Structure of PDB 6t83 Chain J Binding Site BS01

Receptor Information

>6t83 Chain J (length=124) Species: 4932 (Saccharomyces cerevisiae)

AKQSLDVSSDRRKARKAYFTAPSSQRRVLLSAPLSKELRAQYGIKALPIR
RDDEVLVVRGSKKGQEGKISSVYRLKFAVQVDKVTKEKVNGASVPINLHP
SKLVITKLHLDKDRKALIQRKGGK

Ligand information

>6t83 Chain Aa (length=3127)

uugaccucaaaucagguaggaguacccgcugaacuuaagcauaucaauaa
gcggaggaaaagaaaccaaccgggauugccuuaguaacggcgagugaagc
ggcaaaagcucaaauuugaaaucugguaccuucggugcccgaguuguaau
uuggagagggcaacuuuggggccguuccuugucuauguuccuuggaacag
gacgucauagagggugagaaucccguguggcgaggagugcgguucuuugu
aaagugccuucgaagagucgaguuguuugggaaugcagcucuaagugggu
gguaaauuccaucuaaagcuaaauauuggcgagagaccgauagcgaacaa
guacagugauggaaagaugaaaagaacuuugaaaagagagugaaaaagua
cgugaaauuguugaaagggaagggcauuugaucagacaggccagcaucag
uuuugguggcaggauaaauccauaggaauguagcuugccucgguaaguau
uauagccugugggaauacugccagcugggacugaggacugcgacguaagu
caaggaugcuggcauaaugguuauaugccgcccgucuugaaacacggacc
aaggagucuaacgucuaugcgaguguuuggguguaaaacccauacgcgua
augaaagugaacguagguuggggccucgcaagaggugcacaaucgaccga
uccugaugucuucggauggauuugaguaagagcauagcuguugggacccg
aaagauggugaacuaugccugaauagggugaagccagaggaaacucuggu
ggaggcucguagcgguucugacgugcaaaucgaucgucgaauuuggguau
aggggcgaaagacuaaucgaaccaucuaguagcugguuccugccgaaguu
ucccucaggauagcagaagcucguaucaguuuuaugagguaaagcgaaug
auuagagguuccggggucgaaaugaccuugaccuauucucaaacuuuaaa
uauguaagaaguccuuguuacuuaauugaacguggacauuugaaugaaga
gcuuuuagugggccauuuuugguaagcagaacuggcgaugcgggaugaac
cgaacguagaguuaaggugccggaauacacgcucaucagacaccacaaaa
gguguuaguucaucuagacagccggacgguggccauggaagucggaaucc
gcuaaggaguguguaacaacucaccggccgaaugaacuagcccugaaaau
ggauggcgcucaagcguguuaccuauacucuaccgucaggguuaugaugc
ccugacgaguaggcaggcguggaggucagugacgaagccuagaccguaag
gucgggucgaacggccucuagugcagaucuuggugguaguagcaaauauu
caaaugagaacuuugaagacugaaguggggaaagguuccacgucaacagc
aguuggacguggguuagucgauccuaagagauggggaagcuccguuucaa
aggccugcaggccaccaucgaaagggaauccgguuaagauuccggaaccu
ggauauggauucuucacgguaacguaacugaauguggagacgucggcgcg
agcccugggaggaguuaucuuuucuucuuaacagcuuaucaccccggaau
ugguuuauccggagauggggucuuauggcuggaagaggccagcaccuuug
cuggcuccggugcgcuugugacggcccgugaaaauccacaggaaggaaua
guuuucaugccaggucguacugauaaccgcagcaggucuccaaggugaac
agccucuaguugauagaauaauguagauaagggaagucggcaaaauagau
ccguaacuucgggauaaggauuggcucuaagggucggacgaucaacuuag
aacugguacggacaaggggaaucugacugucuaauuaaaacauagcauug
cgauggucagaaagugauguugacgcaaugugauuucugcccagugcucu
gaaugucaaagugaagaaauucaaccaagcgcggguaaacggcgggagua
acuaugacucucuuaagguagccaaaugccucgucaucuaauuagugacg
cgcaugaauggauuaacgagauucccacugucccuaucuacuaucuagcg
aaaccacagccaagggaacgggcuuggcagaaucagcggggaaagaagac
ccuguugagcuugacucuaguuugacauugugaagaguuucuuuacuuau
ucaaugaagcggagcuggaauucauuuuccacguucuagcauucaagguc
ccauucggggcugauccggguugaagacauugucagguggggaguuuggc
uggggcggcacaucuguuaaacgauaacgcagauguccuaaggggggcuc
auggagaacagaaaucuccaguagaacaaaaggguaaaagcccccuugau
uuugauuuucagugugaauacaaaccaugaaaguguggccuaucgauccu
uuagucccucggaauuugaggcuagaggugccagaaaaguuaccacaggg
auaacuggcuuguggcagucaagcguucauagcgacauugcuuuuugauu
cuucgaugucggcucuuccuaucauaccgaagcagaauucgguaagcguu
ggauuguucacccacuaauagggaacgugagcuggguuuagaccgucgug
agacagguuaguuuuacccuacugaugaauguuaccgcaauaguaauuga
acuuaguacgagaggaacaguucauucggauaauugguuuuugcggcugu
cugaucaggcauugccgcgaagcuaccauccgcuggauuauggcugaacg
ccucuaagucagaauccaugcuagaacgcggugauuuugcuccacacaau
auagauggauacgaauaaggcguccuuguggcgucgcugaaccauagcag
gcuagcaacggugcacuuggcggaaaggccuugggugcuugcuggcgaau
ugcaaugucauuuugcguggggauaaaucauuuguauacgacuuagaugu
acaacgggguauuguaagcaguagaguagccuuguuguuacgaucugcug
agauuaagccuuuguugucugauuugu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6t83 Molecular mechanism of translational stalling by inhibitory codon combinations and poly(A) tracts.
• Resolution: 4.0 Å
• Binding residue (original residue number in PDB): A2 K3 S9 S10 R12 Y19 L30 S32 P34 K37 R40 K46 A47 V59 R60 G61 S62 K87 K89 V90 V95 N98 H100 S102 K103 R121 K122 K125
• Binding residue (residue number reindexed from 1): A1 K2 S8 S9 R11 Y18 L29 S31 P33 K36 R39 K45 A46 V58 R59 G60 S61 K86 K88 V89 V94 N97 H99 S101 K102 R120 K121 K124

Gene Ontology

Molecular Function

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

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006412 translation
• GO:0042273 ribosomal large subunit biogenesis

Cellular Component

• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0015934 large ribosomal subunit
• GO:0022625 cytosolic large ribosomal subunit
• GO:0032991 protein-containing complex
• GO:0043232 intracellular non-membrane-bounded organelle
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:6t83, PDBe:6t83, PDBj:6t83
• PDBsum: 6t83
• PubMed: 31858614
• UniProt: P05743|RL26A_YEAST Large ribosomal subunit protein uL24A (Gene Name=RPL26A)