Structure of PDB 3j78 Chain 90 Binding Site BS01

Receptor Information

>3j78 Chain 90 (length=52) Species: 4932 (Saccharomyces cerevisiae)

IIEPSLKALASKYNCDKSVCRKCYARLPPRATNCRKRKCGHTNQLRPKKK
LK

Ligand information

>3j78 Chain 2S (length=3302)

uugaccucaaaucagguaggaguacccgcugaacuuaagcauaucaauaa
gcggaggaaaagaaaccaaccgggauugccuuaguaacggcgagugaagc
ggcaaaagcucaaauuugaaaucugguaccuucggugcccgaguuguaau
uuggagagggcaacuuuggggccguuccuugucuauguuccuuggaacag
gacgucauagagggugagaaucccguguggcgaggagugcgguucuuugu
aaagugccuucgaagagucgaguuguuugggaaugcagcucuaagugggu
gguaaauuccaucuaaagcuaaauauuggcgagagaccgauagcgaacaa
guacagugauggaaagaugaaaagaacuuugaaaagagagugaaaaagua
cgugaaauuguugaaagggaagggcauuugaucagacaugguguuuugua
uuucacuggccagcaucaguuuugguggcaggauaaauccauaggaaugu
agcuugccucgguaaguauuauagccugugggaauacugccagcugggac
ugaggacugcgacguaagucaaggaugcuggcauaaugguuauaugccgc
ccgucuugaaacacggaccaaggagucuaacgucuaugcgaguguuuggg
uguaaaacccauacgcguaaugaaagugaacguagguuggggccucgcaa
gaggugcacaaucgaccgauccugaugucuucggauggauuugaguaaga
gcauagcuguugggacccgaaagauggugaacuaugccugaauaggguga
agccagaggaaacucugguggaggcucguagcgguucugacgugcaaauc
gaucgucgaauuuggguauaggggcgaaagacuaaucgaaccaucuagua
gcugguuccugccgaaguuucccucaggauagcagaagcucguaucaguu
uuaugagguaaagcgaaugauuagagguuccggggucgaaaugaccuuga
ccuauucucaaacuuuaaauauguaagaaguccuuguuacuuaauugaac
guggacauuugaaugaagagcuuuuagugggccauuuuugguaagcagaa
cuggcgaugcgggaugaaccgaacguagaguuaaggugccggaauacacg
cucaucagacaccacaaaagguguuaguucaucuagacagccggacggug
gccauggaagucggaauccgcuaaggaguguguaacaacucaccggccga
augaacuagcccugaaaauggauggcgcucaagcguguuaccuauacucu
accgucaggguugauaugaugcccugacgaguaggcaggcguggagguca
gugacgaagccuagaccguaaggucgggucgaacggccucuagugcagau
cuuggugguaguagcaaauauucaaaugagaacuuugaagacugaagugg
ggaaagguuccacgucaacagcaguuggacguggguuagucgauccuaag
agauggggaagcuccguuucaaaggccugauuuuaugcaggccaccaucg
aaagggaauccgguuaagauuccggaaccuggauauggauucuucacggu
aacguaacugaauguggagacgucggcgcgagcccugggaggaguuaucu
uuucuucuuaacagcuuaucaccccggaauugguuuauccggagaugggg
ucuuauggcuggaagaggccagcaccuuugcuggcuccggugcgcuugug
acggcccgugaaaauccacaggaaggaauaguuuucaugccaggucguac
ugauaaccgcagcaggucuccaaggugaacagccucuaguugauagaaua
auguagauaagggaagucggcaaaauagauccguaacuucgggauaagga
uuggcucuaagggucggguagugagggccuuggucagacgcagcgggccu
uguuguagacggccuugguaggucucuuguagaccgucgcuugcuacaac
gaucaacuuagaacugguacggacaaggggaaucugacugucuaauuaaa
acauagcauugcgauggucagaaagugauguugacgcaaugugauuucug
cccagugcucugaaugucaaagugaagaaauucaaccaagcgcggguaaa
cggcgggaguaacuaugacucucuuaagguagccaaaugccucgucaucu
aauuagugacgcgcaugaauggauuaacgagauucccacugucccuaucu
acuaucuagcgaaaccacagccaagggaacgggcuuggcagaaucagcgg
ggaaagaagacccuguugagcuugacucuaguuugacauugugaagagac
auagaggguguagaauaagugggagcuucggcgccagugaaauaccacua
ccuuuauaguuucuuuacuuauucaaugaagcggagcuggaauucauuuu
ccacguucuagcauucaaggucccauucggggcugauccggguugaagac
auugucagguggggaguuuggcuggggcggcacaucuguuaaacgauaac
gcagauguccuaaggggggcucauggagaacagaaaucuccaguagaaca
aaaggguaaaagcccccuugauuuugauuuucagugugaauacaaaccau
gaaaguguggccuaucgauccuuuagucccucggaauuugaggcuagagg
ugccagaaaaguuaccacagggauaacuggcuuguggcagucaagcguuc
auagcgacauugcuuuuugauucuucgaugucggcucuuccuaucauacc
gaagcagaauucgguaagcguuggauuguucacccacuaauagggaacgu
gagcuggguuuagaccgucgugagacagguuaguuuuacccuacugauga
auguuaccgcaauaguaauugaacuuaguacgagaggaacaguucauucg
gauaauugguuuuugcggcugucugaucaggcauugccgcgaagcuacca
uccgcuggauuauggcugaacgccucuaagucagaauccaugcuagaacg
cggugauuucuuugcuccacacaauauagauggauacgaauaaggcgucc
uuguggcgucgcugaaccauagcaggcuagcaacggugcacuuggcggaa
aggccuugggugcuugcuggcgaauugcaaugucauuuugcguggggaua
aaucauuuguauacgacuuagauguacaacgggguauuguaagcaguaga
guagccuuguuguuacgaucugcugagauuaagccuuuguugucugauuu
gu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3j78 Structures of Yeast 80S Ribosome-tRNA Complexes in the Rotated and Nonrotated Conformations.
• Resolution: 6.3 Å
• Binding residue (original residue number in PDB): R97 Y100 R102 N109 R111 K112 R113 K114 G116 H117 N119 R122 K125
• Binding residue (residue number reindexed from 1): R21 Y24 R26 N33 R35 K36 R37 K38 G40 H41 N43 R46 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:3j78, PDBe:3j78, PDBj:3j78
• PDBsum: 3j78
• PubMed: 25043550
• UniProt: P0CH08|RL40A_YEAST Ubiquitin-ribosomal protein eL40A fusion protein (Gene Name=RPL40A)