Structure of PDB 6snt Chain aj Binding Site BS01

Receptor Information

>6snt Chain aj (length=112) Species: 4932 (Saccharomyces cerevisiae)

AQRVTFRRRNPYNTRSNKIKVVKTPGGILRAQHVKKLATRPKCGDCGSAL
QGISTLRPRQYATVSKTHKTVSRAYGGSRCANCVKERIIRAFLIEEQKIV
KKVVKEQTEAAK

Ligand information

>6snt Chain 1 (length=3184)

uugaccucaaaucagguaggaguacccgcugaacuuaagcauaucaauaa
gcggaggaaaagaaaccaaccgggauugccuuaguaacggcgagugaagc
ggcaaaagcucaaauuugaaaucugguaccuucggugcccgaguuguaau
uuggagagggcaacuuuggggccguuccuugucuauguuccuuggaacag
gacgucauagagggugagaaucccguguggcgaggagugcgguucuuugu
aaagugccuucgaagagucgaguuguuugggaaugcagcucuaagugggu
gguaaauuccaucuaaagcuaaauauuggcgagagaccgauagcgaacaa
guacagugauggaaagaugaaaagaacuuugaaaagagagugaaaaagua
cgugaaauuguugaaagggaagggcauuugaucagacaugguguuuugua
uuucacuggccagcaucaguuuugguggcaggauaaauccauaggaaugu
agcuugccucgguaaguauuauagccugugggaauacugccagcugggac
ugaggacugcgacguaagucaaggaugcuggcauaaugguuauaugccgc
ccgucuugaaacacggaccaaggagucuaacgucuaugcgaguguuuggg
uguaaaacccauacgcguaaugaaagugaacguagguuggggccucgcaa
gaggugcacaaucgaccgauccugaugucuucggauggauuugaguaaga
gcauagcuguugggacccgaaagauggugaacuaugccugaauaggguga
agccagaggaaacucugguggaggcucguagcgguucugacgugcaaauc
gaucgucgaauuuggguauaggggcgaaagacuaaucgaaccaucuagua
gcugguuccugccgaaguuucccucaggauagcagaagcucguaucaguu
uuaugagguaaagcgaaugauuagagguuccggggucgaaaugaccuuga
ccuauucucaaacuuuaaauauguaagaaguccuuguuacuuaauugaac
guggacauuugaaugaagagcuuuuagugggccauuuuugguaagcagaa
cuggcgaugcgggaugaaccgaacguagaguuaaggugccggaauacacg
cucaucagacaccacaaaagguguuaguucaucuagacagccggacggug
gccauggaagucggaauccgcuaaggaguguguaacaacucaccggccga
augaacuagcccugaaaauggauggcgcucaagcguguuaccuauacucu
accgucaggguugauaugaugcccugacgaguaggcaggcguggagguca
gugacgaagccuagaccguaaggucgggucgaacggccucuagugcagau
cuuggugguaguagcaaauauucaaaugagaacuuugaagacugaagugg
ggaaagguuccacgucaacagcaguuggacguggguuagucgauccuaag
agauggggaagcuccguuucaaaggccugauuuuaugcaggccaccaucg
aaagggaauccgguuaagauuccggaaccuggauauggauucuucacggu
aacguaacugaauguggagacgucggcgcgagcccugggaggaguuaucu
uuucuucuuaacagcuuaucaccccggaauugguuuauccggagaugggg
ucuuauggcuggaagaggccagcaccuuugcuggcuccggugcgcuugug
acggcccgugaaaauccacaggaaggaauaguuuucaugccaggucguac
ugauaaccgcagcaggucuccaaggugaacagccucuaguugauagaaua
auguagauaagggaagucggcaaaauagauccguaacuucgggauaagga
uuggcucuaagggucggguacgaucaacuuagaacugguacggacaaggg
gaaucugacugucuaauuaaaacauagcauugcgauggucagaaagugau
guugacgcaaugugauuucugcccagugcucugaaugucaaagugaagaa
auucaaccaagcgcggguaaacggcgggaguaacuaugacucucuuaagg
uagccaaaugccucgucaucuaauuagugacgcgcaugaauggauuaacg
agauucccacugucccuaucuacuaucuagcgaaaccacagccaagggaa
cgggcuuggcagaaucagcggggaaagaagacccuguugagcuugacucu
aguuugacauugugaagagacauagagggcuaccuuuauaguuucuuuac
uuauucaaugaagcggagcuggaauucauuuuccacguucuagcauucaa
ggucccauucggggcugauccggguugaagacauugucagguggggaguu
uggcuggggcggcacaucuguuaaacgauaacgcagauguccuaaggggg
gcucauggagaacagaaaucuccaguagaacaaaaggguaaaagcccccu
ugauuuugauuuucagugugaauacaaaccaugaaaguguggccuaucga
uccuuuagucccucggaauuugaggcuagaggugccagaaaaguuaccac
agggauaacuggcuuguggcagucaagcguucauagcgacauugcuuuuu
gauucuucgaugucggcucuuccuaucauaccgaagcagaauucgguaag
cguuggauuguucacccacuaauagggaacgugagcuggguuuagaccgu
cgugagacagguuaguuuuacccuacugaugaauguuaccgcaauaguaa
uugaacuuaguacgagaggaacaguucauucggauaauugguuuuugcgg
cugucugaucaggcauugccgcgaagcuaccauccgcuggauuauggcug
aacgccucuaagucagaauccaugcuagaacgcggugauuucuuugcucc
acacaauauagauggauacgaauaaggcguccuuguggcgucgcugaacc
auagcaggcuagcaacggugcacuuggcggaaaggccuugggugcuugcu
ggcgaauugcaaugucauuuugcguggggauaaaucauuuguauacgacu
uagauguacaacgggguauuguaagcaguagaguagccuuguuguuacga
ucugcugagauuaagccuuuguugucugauuugu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6snt RQT complex dissociates ribosomes collided on endogenous RQC substrate SDD1.
• Resolution: 2.8 Å
• Binding residue (original residue number in PDB): A2 R4 V5 F7 R8 R9 R10 N11 P12 Y13 N14 T15 R16 S17 K24 T25 P26 G27 L30 R31 Q33 K36 K37 L38 T40 R41 K43 G45 Q52 G53 I54 S55 T56 R58 P59 R60 Y62 S66 K67 K70 T71 S73 R74 Y76 G78 R91 A92 I95 Q98 K99 K102
• Binding residue (residue number reindexed from 1): A1 R3 V4 F6 R7 R8 R9 N10 P11 Y12 N13 T14 R15 S16 K23 T24 P25 G26 L29 R30 Q32 K35 K36 L37 T39 R40 K42 G44 Q51 G52 I53 S54 T55 R57 P58 R59 Y61 S65 K66 K69 T70 S72 R73 Y75 G77 R90 A91 I94 Q97 K98 K101

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006412 translation
• GO:0042254 ribosome biogenesis

Cellular Component

• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0022625 cytosolic large ribosomal subunit
• GO:0030687 preribosome, large subunit precursor
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:6snt, PDBe:6snt, PDBj:6snt
• PDBsum: 6snt
• PubMed: 32203490
• UniProt: P87262|RL34A_YEAST Large ribosomal subunit protein eL34A (Gene Name=RPL34A)