Structure of PDB 6tnu Chain AG Binding Site BS01

Receptor Information

>6tnu Chain AG (length=169) Species: 4932 (Saccharomyces cerevisiae)

QNPMRDLKIEKLVLNISVGESGDRLTRASKVLEQLSGQTPVQSKARYTVR
TFGIRRNEKIAVHVTVRGPKAEEILERGLKVKEYQLRDRNFSATGNFGFG
IDEHIDLGIKYDPSIGIFGMDFYVVMNRPGARVTRRKRCKGTVGNSHKTT
KEDTVSWFKQKYDADVLDK

Ligand information

>6tnu Chain BQ (length=3184)

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
uuggcucuaagggucggguacgaucaacuuagaacugguacggacaaggg
gaaucugacugucuaauuaaaacauagcauugcgauggucagaaagugau
guugacgcaaugugauuucugcccagugcucugaaugucaaagugaagaa
auucaaccaagcgcggguaaacggcgggaguaacuaugacucucuuaagg
uagccaaaugccucgucaucuaauuagugacgcgcaugaauggauuaacg
agauucccacugucccuaucuacuaucuagcgaaaccacagccaagggaa
cgggcuuggcagaaucagcggggaaagaagacccuguugagcuugacucu
aguuugacauugugaagagacauagagggcuaccuuuauaguuucuuuac
uuauucaaugaagcggagcuggaauucauuuuccacguucuagcauucaa
ggucccauucggggcugauccggguugaagacauugucagguggggaguu
uggcuggggcggcacaucuguuaaacgauaacgcagauguccuaaggggg
gcucauggagaacagaaaucuccaguagaacaaaaggguaaaagcccccu
ugauuuugauuuucagugugaauacaaaccaugaaaguguggccuaucga
uccuuuagucccucggaauuugaggcuagaggugccagaaaaguuaccac
agggauaacuggcuuguggcagucaagcguucauagcgacauugcuuuuu
gauucuucgaugucggcucuuccuaucauaccgaagcagaauucgguaag
cguuggauuguucacccacuaauagggaacgugagcuggguuuagaccgu
cgugagacagguuaguuuuacccuacugaugaauguuaccgcaauaguaa
uugaacuuaguacgagaggaacaguucauucggauaauugguuuuugcgg
cugucugaucaggcauugccgcgaagcuaccauccgcuggauuauggcug
aacgccucuaagucagaauccaugcuagaacgcggugauuucuuugcucc
acacaauauagauggauacgaauaaggcguccuuguggcgucgcugaacc
auagcaggcuagcaacggugcacuuggcggaaaggccuugggugcuugcu
ggcgaauugcaaugucauuuugcguggggauaaaucauuuguauacgacu
uagauguacaacgggguauuguaagcaguagaguagccuuguuguuacga
ucugcugagauuaagccuuuguugucugauuugu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6tnu The Ccr4-Not complex monitors the translating ribosome for codon optimality.
• Resolution: 3.1 Å
• Binding residue (original residue number in PDB): K16 N20 S22 G24 R51 Y52 F57 H68 R94 N95 S97 A98 N101 F104 G105 D107 G124 M125 Y128 R140 K142
• Binding residue (residue number reindexed from 1): K11 N15 S17 G19 R46 Y47 F52 H63 R89 N90 S92 A93 N96 F99 G100 D102 G119 M120 Y123 R135 K137

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0019843 rRNA binding

Biological Process

• GO:0000027 ribosomal large subunit assembly
• GO:0002181 cytoplasmic translation
• GO:0006412 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:6tnu, PDBe:6tnu, PDBj:6tnu
• PDBsum: 6tnu
• PubMed: 32299921
• UniProt: P0C0W9|RL11A_YEAST Large ribosomal subunit protein uL5A (Gene Name=RPL11A)