuagugacgcgcaugaauggauuaacgag
auucccacugucccuaucuacuaucuagcgaaaccacagccaagggaacg
ggcuuggcagaaucagcggggaaagaagacccuguugagcuugacucuag
uuugacauugugaagagacauagaggguguagaauaagugggagcuucgg
cgccagugaaauaccacuaccuuuauaguuucuuuacuuauucaaugaag
cggagcuggaauucauuuuccacguucuagcauucaaggucccauucggg
gcugauccggguugaagacauugucagguggggaguuuggcuggggcggc
acaucuguuaaacgauaacgcagauguccuaaggggggcucauggagaac
agaaaucuccaguagaacaaaaggguaaaagcccccuugauuuugauuuu
cagugugaauacaaaccaugaaaguguggccuaucgauccuuuagucccu
cggaauuugaggcuagaggugccagaaaaguuaccacagggauaacuggc
uuguggcagucaagcguucauagcgacauugcuuuuugauucuucgaugu
cggcucuuccuaucauaccgaagcagaauucgguaagcguuggauuguuc
acccacuaauagggaacgugagcuggguuuagaccgucgugagacagguu
aguuuuacccuacugaugaauguuaccgcaauaguaauugaacuuaguac
gagaggaacaguucauucggauaauugguuuuugcggcugucugaucagg
cauugccgcgaagcuaccauccgcuggauuauggcugaacgccucuaagu
cagaauccaugcuagaacgcggugauuucuuugcuccacacaauauagau
ggauacgaauaaggcguccuuguggcgucgcugaaccauagcaggcuagc
aacggugcacuuggcggaaaggccuugggugcuugcuggcgaauugcaau
gucauuuugcguggggauaaaucauuuguauacgacuuagauguacaacg
ggguauuguaagcaguagaguagccuuguuguuacgaucugcugagauua
agccuuuguugucugauuugu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8y0u dormant ribosome with STM1
• Resolution: 3.59 Å
• Binding residue (original residue number in PDB): A2 R4 V5 T6 F7 R8 R9 R10 N11 P12 Y13 N14 T15 S17 K24 T25 P26 G27 R31 Q33 K36 K37 T40 R41 P42 Q52 G53 S55 T56 R58 P59 R60 S66 T68 K70 S73 R74 Y76 G78 R80 R88 R91 A92 I95 E96 K102
• Binding residue (residue number reindexed from 1): A1 R3 V4 T5 F6 R7 R8 R9 N10 P11 Y12 N13 T14 S16 K23 T24 P25 G26 R30 Q32 K35 K36 T39 R40 P41 Q51 G52 S54 T55 R57 P58 R59 S65 T67 K69 S72 R73 Y75 G77 R79 R87 R90 A91 I94 E95 K101

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006412 translation
• GO:0042254 ribosome biogenesis

Cellular Component

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

External links

• PDB: RCSB:8y0u, PDBe:8y0u, PDBj:8y0u
• PDBsum: 8y0u
• PubMed: 38698775
• UniProt: P87262|RL34A_YEAST Large ribosomal subunit protein eL34A (Gene Name=RPL34A)