Structure of PDB 7aqd Chain Q Binding Site BS01

Receptor Information

>7aqd Chain Q (length=117) Species: 224308 (Bacillus subtilis subsp. subtilis str. 168)

PRVKGGTVTRKRRKKVLKLAKGYFGSKHTLYKVANQQVMKSGNYAFRDRR
QKKRDFRKLWITRINAAARMNGLSYSRLMHGLKLSGIEVNRKMLADLAVN
DLTAFNQLADAAKAQLN

Ligand information

>7aqd Chain A (length=2918)

uuaaguuagaaagggcgcacgguggaugccuuggcacuaggagccgauga
aggacgggacgaacaccgauaugcuucggggagcuguaagcaagcuuuga
uccggagauuuccgaauggggaaacccaccacucguaauggagugguauc
cauaucugaauucauaggauaugagaaggcagacccggggaacugaaaca
ucuaaguacccggaggaagagaaagcaaaugcgauucccugaguagcggc
gagcgaaacgggaucagcccaaaccaagaggcuugccucuugggguugua
ggacacucuguacggaguuacaaaggaacgagguagaugaagaggucugg
aaaggcccgccauaggagguaacagcccuguagucaaaacuucguucucu
ccugaguggauccugaguacggcggaacacgugaaauuccgucggaaucc
gggaggaccaucucccaaggcuaaauacucccuagugaccgauagugaac
caguaccgugagggaaaggugaaaagcaccccggaaggggagugaaagag
auccugaaaccgugugccuacaaguagucagagcccguuaacgggugaug
gcgugccuuuuguagaaugaaccggcgaguuacgaucucgugcaagguua
agcagaagaugcggagccgcagcgaaagcgagucugaauagggcgcauga
guacguggucguagacccgaaaccaggugaucuacccauguccaggguga
aguucagguaacacugaauggaggcccgaacccacgcacguugaaaagug
cggggaugagguguggguaggggugaaaugccaaucgaaccuggagauag
cugguucucuccgaaauagcuuuagggcuagccucaagguaagagucuug
gagguagagcacugauuggacuaggggccccuaccggguuaccgaauuca
gucaaacuccgaaugccaaugacuuauccuugggagucagacugcgagug
auaagauccguagucgaaagggaaacagcccagaccgccagcuaaggucc
caaaguauacguuaaguggaaaaggauguggaguugcuuagacaaccagg
auguuggcuuagaagcagccaccauuuaaagagugcguaauagcucacug
gucgagugacucugcgccgaaaauguaccggggcuaaacguaucaccgaa
gcugcggacuguucuucgaacagugguaggagagcguucuaagggcugug
aagccagaccggaaggacugguggagcgcuuagaagugagaaugccggua
ugaguagcgaaagaggggugagaauccccuccaccgaaugccuaagguuu
ccugaggaaggcucguccgcucaggguuagucgggaccuaagccgaggcc
gaaaggcguaggcgauggacaacagguugauauuccuguaccaccuccuc
accauuugagcaauggggggacgcaggaggauaggguaagcgcgguauug
gauauccgcguccaagcaguuaggcugggaaauaggcaaauccguuuccc
auaagccugagcugugauggcgagcgaaauauaguagcgaaguuccugau
uccacacugccaagaaaagccucuagcgaggugagaggugcccguaccgc
aaaccgacacagguaggcgaggagagaauccuaaggugaucgagagaacu
cucguuaaggaacucggcaaaaugaccccguaacuucgggagaaggggug
cucuguuagggugcaagcccgagagagccgcagugaauaggcccaggcga
cuguuuagcaaaaacacaggucucugcgaagccguaaggcgaaguauagg
ggcugacgccugcccggugcuggaagguuaagaggagcgcuuagcguaag
cgaaggugcgaauugaagccccaguaaacggcggccguaaacgguccuaa
gguagcgaaauuccuugucggguaaguuccgacccgcacgaaaggcgcaa
cgaucugggcacugucucaacgagagacucggugaaauuauaguaccugu
gaagaugcagguuacccgcgacaggacggaaagaccccguggagcuuuac
ugcagccugauauugaauguugguacagcuuguacaggauagguaggagc
cuuggaaaccggagcgccagcuucgguggaggcaucggugggauacuacc
cuggcuguauugaccuucuaacccgccgcccuuaucgggcggggagacag
ugucaggugggcaguuugacuggggcggucgccuccuaaaagguaacgga
ggcgcccaaagguucccucagaaugguuggaaaucauucgcagaguguaa
aggcacaagggagcuugacugcgagaccuacaagucgagcagggacgaaa
gucgggcuuagugauccggugguuccgcauggaagggccaucgcucaacg
gauaaaagcuaccccggggauaacaggcuuaucucccccaagaguccaca
ucgacggggagguuuggcaccucgaugucggcucaucgcauccuggggcu
guagucggucccaaggguugggcuguucgcccauuaaagcgguacgcgag
cuggguucagaacgucgugagacaguucggucccuauccgucgcgggcgc
aggaaauuugagaggagcuguccuuaguacgagaggaccgggauggacgc
accgcugguguaccaguuguucugccaagggcaucgcuggguagcuaugu
gcggacgggauaagugcugaaagcaucuaagcaugaagccccccucaaga
ugagauuucccauuccgcaaggaaguaagaucccugaaagaugaucaggu
ugauaggucugagguggaaguguggcgacacauggagcugacagauacua
aucgaucgaggacuuaac

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7aqd Mimicry of Canonical Translation Elongation Underlies Alanine Tail Synthesis in RQC.
• Resolution: 3.1 Å
• Binding residue (original residue number in PDB): P2 R3 V4 K5 T8 V9 T10 R11 R13 R14 K15 K16 K19 G23 Y24 F25 G26 S27 K28 H29 T30 L31 K33 V34 N36 Q37 Q38 K41 S42 Y45 A46 F47 R48 D49 R50 R51 K53 K54 R55 F57 R58 W61 I62 N66 R70 S75 Y76 S77 H81 K84 R92 K93
• Binding residue (residue number reindexed from 1): P1 R2 V3 K4 T7 V8 T9 R10 R12 R13 K14 K15 K18 G22 Y23 F24 G25 S26 K27 H28 T29 L30 K32 V33 N35 Q36 Q37 K40 S41 Y44 A45 F46 R47 D48 R49 R50 K52 K53 R54 F56 R57 W60 I61 N65 R69 S74 Y75 S76 H80 K83 R91 K92

Gene Ontology

Molecular Function

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

Biological Process

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

Cellular Component

• GO:0005840 ribosome
• GO:0022625 cytosolic large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:7aqd, PDBe:7aqd, PDBj:7aqd
• PDBsum: 7aqd
• PubMed: 33259811
• UniProt: P55873|RL20_BACSU Large ribosomal subunit protein bL20 (Gene Name=rplT)