Structure of PDB 6tb3 Chain AX Binding Site BS01

Receptor Information

>6tb3 Chain AX (length=183) Species: 559292 (Saccharomyces cerevisiae S288C)

ARYGATSTNPAKSASARGSYLRVSFKNTRETAQAINGWELTKAQKYLEQV
LDHQRAIPFRRFNSSIGRTAQGKEFGVTKARWPAKSVKFVQGLLQNAAAN
AEAKGLDATKLYVSHIQVNQAPKQRRRTYRAHGRINKYESSPSHIELVVT
EKEEAVAKAAEKKVVRLTSRQRGRIAAQKRIAA

Ligand information

>6tb3 Chain BQ (length=3223)

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
aguuugacauugugaagagacauagaggguguagaauaagugggagcuuc
ggcgccagugaaauaccacuaccuuuauaguuucuuuacuuauucaauga
agcggagcuggaauucauuuuccacguucuagcauucaaggucccauucg
gggcugauccggguugaagacauugucagguggggaguuuggcuggggcg
gcacaucuguuaaacgauaacgcagauguccuaaggggggcucauggaga
acagaaaucuccaguagaacaaaaggguaaaagcccccuugauuuugauu
uucagugugaauacaaaccaugaaaguguggccuaucgauccuuuagucc
cucggaauuugaggcuagaggugccagaaaaguuaccacagggauaacug
gcuuguggcagucaagcguucauagcgacauugcuuuuugauucuucgau
gucggcucuuccuaucauaccgaagcagaauucgguaagcguuggauugu
ucacccacuaauagggaacgugagcuggguuuagaccgucgugagacagg
uuaguuuuacccuacugaugaauguuaccgcaauaguaauugaacuuagu
acgagaggaacaguucauucggauaauugguuuuugcggcugucugauca
ggcauugccgcgaagcuaccauccgcuggauuauggcugaacgccucuaa
gucagaauccaugcuagaacgcggugauuucuuugcuccacacaauauag
auggauacgaauaaggcguccuuguggcgucgcugaaccauagcaggcua
gcaacggugcacuuggcggaaaggccuugggugcuugcuggcgaauugca
augucauuuugcguggggauaaaucauuuguauacgacuuagauguacaa
cgggguauuguaagcaguagaguagccuuguuguuacgaucugcugagau
uaagccuuuguugucugauuugu

