Structure of PDB 6tb3 Chain AR Binding Site BS01

Receptor Information

>6tb3 Chain AR (length=148) Species: 559292 (Saccharomyces cerevisiae S288C)

PSRFTKTRKHRGHVSAGKGRIGKHRKHPGGRGMAGGQHHHRINMDKYHPG
YFGKVGMRYFHKQQAHFWKPVLNLDKLWTLIPEDKRDQYLKSASKETAPV
IDTLAAGYGKILGKGRIPNVPVIVKARFVSKLAEEKIRAAGGVVELIA

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): P2 S3 R4 T6 K7 T8 R9 K10 H11 R12 G13 H14 V15 S16 A17 G18 K19 G20 R21 I22 G23 H25 R26 K27 H28 P29 G30 G31 R32 G33 M34 G36 H39 H40 H41 R42 I43 N44 Y52 F53 G54 K55 V56 G57 M58 R59 Y60 F61 H62 K63 Q64 H67 V72 N74 K77 K111 L113 G114 K115 R117 S131 K132 L133
• Binding residue (residue number reindexed from 1): P1 S2 R3 T5 K6 T7 R8 K9 H10 R11 G12 H13 V14 S15 A16 G17 K18 G19 R20 I21 G22 H24 R25 K26 H27 P28 G29 G30 R31 G32 M33 G35 H38 H39 H40 R41 I42 N43 Y51 F52 G53 K54 V55 G56 M57 R58 Y59 F60 H61 K62 Q63 H66 V71 N73 K76 K110 L112 G113 K114 R116 S130 K131 L132

Gene Ontology

Molecular Function

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

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006412 translation

Cellular Component

• GO:0005634 nucleus
• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0015934 large ribosomal subunit
• GO:0022625 cytosolic large ribosomal subunit
• GO:0043232 intracellular non-membrane-bounded organelle
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:6tb3, PDBe:6tb3, PDBj:6tb3
• PDBsum: 6tb3
• PubMed: 32299921
• UniProt: P02406|RL28_YEAST Large ribosomal subunit protein uL15 (Gene Name=RPL28)