Structure of PDB 4v88 Chain Dm Binding Site BS01

Receptor Information

>4v88 Chain Dm (length=52) Species: 559292 (Saccharomyces cerevisiae S288C)

IIEPSLKALASKYNCDKSVCRKCYARLPPRATNCRKRKCGHTNQLRPKKK
LK

Ligand information

>4v88 Chain A5 (length=3150)

uugaccucaaaucagguaggaguacccgcugaacuuaagcauaucaauaa
gcggaggaaaagaaaccaaccgggauugccuuaguaacggcgagugaagc
ggcaaaagcucaaauuugaaaucugguaccuucggugcccgaguuguaau
uuggagagggcaacuuuggggccguuccuugucuauguuccuuggaacag
gacgucauagagggugagaaucccguguggcgaggagugcgguucuuugu
aaagugccuucgaagagucgaguuguuugggaaugcagcucuaagugggu
gguaaauuccaucuaaagcuaaauauuggcgagagaccgauagcgaacaa
guacagugauggaaagaugaaaagaacuuugaaaagagagugaaaaagua
cgugaaauuguugaaagggaagggcauuugaucagacauggcugggccag
caucaguuuugguggcaggauaaauccauaggaauguagcuugccucggu
aaguauuauagccugugggaauacugccagcugggacugaggacugcgac
guaagucaaggaugcuggcauaaugguuauaugccgcccgucuugaaaca
cggaccaaggagucuaacgucuaugcgaguguuuggguguaaaacccaua
cgcguaaugaaagugaacguagguuggggccucgcaagaggugcacaauc
gaccgauccugaugucuucggauggauuugaguaagagcauagcuguugg
gacccgaaagauggugaacuaugccugaauagggugaagccagaggaaac
ucugguggaggcucguagcgguucugacgugcaaaucgaucgucgaauuu
ggguauaggggcgaaagacuaaucgaaccaucuaguagcugguuccugcc
gaaguuucccucaggauagcagaagcucguaucaguuuuaugagguaaag
cgaaugauuagagguuccggggucgaaaugaccuugaccuauucucaaac
uuuaaauauguaagaaguccuuguuacuuaauugaacguggacauuugaa
ugaagagcuuuuagugggccauuuuugguaagcagaacuggcgaugcggg
augaaccgaacguagaguuaaggugccggaauacacgcucaucagacacc
acaaaagguguuaguucaucuagacagccggacgguggccauggaagucg
gaauccgcuaaggaguguguaacaacucaccggccgaaugaacuagcccu
gaaaauggauggcgcucaagcguguuaccuauacucuaccgucaggguug
auaugaugcccugacgaguaggcaggcguggaggucagugacgaagccua
gaccguaaggucgggucgaacggccucuagugcagaucuuggugguagua
gcaaauauucaaaugagaacuuugaagacugaaguggggaaagguuccac
gucaacagcaguuggacguggguuagucgauccuaagagauggggaagcu
ccguuucaaaggccugauuuuaugcaggccaccaucgaaagggaauccgg
uuaagauuccggaaccuggauauggauucuucacgguaacguaacugaau
guggagacgucggcgcgagcccugggaggaguuaucuuuucuucuuaaca
gcuuaucaccccggaauugguuuauccggagauggggucuuauggcugga
agaggccagcaccuuugcuggcuccggugcgcuugugacggcccgugaaa
auccacaggaaggaauaguuuucaugccaggucguacugauaaccgcagc
aggucuccaaggugaacagccucuaguugauagaauaauguagauaaggg
aagucggcaaaauagauccguaacuucgggauaaggauuggcucuaaggg
ucggacgaucaacuuagaacugguacggacaaggggaaucugacugucua
auuaaaacauagcauugcgauggucagaaagugauguugacgcaauguga
uuucugcccagugcucugaaugucaaagugaagaaauucaaccaagcgcg
gguaaacggcgggaguaacuaugacucucuuaagguagccaaaugccucg
ucaucuaauuagugacgcgcaugaauggauuaacgagauucccacugucc
cuaucuacuaucuagcgaaaccacagccaagggaacgggcuuggcagaau
cagcggggaaagaagacccuguugagcuugacucuaguuugacauuguga
agagacguuucuuuacuuauucaaugaagcggagcuggaauucauuuucc
acguucuagcauucaaggucccauucggggcugauccggguugaagacau
ugucagguggggaguuuggcuggggcggcacaucuguuaaacgauaacgc
agauguccuaaggggggcucauggagaacagaaaucuccaguagaacaaa
aggguaaaagcccccuugauuuugauuuucagugugaauacaaaccauga
aaguguggccuaucgauccuuuagucccucggaauuugaggcuagaggug
ccagaaaaguuaccacagggauaacuggcuuguggcagucaagcguucau
agcgacauugcuuuuugauucuucgaugucggcucuuccuaucauaccga
agcagaauucgguaagcguuggauuguucacccacuaauagggaacguga
gcuggguuuagaccgucgugagacagguuaguuuuacccuacugaugaau
guuaccgcaauaguaauugaacuuaguacgagaggaacaguucauucgga
uaauugguuuuugcggcugucugaucaggcauugccgcgaagcuaccauc
cgcuggauuauggcugaacgccucuaagucagaauccaugcuagaacgcg
gugauuucuuugcuccacacaauauagauggauacgaauaaggcguccuu
guggcgucgcugaaccauagcaggcuagcaacggugcacuuggcggaaag
gccuugggugcuugcuggcgaauugcaaugucauuuugcguggggauaaa
ucauuuguauacgacuuagauguacaacgggguauuguaagcaguagagu
agccuuguuguuacgaucugcugagauuaagccuuuguugucugauuugu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4v88 The structure of the eukaryotic ribosome at 3.0 angstrom resolution.
• Resolution: 3.0 Å
• Binding residue (original residue number in PDB): R97 Y100 R102 P104 N109 R111 K112 R113 K114 G116 H117 N119 R122 K124 K125
• Binding residue (residue number reindexed from 1): R21 Y24 R26 P28 N33 R35 K36 R37 K38 G40 H41 N43 R46 K48 K49

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:0006412 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

External links

• PDB: RCSB:4v88, PDBe:4v88, PDBj:4v88
• PDBsum: 4v88
• PubMed: 22096102
• UniProt: P0CH08|RL40A_YEAST Ubiquitin-ribosomal protein eL40A fusion protein (Gene Name=RPL40A)