Structure of PDB 8pfr Chain RO Binding Site BS01

Receptor Information
>8pfr Chain RO (length=50) Species: 4932 (Saccharomyces cerevisiae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
EPSLKALASKYNCDKSVCRKCYARLPPRATNCRKRKCGHTNQLRPKKKLK
Ligand information
>8pfr Chain A (length=3038) [Search RNA sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
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
cuucgggauaaggauuggcucuaagggucggacgaucaacuuagaacugg
uacggacaaggggaaucugacugucuaauuaaaacauagcauugcgaugg
ucagaaagugauguugacgcaaugugauuucugcccagugcucugaaugu
caaagugaagaaauucaaccaagcgcggguaaacggcggaagguagccaa
augccucgucaucuaauuagugacgcgcaugaauggauuaacgagauucc
cacugucccuaucuacuaucuagcgaaaccacagccaagggaacgggcuu
ggcagaaucagcggggaaagaagacccuguugagcuugacucuaguuuga
cauugugaaguacuuauucaaugaagcggagcuggaccacguucuagcau
ucaaggucccauucggggcugauccggguugaagacauugucaggugggg
aguuuggcuggggcggcacaucuguuaaacgauaacgcagauguccuaag
gggggcucauggagaacagaaaucuccaguagaacaaaaggguaaaagcc
cccuugauuuugauuuucagugugaauacaaaccaugaaaguguggccua
ucgauccuuuagucccucggaauuugaggcuagaggugccagaaaaguua
ccacagggauaacuggcuuguggcagucaagcguucauagcgacauugcu
uuuugauucuucgaugucggcucuuccuaucauaccgaagcagaauucgg
uaagcguuggauuguucacccacuaauagggaacgugagcuggguuuaga
ccgucgugagacagguuaguuuuacccuacugaugaauguuaccgcaaua
guaauugaacuuaguacgagaggaacaguucauucggauaauugguuuuu
gcggcugucugaucaggcauugccgcgaagcuaccauccgcuggauuaug
gcugaacgccucuaagucagaauccaugcuagaacgcggugauuucuuug
cuccacacaauauagauggauacgaauaaggcguccuuguggcgucgcug
aaccauagcaggcuagcaacggugcacuuggcggaaaggccuugggugcu
ugcuggcgaauugcaaugucauuuugcguggggauaaaucauuuguauac
gacuuagauguacaacgggguauuguaagcaguagaguagccuuguuguu
acgaucugcugagauuaagccuuuguugucugauuugu
........................<<<<<<.....<......>......>
>>>>.>.........<<....>>..<<<<<......<<.....>>.....
>>>>>..[[[..<<.......<<.<<<<<<...>>>>>>.>>.......>
>....<<<<<<<.<<<<<<<<<<<<<<<<<<<<<....<<<<......>>
>>.(.......<<<......)>>>..>.>>>>>>>>..>>>>>>>>....
>>>>>>>>>>>........<<<<<<<........>>>>>>>.....((((
(..<<<<<<)))))..]]]...............................
...<<....>>...............<<<<....>>>>............
......................<<<<<.<<<<<......<<<<<<<.<<<
<<<<<<<<<<<<.....<<<<<<<<<......<<<<<......>>>>>..
.....>>>>>>>.>.>.>>>>>.>>>>>>>>>>........<<<....>>
>.....>>>>>>>.....>>>>>.>>>>>..<<<<........>>>><<<
<<<....<<<<<<.<<<<<<..<<<...<<<<.....>>>>...>>>...
<<....>>.......<<<<<..<<<<<....>>>>>...>>>>>.<<<<<
<<<...<<....>>...>>>.>>>.>>....>>>>>>.>>>>>>..<<.<
..<<<<<<<.....<<<<<<<<<..<<<....<<<<<<<....>>>>>>>
.....>>>...<<<..<<.<<........>>>>.>>>....>>>>>>>>>
...<<.......>>......>>>>>>...>..>.>>..<<<<<<....<.
<<<....>>>.><<<<<<<<<<...<<<.<<<<<<<.....<<<....<<
<....<<<<...<<....>>.>>>>....>>>..>.>>.....>>>>>..
.<<<<.<<<<.<......>>>>>.>>>>.....>>>>>.>>>>>>>>.>>
..<<<<.<<<<<.....>>>>>.>>>>....<<<......>>>...<<<<
<<<..<<<<(((.....<<<<<<......<..........<<<.<<<<<<
<<<<..........>>>>>>>>>>>>>..........))).>....>>>>
>>.>>>>..>>>>>>><<<<<<<<<.........>>>>>>>>>....>>>
>>><.<<<<<<<..<<......<<<<.<<<<....>>>>>>>>...>>.>
>>>>>>..>.....>>>>>><<<....<<.....<<<<<<.......>>>
