Structure of PDB 6q8y Chain BC Binding Site BS01

Receptor Information

>6q8y Chain BC (length=109) Species: 4932 (Saccharomyces cerevisiae)

LKDVVTREYTINLHKRLHGVSFKKRAPRAVKEIKKFAKLHMGTDDVRLAP
ELNQAIWKRGVKGVEYRLRLRISRKRNEEEDAKNPLFSYVEPVLVASAKG
LQTVVVEED

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): R10 T13 N15 H17 K18 R19 H21 G22 V23 S24 F25 K26 R31 K34 H43 P53 N56 Q57 W60 R62 K65 Y69 R70 K102 L104 Q105 T106 V108
• Binding residue (residue number reindexed from 1): R7 T10 N12 H14 K15 R16 H18 G19 V20 S21 F22 K23 R28 K31 H40 P50 N53 Q54 W57 R59 K62 Y66 R67 K99 L101 Q102 T103 V105

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006412 translation
• GO:0006450 regulation of translational fidelity

Cellular Component

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

External links

• PDB: RCSB:6q8y, PDBe:6q8y, PDBj:6q8y
• PDBsum: 6q8y
• PubMed: 30911188
• UniProt: P0C2H8|RL31A_YEAST Large ribosomal subunit protein eL31A (Gene Name=RPL31A)