........................<<<<<<.....<<....>>......>
>>>>.>...<.....<<....>>..<<<<<......<<.....>>.....
>>>>>..<<<...<.......<<.<<<<<<...>>>>>>.>>.......>
.....<<<<<<.<<<<<<<<<<<<<<<<<<<<<<....<<<<......>>
>>.(.......<<<......)>>>..>.>>>>>>>>..>>>>>>>>....
>>>>>>>>>>>........<<<<<<<........>>>>>>>.....<<<<
<..((((((>>>>>..>>>....>..........................
...<<....>>...............<<<<....>>>>............
......................<<<<<.<<<<<.................
........<<<<<<<.<<<<<<<<<<<<<<<.....<<<<<<<<<.....
.<<<<<<....>>>>>>.......>>>>>>>.>.>.>>>>>.>>>>>>>>
>>........<<<....>>>.....>>>>>>>.....>>>>>.>>>>>..
<<<<........>>>><<<<<<....<<<<<<.<<<<<<..<<<...<<<
<.....>>>>...>>>...<<....>>.......<<<<<..<<<<<....
>>>>>...>>>>>.<<<<<<<<...<<....>>...>>>.>>>.>>....
>>>>>>.>>>>>>..<<.<..<<<<<<<.....<<<<<<<<<..<<<...
.<<<<<<<....>>>>>>>.....>>>...<<<..<<.<<........>>
>>.>>>....>>>>>>>>>...<<.......>>......>>>>>>...>.
.>.>>..<<<<<<....<.<<<....>>>.><<<<<<<<<<....<<.<<
<<<<<.....<<<....<<<....<<<<...<<<<<<.....>>>>>>.>
>>>....>>>..>.>>.....>>>>>...<<<<.<<<<.<......>>>>
>.>>>>.....>>>>..>>>>>>>>.>>..<<<<.<<<<<.....>>>>>
.>>>>....<<<......>>>...<<<<<<<..<<<<(((.....<<<<<
<.....<<..........<<<.<<<<<<<<<<.......<<<<<.<<...
.<<.........>>....>>.........<<......>>...>>>>>...
>>>>>>>>>>>>>..........))).>>...>>>>>>.>>>>..>>>>>
>><<<<<<<<<.........>>>>>>>>>....>>>>>><.<<<<<<<<.
<<......<<<<.<<<<....>>>>>>>>...>>>>>>>>>>..>.....
>>>>>><<.....<<.....<<<<<<.......>>>>>><<<<.....<<
<<<.<<...<<<<<<...<<.....>>.>>>>>>....((<<<<<<...<
<....<<<....>>>........<<<<<.<.....>..>>>>>....>>.
...>>...<<<<<........>>>>>))<<<<.<<<<<.<.....<<<..
..>>>.......<<<<<<...<<<<.<<<<<<<<<<<<<<<<<<..[[[.
.>>>>>><...<<<<<....<<<<<<....<<<.....>>>....>>>>>
>.....>>>>>....><<<<<<<......>>>>>>>>>>>.>.>>>>>>>
.>>>>.........>>>>>>..........>.>..>>>>>>>>>>>>..>
>.....<<......>>>>>>>.<<<<.....>>>>..>>>>..<<<<...
..<<<<<<<.<<.........<.....<<<<<....<....>.....>>>
>><<.<<<<<<<<<<<....>>>>>..>>>>>>.>>............<<
<<<<<<<..<<<.........>>>..<<<<<<<....<<<<.....>>>>
......>>>>>>>...<<..<<<..<<<<<<.....<<.....<<<<...
.>>>>.....>>..>>>>..>>>>><<<<<<.......>>>>>>......
..<...........<<<<<.......>>>>>.....>.....>>....>>
.>>>>>>>..>..>>.>>>>>>>..>>>>>>....>>....<<<<<....
....>>>>>....<<<<<..<<<.<<......<<<<.<<<<<<..<<<<<
.<<<<<<<<..<<<<<<<<<<.<<.<<.<..........<.<<.......
...............>>.>..>>>.>>..>>>>>>>>>>...<<<<<...
..<<<<..<<<<<......>>>>>...............<<<<<<....>
>>>>>..>>>>..>>>>>.....>>>>>>>>..>>>>>...<<<.....>
>>..<<<<<<...........>>>>>>..<<...<<<<<<<...<<<<<<
.......>>>>>>.....<<...(((>>....>>>>>>>...<<<.<<<<
<.......>>>>.>>>>.<<<....>>>.>>)))......<<<<<<<..<
<<<.))))))>>>>>>>>>>>.........>>>>..>>>>>>.......<
<.<.<.<<<<<<...<<.......>>...>>>>>>...>>..>>......
.<<<<<.<<<<<<..<.<<<<<<<......>>>>>>>...>.<<<.....
....>>>.....>>>>>..>...>>>.>>....<<<<<<<....>>>.>>
>>....>>..>>>.>>>>>....<<<<<<<<..<<<<.<.<<<<<<....
...........>>>>>>.><<<<<...<<<<....<<<<<<<<<<]]].>
>>>>..>>>>>...>>>>..>>>>>.<<<<...<<<<<...........>
>>>>...>>>>.>>>>....>>>>>>>>.......<<<<<<.<<<.<<..
..<<..........<<<<<<.....>>>>>>......>>.......<<<<
<<...<<<<<.<..<<<......>>>..>.>>>>>.>>>>>>........
.....>>.>>>.>>>>>>..<<<<<.<.............>.....<<<<
<<<<<.<<<....<<<<.<..<<<<<......>>>>>..>>>>>...>>>
....>>>>.>>>>>..>>>>>..

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6tb3 The Ccr4-Not complex monitors the translating ribosome for codon optimality.
• Resolution: 2.8 Å
• Binding residue (original residue number in PDB): R3 Y4 S16 R18 Y21 R23 S25 F26 K27 R30 Q34 N37 K43 Q55 R56 R62 F63 S65 S66 I67 G68 R69 A71 Q72 K74 E75 K80 R82 W83 P84 K86 N97 A100 N101 H116 Q118 V119 K124 R127 Y130 R131 A132 H133 G134 R135 I136 N137 K138 Y139 E140 S141 R167 T169 S170 R171 Q172 R173 G174 R175 A178 R181 I182
• Binding residue (residue number reindexed from 1): R2 Y3 S15 R17 Y20 R22 S24 F25 K26 R29 Q33 N36 K42 Q54 R55 R61 F62 S64 S65 I66 G67 R68 A70 Q71 K73 E74 K79 R81 W82 P83 K85 N96 A99 N100 H115 Q117 V118 K123 R126 Y129 R130 A131 H132 G133 R134 I135 N136 K137 Y138 E139 S140 R166 T168 S169 R170 Q171 R172 G173 R174 A177 R180 I181

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome

Biological Process

• GO:0000448 cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
• GO:0002181 cytoplasmic translation
• GO:0006412 translation

Cellular Component

• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0015934 large ribosomal subunit
• GO:0022625 cytosolic large ribosomal subunit
• GO:0030687 preribosome, large subunit precursor
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:6tb3, PDBe:6tb3, PDBj:6tb3
• PDBsum: 6tb3
• PubMed: 32299921
• UniProt: P05740|RL17A_YEAST Large ribosomal subunit protein uL22A (Gene Name=RPL17A)