Structure of PDB 8p8m Chain RC Binding Site BS01

Receptor Information

>8p8m Chain RC (length=97) Species: 4932 (Saccharomyces cerevisiae)

SINQKLALVIKSGKYTLGYKSTVKSLRQGKSKLIIIAANTPVLRKSELEY
YAMLSKTKVYYFQGGNNELGTAVGKLFRVGVVSILEAGDSDILTTLA

Ligand information

>8p8m Chain A (length=3035)

uugaccucaaaucagguaggaguacccgcugaacuuaagcauaucaauaa
gcggaggaaaagaaaccaaccgggauugccuuaguaacggcgagugaagc
ggcaaaagcucaaauuugaaaucugguaccuucggugcccgaguuguaau
uuggagagggcaacuuuggggccguuccuugucuauguuccuuggaacag
gacgucauagagggugagaaucccguguggcgaggagugcgguucuuugu
aaagugccuucgaagagucgaguuguuugggaaugcagcucuaagugggu
gguaaauuccaucuaaagcuaaauauuggcgagagaccgauagcgaacaa
guacagugauggaaagaugaaaagaacuuugaaaagagagugaaaaagua
cgugaaauuguugaaagggaagggcauuugaucagacaggccagcaucag
uuuugguggcaggauaaauccauaggaauguagcuugccucgguaaguau
uauagccugugggaauacugccagcugggacugaggacugcgacguaagu
caaggaugcuggcauaaugguuauaugccgcccgucuugaaacacggacc
aaggagucuaacgucuaugcgaguguuuggguguaaaacccauacgcgua
augaaagugaacguagguuggggccucgcaagaggugcacaaucgaccga
uccugaugucuucggauggauuugaguaagagcauagcuguugggacccg
aaagauggugaacuaugccugaauagggugaagccagaggaaacucuggu
ggaggcucguagcgguucugacgugcaaaucgaucgucgaauuuggguau
aggggcgaaagacuaaucgaaccaucuaguagcugguuccugccgaaguu
ucccucaggauagcagaagcucguaucaguuuuaugagguaaagcgaaug
auuagagguuccggggucuugaccuauucucaaacuuuaaauauguaaga
aguccuuguuacuuaauugaacguggacauuugaaugaagagcuuuuagu
gggccauuuuugguaagcagaacuggcgaugcgggaugaaccgaacguag
aguuaaggugccggaauacacgcucaucagacaccacaaaagguguuagu
ucaucuagacaggaaugaacuagcccugaaaauggauggcgcucaagcgu
guuaccuauacucuaccgucaggguugauaugaugcccugacgaguaggc
aggcguggaggucagugacgaagccuagaccguaaggucgggucgaacgg
ccucuagugcagaucuuggugguaguagcaaauauucaaaugagaacuuu
gaagacugaaguggggaaagguuccacgucaacagcaguuggacgugggu
uagucgauccuaagagauggggaagcuccguuucaaaggccugauuuuau
gcaggccaccaucgaaagggaauccgguuaagauuccggaaccuggauau
ggauucuucacgguaacguaacugaauguggagacgucggcgcgagcccu
gggaggaguuaucuuuucuucuuaacagcuuaucaccccggaauugguuu
auccggagauggggucuuauggcuggaagaggccagcaccuuugcuggcu
ccggugcgcuugugacggcccgugaaaauccacaggaaggaauaguuuuc
augccaggucguacugauaaccgcagcaggucuccaaggugaacagccuc
uaguugauagaauaauguagauaagggaagucggcaaaauagauccguaa
cuucgggauaaggauuggcucuaagggucgguacgaucaacuuagaacug
guacggacaaggggaaucugacugucuaauuaaaacauagcauugcgaug
gucagaaagugauguugacgcaaugugauuucugcccagugcucugaaug
ucaaagugaagaaauucaaccaagcgcggguaaacggcggaagguagcca
aaugccucgucaucuaauuagugacgcgcaugaauggauuaacgagauuc
ccacugucccuaucuacuaucuagcgaaaccacagccaagggaacgggcu
uggcagaaucagcggggaaagaagacccuguugagcuugacucuaguuug
acauugugaaguacuuauucaaugaagcggagcucacguucuagcauuca
aggucccauucggggcugauccggguugaagacauugucagguggggagu
uuggcuggggcggcacaucuguuaaacgauaacgcagauguccuaagggg
ggcucauggagaacagaaaucuccaguagaacaaaaggguaaaagccccc
uugauuuugauuuucagugugaauacaaaccaugaaaguguggccuaucg
auccuuuagucccucggaauuugaggcuagaggugccagaaaaguuacca
cagggauaacuggcuuguggcagucaagcguucauagcgacauugcuuuu
ugauucuucgaugucggcucuuccuaucauaccgaagcagaauucgguaa
gcguuggauuguucacccacuaauagggaacgugagcuggguuuagaccg
ucgugagacagguuaguuuuacccuacugaugaauguuaccgcaauagua
auugaacuuaguacgagaggaacaguucauucggauaauugguuuuugcg
gcugucugaucaggcauugccgcgaagcuaccauccgcuggauuauggcu
gaacgccucuaagucagaauccaugcuagaacgcggugauuucuuugcuc
cacacaauauagauggauacgaauaaggcguccuuguggcgucgcugaac
cauagcaggcuagcaacggugcacuuggcggaaaggccuugggugcuugc
uggcgaauugcaaugucauuuugcguggggauaaaucauuuguauacgac
uuagauguacaacgggguauuguaagcaguagaguagccuuguuguuacg
aucugcugagauuaagccuuuguugucugauuugu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8p8m Yeast 60S ribosomal subunit, RPL39 deletion
• Resolution: 2.66 Å
• Binding residue (original residue number in PDB): L25 G26 Y27 K28 S29 P49 V50 R52 S54 F85 R86 G88
• Binding residue (residue number reindexed from 1): L17 G18 Y19 K20 S21 P41 V42 R44 S46 F77 R78 G80

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0030627 pre-mRNA 5'-splice site binding

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006364 rRNA processing
• GO:0048025 negative regulation of mRNA splicing, via spliceosome

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:8p8m, PDBe:8p8m, PDBj:8p8m
• PDBsum: 8p8m
• UniProt: P14120|RL30_YEAST Large ribosomal subunit protein eL30 (Gene Name=RPL30)