Structure of PDB 6sj6 Chain M Binding Site BS01

Receptor Information

>6sj6 Chain M (length=145) Species: 93061 (Staphylococcus aureus subsp. aureus NCTC 8325)

MRQTFMANESNIERKWYVIDAEGQTLGRLSSEVASILRGKNKVTYTPHVD
TGDYVIVINASKIEFTGNKETDKVYYRHSNHPGGIKSITAGELRRTNPER
LIENSIKGMLPSTRLGEKQGKKLFVYGGAEHPHAAQQPENYELRG

Ligand information

>6sj6 Chain A (length=2585)

uuaaguuauuaagggcgcacgguggaugccuuggcacuagaagccgauga
aggacguuacuaacgacgauaugcuuuggggagcuguaaguaagcuuuga
uccagagauuuccgaauggggaaacccagcaugaguuaugucauguuauc
gauaugugaauacauagcauaucagaaggcacacccggagaacugaaaca
ucuuaguacccggaggaagagaaagaaaucgauucccuuaguagcggcga
gcgaaacgggaagagcccaaaccaacaagcuugcuuguugggguuguagg
acacucuauacggaguuacaaaggacgacauuagacgaaucaucuggaaa
gaugaaucaaagaagguaauaauccuguagucgaaaauguugucucucuu
gaguggauccugaguacgacggagcacgugaaauuccgucggaaucuggg
aggaccaucuccuaaggcuaaauacucucuagugaccgauagugaaccag
uaccgugagggaaaggugaaaagcaccccggaaggggagugaaauagaac
cugaaaccgugugcuuacaaguagucagagcccguuaaugggugauggcg
ugccuuuuguagaaugaaccggcgaguuacgauuugaugcaagguuaagc
aguaaauguggagccguagcgaaagcgagucuguagggcguuuaguauuu
ggucguagacccgaaaccaggugaucuacccuuggucagguugaaguuca
gcugaauggaggaccgaaccgacuuacguugaaaagugagcggaugaacu
gaggguagcggagaaauuccaaucgaaccuggagauagcugguucucucc
gaaauagcuuuagggcuagccucaagugaugauuauuggagguagagcac
uguuuggacgaggggccgguuaccgaauucagacaaacuccgaaugccaa
uuaauuuaacuugggagucagaacaugggugauaagguccguguucgaaa
gggaaacagcccagaccaccagcuaaggucccaaaauauauguuaagugg
aaaaggauguggcguugccgugacacugcgccgaaaauguaccggggcua
aacauauuaccgaagcuguggauuguccuuuggacaaugguaggagagcg
uucuaagggcguugaagcaugaucguaaggacauguggagcgcuuagaag
ugagaaugccggugugaguagcgaaagacgggugagaaucccguccaccg
auugacuaagguuuccagaggaaggcucguccgcucuggguuagucgggu
ccuaagcugaggccgacaggcguaggcgauggauaacagguugauauucc
uguaccaccuauaaucguuuuaaucgauggggggacgcaguaggauaggc
gaagcgugcgauuggauucguugauuucacacugccgagaaaagccucua
gauagaaaauaggugcccguaccgcaaaccgacacagguagucaagauga
gaauucuaaggugagcgagcgaacucucguuaaggaacucggcaaaauga
ccccguaacuucgggagaaggggugcucuuuaggguuaacgcccagaaga
gccgcagugaauaggcccaagcgacuguuuaucaaaaacacaggucucug
cuaaaccguaaggugauguauaggggcugacgccugcccggugaguaaac
ggcgaagguagcgaaauuccuugucggguaaguuccgacccgcacgaaag
gcguaacgauuugggcacugucucaacgagagacucggugaaaucauagu
accugugaagaugcagguuacccgcgacaggacggaaagaccccguggag
cuuuacuguagccugauauugaaauucggcacacuguguuggcuuucuaa
cccgcaccacucguggugggagacagugucaggcgggcaguuugacuggg
gcggucgccuccuaaaagguaacggaggcgcucaaagguucccucagaau
gguuggaaaucauucauagaguguaaaggcauaagggagcuugacugcga
gaccuacaagucgagcagggucgaaagacggacuuagugauccggugguu
ccgcauggaagggccaucgcucaacggauaaaagcuaccccggggauaac
aggcuuaucucccccaagaguucacaucgacggggagguuuggcaccucg
augucggcucaucgcauccuggggcuguagucggucccaaggguugggcu
guucgcccauuaaagcgguacgcgagcuggguucagaacgucgugagaca
guucggucccuauccgucgugggcguaggaaauuugagaggagcuguccu
uaguacgagaggaccgggauggacauaccucugguguaccaguugucgug
ccaacggcauagcuggguagcuauguguggacgggauaagugcugaaagc
aucuaagcaugaagccccccucaagaugagauuucccaauuauaagaucc
cucaaagaugaugagguuaauagguucgagguggaagcauggugacaugu
ggagcugacgaauacuaaucgaucgaagacuuaau

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6sj6 Mechanism of ribosome shutdown by RsfS in Staphylococcus aureus revealed by integrative structural biology approach.
• Resolution: 3.23 Å
• Binding residue (original residue number in PDB): M1 T4 W16 G27 R28 S31 R38 K40 P47 H48 T66 K69 Y76 R77 H78 S79 K86 R100 E103 S105 G108 M109 P111 R114 K121 H133 A135 Q136 Q137
• Binding residue (residue number reindexed from 1): M1 T4 W16 G27 R28 S31 R38 K40 P47 H48 T66 K69 Y76 R77 H78 S79 K86 R100 E103 S105 G108 M109 P111 R114 K121 H133 A135 Q136 Q137

Gene Ontology

Molecular Function

• GO:0003729 mRNA binding
• GO:0003735 structural constituent of ribosome

Biological Process

• GO:0006412 translation
• GO:0017148 negative regulation of translation

Cellular Component

• GO:0005737 cytoplasm
• GO:0005840 ribosome
• GO:0022625 cytosolic large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:6sj6, PDBe:6sj6, PDBj:6sj6
• PDBsum: 6sj6
• PubMed: 32245971
• UniProt: Q2FW38|RL13_STAA8 Large ribosomal subunit protein uL13 (Gene Name=rplM)