Structure of PDB 6r86 Chain J Binding Site BS02

Receptor Information

>6r86 Chain J (length=222) Species: 4932 (Saccharomyces cerevisiae)

AEQVAAERAARKAANKEKRAIILERNAAYQKEYETAERNIIQAKRDAKAA
GSYYVEAQHKLVFVVRIKGINKIPPKPRKVLQLLRLTRINSGTFVKVTKA
TLELLKLIEPYVAYGYPSYSTIRQLVYKRGFGKINKQRVPLSDNAIIEAN
LGKYGILSIDDLIHEIITVGPHFKQANNFLWPFKLSNPSGGWGVPRKFKH
FIQGGSFGNREEFINKLVKSMN

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): R30 R33 N37 R41 R67 K70 K90 G91 I92 N93 K94 P97 K98 K101 L105 R107 I111 N112 A122 E125 L126 L129 S142 R145 K150 R151 K155 K158 Q159 R160 D165 K196 N200 K206 L207 N209 P210 S211 G212 G213 W214 R218 K219 K241
• Binding residue (residue number reindexed from 1): R8 R11 N15 R19 R45 K48 K68 G69 I70 N71 K72 P75 K76 K79 L83 R85 I89 N90 A100 E103 L104 L107 S120 R123 K128 R129 K133 K136 Q137 R138 D143 K174 N178 K184 L185 N187 P188 S189 G190 G191 W192 R196 K197 K219

Gene Ontology

Molecular Function

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

Biological Process

• GO:0000463 maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
• GO:0000470 maturation of LSU-rRNA
• GO:0002181 cytoplasmic translation
• GO:0042273 ribosomal large subunit biogenesis

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:6r86, PDBe:6r86, PDBj:6r86
• PDBsum: 6r86
• PubMed: 31189955
• UniProt: P05737|RL7A_YEAST Large ribosomal subunit protein uL30A (Gene Name=RPL7A)