Structure of PDB 5myj Chain BU Binding Site BS01

Receptor Information

>5myj Chain BU (length=101) Species: 416870 (Lactococcus cremoris subsp. cremoris MG1363)

YAIIKTGGKQVKVEEGSVIYVEKLNVEAGQTVTFDEVIFVGGETTKVGAP
LVEGATVVGEVEKHGKQKKVVTFQYKPKKHSHRKQGHRQPYTKVVIKSVN
A

Ligand information

>5myj Chain BA (length=2897)

caaaguuaauaagggcgcacgguggaugccuuggcacuaagagccgauga
aggacgugacuaacgacgauauucuagggggagcaguaaguacgcauuga
ucccuaggucuccgaauggggaaacccagcuguuacuagcaguuauucau
gagugaauacauagcucauguaaagguaacgcagagaacugaaacaucua
aguaccugcaggaagagaaaguaaaaacgauuucguaaguagcggcgagc
gaacgcgaagaagggcaaaccaagaagcuugcuucuugggguuguaggac
ugcaacguggacuuaagcauuauagucgaauaaccugggaagguuaauca
aagaggguaauaaucccguagacaaaauagcgcuuauaccuagcaguauc
cugaguagggcuggacacgcgaaauccaguuugaauccgggaggaccauc
ucccaacccuaaauacuccuuagugaccgauagugaaccaguaccgugag
ggaaaggugaaaagaaccccgagaggggagugaaauagcaccugaaaccg
ugugccuacaagaaguucgagcccguuaaugggugagagcgugccuuuug
uagaaugaaccggcgaguuacguuaugaugcgagguuaaguugaagagac
ggagccguagggaaaccgagucugaauagggcgacuuaguaucaugaugu
agacccgaaaccuagugaccuauccaugagcagggugaaggugugguaag
acgcacuggaggcccgaaccaggacacguugaaaaguguuuggaugacuu
guggauagcggagaaauuccaaacgaacugggagauagcugguucucucc
gaaauagcuuuagggcuagcgucgaaauguaaguguauuggagguagagc
acuguuugggugagggguccgucuaggauuaccaaucucagauaaacucc
gaaugcuaauacacauguucggcagucagacugcgagugcuaagauccgu
agucgaaagggaaacagcccagaccaacagcuaaggucccaaaauauaug
uuaaguggaaaaggaugugggguugcacagacaacuaggauguuagcuca
gaagcagcuaucauucaaagagugcguaauagcucacuagucgagugacc
cugcgccgaaaauguaccggggcuaaacauauuaccgaagcuuuggauug
auauuuuaucaaugguaggagagcguucuuaaccgcaaugaagguauacc
gugaggagugcuggagcguuaagaagugagaaugccgguaugaguagcgc
aagauaagugagaaucuuauccaccguaagacuaagguuuccaggggaag
gcucguccgcccuggguuagucgggaccuaaggcgaggccgaaaggcgua
gucgauggacaacugguugauauuccaguacuagauaugaucgugaugga
gggacgcaguaggcuaagagaugccaguuaauggauccuggucuaagcag
ugaggugugagaugugucaaaugcauuucucucuaacauugagcugugau
ggggaagcaacuacgguugcgaacucucugaugucacacugccaagaaaa
gcuucuagcguaaagucauaucuacccguaccgcaaaccgacacagguag
ucgaggcgaguagccucaggugaucgagagaacucucguuaaggaacucg
gcaaaauagccccguaacuucgggagaaggggugcugguguaaaagccag
ccgcagugaauaggcccaagcaacuguuuaucaaaaacacagcucucugc
uaaaccgcaaggugauguauagggggugacgccugcccggugcuggaagg
uuaagaggagugcuuagacguaagucgaagguaugaauugaagccccagu
aaacggcggccguaacuauaacgguccuaagguagcgaaauuccuugucg
gguaaguuccgacccgcacgaaaggcguaaugauuugggcacugucucaa
cgagagacucggugaaauuuuaguaccugugaagaugcagguuacccgcg
acaggacggaaagaccccauggagcuuuacuguaguuugauauugaguac
cuguaagucauguacaggauagguaggagccauugaaauagggacgcuag
uuucuauugaggcguuguugggauacuacccuugacuuaugguuacucua
acccgcuggcauaaucggccagggagacagugucugacggacaguuugac
uggggcggucgccuccuaaagaguaacggaggcgcucaaagguuggcuca
gauugguuggaaaucaaucguagaguguaaagguaaaagccagcuugacu
gcgagagcuacaacucgagcagguaggaaacuaggacuuagugauccggu
gguaccgcauggaagggccaucgcucaacggauaaaagcuacccugggga
uaacaggcuuaucucccccaagaguucacaucgacggggagguuuggcac
cucgaugucggcucgucgcauccuggggcuguagucggucccaaggguug
ggcuguucgcccauuaaagcggcacgcgagcuggguucagaacgucguga
gacaguucggucccuauccgucgcgggcguagguaauuugagaggaucug
uccuuaguacgagaggaccgggauggacuuaccgcugguguaccaguugu
uccgccaggagcacggcuggauagcuauguagggaagggauaagcgcuga
aagcaucuaagugcgaagcccaccucaagaugagauuacccauucguaag
aauuaagagcccagagagaugaucugguagauaggcuggaaguggaagag
uugcgagacuuggagcggaccaguacuaaucgcucgaggacuuuacc

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5myj A general mechanism of ribosome dimerization revealed by single-particle cryo-electron microscopy.
• Resolution: 5.6 Å
• Binding residue (original residue number in PDB): G10 G11 K12 Y23 E25 K26 K69 K72 Y78 K79 K81 K82 H83 R86 K87 Q88 G89 H90 R91 Y94
• Binding residue (residue number reindexed from 1): G7 G8 K9 Y20 E22 K23 K66 K69 Y75 K76 K78 K79 H80 R83 K84 Q85 G86 H87 R88 Y91

Gene Ontology

Molecular Function

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

Biological Process

• GO:0006412 translation

Cellular Component

• GO:0005737 cytoplasm
• GO:0005840 ribosome
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:5myj, PDBe:5myj, PDBj:5myj
• PDBsum: 5myj
• PubMed: 28959045
• UniProt: A2RLA4|RL21_LACLM Large ribosomal subunit protein bL21 (Gene Name=rplU)