Structure of PDB 5myj Chain AM Binding Site BS02

Receptor Information

>5myj Chain AM (length=111) Species: 416870 (Lactococcus cremoris subsp. cremoris MG1363)

ARFAGVDIPNEKRIVISLTYVFGVGLQTSKKVLAAAGVSEDIRTKDLTSD
QEDAIRRELDGLKLEGDLRREVSLNIKRLMEIGSYRGMRHRRGLPTRGQN
TKNNARTRKGP

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): I77 K78 M81 R92
• Binding residue (residue number reindexed from 1): I76 K77 M80 R91

Gene Ontology

Molecular Function

• GO:0000049 tRNA binding
• GO:0003676 nucleic acid binding
• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0019843 rRNA binding

Biological Process

• GO:0006412 translation

Cellular Component

• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0015935 small ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:5myj, PDBe:5myj, PDBj:5myj
• PDBsum: 5myj
• PubMed: 28959045
• UniProt: A2RNM9|RS13_LACLM Small ribosomal subunit protein uS13 (Gene Name=rpsM)