>>><<<<.....<<<<<.<<...<<<<<<...<<.....>>.>>>>>>..
..((<<<<<<...<<....<<<....>>>........<<..<<<.....>
.>>..>>....>>....>>...<<<<<........>>>>>))<<<<.<<<
<<<<.....<<<....>>>...<...<<<<<<...<<<<.<<<<<<<.<<
<<<<<<<<..{{{..>>>>>><...<<<<<....<<<<<<....<<<...
..>>>....>>>>>>.....>>>>>....><<<<<<<......>>>>>>>
>>>>...>>>>>>>.>>>>.........>>>>>>...>......>>>..>
>>>>>>>>>>>..>>.....<<......>>>>>>>.<<<<.....>>>>.
.>>>>..<<<<.....<<<<<<<.<<...............<<<<<....
<<..>>.....>>>>><<.<<<<<<<<<<....>>>>..>>>>>>.>>..
..........<<<<<<<<<..<<<.........>>>..<<<<<<<....<
<<<.....>>>>......>>>>>>>.<.<<..<<<..<<<<<<.<...<<
....<<<<<....>>>>.>...>>.>>>>>..>>>>>........<....
.......<<<<<.......>>>>>.....>.....>>.>..>>.>>>>>>
>.....>>.>>>>>>>..>>>>>>...>>>....<<<<<........>>>
>>....[[[[[..{{{.{{......[[[[.{{[[[[..<<<<<.<<<<<<
<<..<<<...>>>...<<<<<.....<<<<..<<<.>>>...........
....<<<<<<....>>>>>>..>>>>..>>>>>.....>>>>>>>>..>>
>>>...<<<.....>>>..<<<<<<...........>>>>>>..<<...<
<<<<<<...<<<<<<.......>>>>>>.....<<...(((>>....>>>
>>>>...<<<.<<<<<.......>>>>.>>>>.<<<....>>>.>>))).
......((((((..((((.>>>>>>))))))))))..........]]]].
.}}]]]].......<<.<.<.<<<<<<...<<.......>>...>>>>>>
...>>.>.>.......<<<<<.<<<<<<..<.<<<<<<<......>>>>>
>>...>.<<<.........>>>.....>>>>>..>...>>>.>>....<<
<<<<<....>>>.>>>>....}}..}}}.]]]]]....<<<<<<<<..<<
<<...<<<<<<...............>>>>>>..<<<<<...<<<<....
<<<<<<<<<<}}}.>>>>>..>>>>>...>>>>..>>>>>.<<<<...<<
<<<...........>>>>>...>>>>.>>>>....>>>>>>>>.......
<<<<<..<<<.<<....<<..........<<<<<<.....>>>>>>....
..>>.......<<<<<<...<<<<<.<..<<<......>>>..>.>>>>>
.>>>>>>.............>>.>>>..>>>>>..<<<<<.<........
.....>.....<<<<<<<<<.<<<....<<<<....<<<<<......>>>
>>...>>>>...>>>....>>>>.>>>>>..>>>>>..
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB8pfr Real-space refinement in PHENIX for cryo-EM and crystallography.
Resolution2.15 Å
Binding residue
(original residue number in PDB)
R97 Y100 R102 R106 N109 R111 K112 R113 K114 G116 H117 N119 R122 K124 K125 K128
Binding residue
(residue number reindexed from 1)
R19 Y22 R24 R28 N31 R33 K34 R35 K36 G38 H39 N41 R44 K46 K47 K50
Gene Ontology
Molecular Function
GO:0003735 structural constituent of ribosome
GO:0008270 zinc ion binding
GO:0031386 protein tag activity
GO:0031625 ubiquitin protein ligase binding
Biological Process
GO:0000027 ribosomal large subunit assembly
GO:0000055 ribosomal large subunit export from nucleus
GO:0002181 cytoplasmic translation
GO:0016567 protein ubiquitination
GO:0019941 modification-dependent protein catabolic process
GO:0042254 ribosome biogenesis
Cellular Component
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0005840 ribosome
GO:0022625 cytosolic large ribosomal subunit
GO:1990904 ribonucleoprotein complex

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Molecular Function

View graph for
Biological Process

View graph for
Cellular Component
External links
PDB RCSB:8pfr, PDBe:8pfr, PDBj:8pfr
PDBsum8pfr
PubMed
UniProtP0CH08|RL40A_YEAST Ubiquitin-ribosomal protein eL40A fusion protein (Gene Name=RPL40A)

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