Structure of PDB 6r86 Chain M Binding Site BS02

Receptor Information

>6r86 Chain M (length=169) Species: 4932 (Saccharomyces cerevisiae)

QNPMRDLKIEKLVLNISVGESGDRLTRASKVLEQLSGQTPVQSKARYTVR
TFGIRRNEKIAVHVTVRGPKAEEILERGLKVKEYQLRDRNFSATGNFGFG
IDEHIDLGIKYDPSIGIFGMDFYVVMNRPGARVTRRKRCKGTVGNSHKTT
KEDTVSWFKQKYDADVLDK

Ligand information

>6r86 Chain 1 (length=3260)

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
agugagagccuuggucagacgcagcguuguagacggccuuggucuugcua
caauuaacgaucaacuuagaacugguacggacaaggggaaucugacuguc
uaauuaaaacauagcauugcgauggucagaaagugauguugacgcaaugu
gauuucugcccagugcucugaaugucaaagugaagaaauucaaccaagcg
cggguaaacggcgggaguaacuaugacucucuuaagguagccaaaugccu
cgucaucuaauuagugacgcgcaugaauggauuaacgagauucccacugu
cccuaucuacuaucuagcgaaaccacagccaagggaacgggcuuggcaga
aucagcggggaaagaagacccuguugagcuugacucuaguuugacauugu
gaagagacauagaggguguagaauaagugggagcuucggcgccagugaaa
uaccacuaccuuuauaguuucuuuacuuauucaaugaagcggagcuggaa
uucauuuuccacguucuagcauucaaggucccauucggggcugauccggg
uugaagacauugucagguggggaguuuggcuggggcggcacaucuguuaa
acgauaacgcagauguccuaaggggggcucauggagaacagaaaucucca
guagaacaaaaggguaaaagcccccuugauuuugauuuucagugugaaua
caaaccaugaaaguguggccuaucgauccuuuagucccucggaauuugag
gcuagaggugccagaaaaguuaccacagggauaacuggcuuguggcaguc
aagcguucauagcgacauugcuuuuugauucuucgaugucggcucuuccu
aucauaccgaagcagaauucgguaagcguuggauuguucacccacuaaua
gggaacgugagcuggguuuagaccgucgugagacagguuaguuuuacccu
acugaugaauguuaccgcaauaguaauugaacuuaguacgagaggaacag
uucauucggauaauugguuuuugcggcugucugaucaggcauugccgcga
agcuaccauccgcuggauuauggcugaacgccucuaagucagaauccaug
cuagaacgcggugauuucuuugcuccacacaauauagauggauacgaaua
aggcguccuuguggcgucgcugaaccauagcaggcuagcaacggugcacu
uggcggaaaggccuugggugcuugcuggcgaauugcaaugucauuuugcg
uggggauaaaucauuuguauacgacuuagauguacaacgggguauuguaa
gcaguagaguagccuuguuguuacgaucugcugagauuaagccuuuguug
ucugauuugu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6r86 Structure and function of Vms1 and Arb1 in RQC and mitochondrial proteome homeostasis.
• Resolution: 3.4 Å
• Binding residue (original residue number in PDB): N20 S22 S48 A50 R51 Y52 F57 H68 R94 N95 S97 T99 G103 F104 G105 G124 D126 Y128 K142
• Binding residue (residue number reindexed from 1): N15 S17 S43 A45 R46 Y47 F52 H63 R89 N90 S92 T94 G98 F99 G100 G119 D121 Y123 K137

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0019843 rRNA binding

Biological Process

• GO:0000027 ribosomal large subunit assembly
• GO:0002181 cytoplasmic translation
• GO:0006412 translation

Cellular Component

• GO:0005634 nucleus
• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0022625 cytosolic large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:6r86, PDBe:6r86, PDBj:6r86
• PDBsum: 6r86
• PubMed: 31189955
• UniProt: Q3E757|RL11B_YEAST Large ribosomal subunit protein uL5B (Gene Name=RPL11B)