Structure of PDB 6q8y Chain AT Binding Site BS01

Receptor Information

>6q8y Chain AT (length=91) Species: 4932 (Saccharomyces cerevisiae)

AKRTKKVGITGKYGVRYGSSLRRQVKKLEIQQHARYDCSFCGKKTVKRGA
AGIWTCSCCKKTVAGGAYTVSTAAAATVRSTIRRLREMVEA

Ligand information

>6q8y Chain BQ (length=3161)

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
ggauggcgcucaagcguguuaccuauacucuaccgucaggguugauauga
ugcccugacgaguaggcaggcguggaggucagugacgaagccuagaccgu
aaggucgggucgaacggccucuagugcagaucuuggugguaguagcaaau
auucaaaugagaacuuugaagacugaaguggggaaagguuccacgucaac
agcaguuggacguggguuagucgauccuaagagauggggaagcuccguuu
caaaggccugauuuuaugcaggccaccaucgaaagggaauccgguuaaga
uuccggaaccuggauauggauucuucacgguaacguaacugaauguggag
acgucggcgcgagcccugggaggaguuaucuuuucuucuuaacagcuuau
caccccggaauugguuuauccggagauggggucuuauggcuggaagaggc
cagcaccuuugcuggcuccggugcgcuugugacggcccgugaaaauccac
aggaaggaauaguuuucaugccaggucguacugauaaccgcagcaggucu
ccaaggugaacagccucuaguugauagaauaauguagauaagggaagucg
gcaaaauagauccguaacuucgggauaaggauuggcucuaagggucgggu
acgaucaacuuagaacugguacggacaaggggaaucugacugucuaauua
aaacauagcauugcgauggucagaaagugauguugacgcaaugugauuuc
ugcccagugcucugaaugucaaagugaagaaauucaaccaagcgcgggua
aacggcgggaguaacuaugacucucuuaagguagccaaaugccucgucau
cuaauuagugacgcgcaugaauggauuaacgagauucccacugucccuau
cuacuaucuagcgaaaccacagccaagggaacgggcuuggcagaaucagc
ggggaaagaagacccuguugagcuugacucuaguuugacauugugaagag
acauagaggccuuuauaguuucuuuacuuauucaaugaagcggagcugga
auucauuuuccacguucuagcauucaaggucccauucggggcugauccgg
guugaagacauugucagguggggaguuuggcuggggcggcacaucuguua
aacgauaacgcagauguccuaaggggggcucauggagaacagaaaucucc
aguagaacaaaaggguaaaagcccccuugauuuugauuuucagugugaau
acaaaccaugaaaguguggccuaucgauccuuuagucccucggaauuuga
ggcuagaggugccagaaaaguuaccacagggauaacuggcuuguggcagu
caagcguucauagcgacauugcuuuuugauucuucgaugucggcucuucc
uaucauaccgaagcagaauucgguaagcguuggauuguucacccacuaau
agggaacgugagcuggguuuagaccgucgugagacagguuaguuuuaccc
uacugaugaauguuaccgcaauaguaauugaacuuaguacgagaggaaca
guucauucggauaauugguuuuugcggcugucugaucaggcauugccgcg
aagcuaccauccgcuggauuauggcugaacgccucuaagucagaauccau
gcuagaacgcggugauuucuuugcuccacacaauauagauggauacgaau
aaggcguccuuguggcgucgcugaaccauagcaggcuagcaacggugcac
uuggcggaaaggccuugggugcuugcuggcgaauugcaaugucauuuugc
guggggauaaaucauuuguauacgacuuagauguacaacgggguauugua
agcaguagaguagccuuguuguuacgaucugcugagauuaagccuuuguu
gucugauuugu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6q8y Structure of the 80S ribosome-Xrn1 nuclease complex.
• Resolution: 3.1 Å
• Binding residue (original residue number in PDB): A2 K3 R4 T5 K6 K7 V8 G9 I10 G12 K13 Y14 G15 V16 R17 Y18 G19 S20 S21 R23 Q33 H34 C42 R49 A51 Y69
• Binding residue (residue number reindexed from 1): A1 K2 R3 T4 K5 K6 V7 G8 I9 G11 K12 Y13 G14 V15 R16 Y17 G18 S19 S20 R22 Q32 H33 C41 R48 A50 Y68

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome
• GO:0046872 metal ion binding
• GO:0070180 large ribosomal subunit rRNA binding

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006412 translation

Cellular Component

• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0022625 cytosolic large ribosomal subunit
• GO:0044391 ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:6q8y, PDBe:6q8y, PDBj:6q8y
• PDBsum: 6q8y
• PubMed: 30911188
• UniProt: P0CX25|RL43A_YEAST Large ribosomal subunit protein eL43A (Gene Name=RPL43A)