Structure of PDB 8p8n Chain LI Binding Site BS01

Receptor Information

>8p8n Chain LI (length=286) Species: 4932 (Saccharomyces cerevisiae)

KSSAYSSRFQTPFRRRREGKTDYYQRKRLVTQHKAKYNTPKYRLVVRFTN
KDIICQIISSTITGDVVLAAAYSHELPRYGITHGLTNWAAAYATGLLIAR
RTLQKLGLDETYKGVEEVEGEYELTEAVEDGPRPFKVFLDIGLQRTTTGA
RVFGALKGASDGGLYVPHSENRFPGWDFETEEIDPELLRSYIFGGHVSQY
MEELADDDEERFSELFKGYLADDIDADSLEDIYTSAHEAIRADPAFKPTE
KKFTKEQYAAESKKYRQTKLSKEERAARVAAKIAAL

Ligand information

>8p8n Chain A (length=3043)

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
cuucgggauaaggauuggcucuaagggucgaucaacuuagaacugguacg
gacaaggggaaucugacugucuaauuaaaacauagcauugcgauggucag
aaagugauguugacgcaaugugauuucugcccagugcucugaaugucaaa
gugaagaaauucaaccaagcgcggguaaacggcggaagguagccaaaugc
cucgucaucuaauuagugacgcgcaugaauggauuaacgagauucccacu
gucccuaucuacuaucuagcgaaaccacagccaagggaacgggcuuggca
gaaucagcggggaaagaagacccuguugagcuugacucuaguuugacauu
gugaaguacuuauucaaugaagcggagcuggaauucauuuuccacguucu
agcauucaaggucccauucggggcugauccggguugaagacauugucagg
uggggaguuuggcuggggcggcacaucuguuaaacgauaacgcagauguc
cuaaggggggcucauggagaacagaaaucuccaguagaacaaaaggguaa
aagcccccuugauuuugauuuucagugugaauacaaaccaugaaagugug
gccuaucgauccuuuagucccucggaauuugaggcuagaggugccagaaa
aguuaccacagggauaacuggcuuguggcagucaagcguucauagcgaca
uugcuuuuugauucuucgaugucggcucuuccuaucauaccgaagcagaa
uucgguaagcguuggauuguucacccacuaauagggaacgugagcugggu
uuagaccgucgugagacagguuaguuuuacccuacugaugaauguuaccg
caauaguaauugaacuuaguacgagaggaacaguucauucggauaauugg
uuuuugcggcugucugaucaggcauugccgcgaagcuaccauccgcugga
uuauggcugaacgccucuaagucagaauccaugcuagaacgcggugauuu
cuuugcuccacacaauauagauggauacgaauaaggcguccuuguggcgu
cgcugaaccauagcaggcuagcaacggugcacuuggcggaaaggccuugg
gugcuugcuggcgaauugcaaugucauuuugcguggggauaaaucauuug
uauacgacuuagauguacaacgggguauuguaagcaguagaguagccuug
uuguuacgaucugcugagauuaagccuuuguugucugauuugu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8p8n Real-space refinement in PHENIX for cryo-EM and crystallography.
• Resolution: 2.15 Å
• Binding residue (original residue number in PDB): K8 R15 F16 Q17 P19 R23 T28 Y31 R35 L36 K43 Y44 T46 K48 P139 R140 F142 F145 I148 L150 R152 T153 P174 H175 S176 N178 R179
• Binding residue (residue number reindexed from 1): K1 R8 F9 Q10 P12 R16 T21 Y24 R28 L29 K36 Y37 T39 K41 P132 R133 F135 F138 I141 L143 R145 T146 P167 H168 S169 N171 R172

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome
• GO:0005515 protein binding
• GO:0008097 5S rRNA binding
• GO:0019843 rRNA binding

Biological Process

• GO:0000027 ribosomal large subunit assembly
• GO:0002181 cytoplasmic translation

Cellular Component

• GO:0005634 nucleus
• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0022625 cytosolic large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8p8n, PDBe:8p8n, PDBj:8p8n
• PDBsum: 8p8n
• UniProt: P26321|RL5_YEAST Large ribosomal subunit protein uL18 (Gene Name=RPL5)