Structure of PDB 8p2f Chain M Binding Site BS01

Receptor Information

>8p2f Chain M (length=144) Species: 93061 (Staphylococcus aureus subsp. aureus NCTC 8325)

MRQTFMANESNIERKWYVIDAEGQTLGRLSSEVASILRGKNKVTYTPHVD
TGDYVIVINASKIEFTGNKETDKVYYRHSNHPGGIKSITAGELRRTNPER
LIENSIKGMLPSTRLGEKQGKKLFVYGGAEHPHAAQQPENYELR

Ligand information

>8p2f Chain A (length=2844)

uuaaguuauuaagggcgcacgguggaugccuuggcacuagaagccgauga
aggacguuacuaacgacgauaugcuuuggggagcuguaaguaagcuuuga
uccagagauuuccgaauggggaaacccagcaugaguuaugucauguuauc
gauaugugaauacauagcauaucagaaggcacacccggagaacugaaaca
ucuuaguacccggaggaagagaaagaaaauucgauucccuuaguagcggc
gagcgaaacgggaagagcccaaaccaacaagcuugcuuguugggguugua
ggacacucuauacggaguuacaaaggacgacauuagacgaaucaucugga
aagaugaaucaaagaagguaauaauccuguagucgaaaauguugucucuc
uugaguggauccugaguacgacggagcacgugaaauuccgucggaaucug
ggaggaccaucuccuaaggcuaaauacucucuagugaccgauagugaacc
aguaccgugagggaaaggugaaaagcaccccggaaggggagugaaauaga
accugaaaccgugugcuuacaaguagucagagcccguuaaugggugaugg
cgugccuuuuguagaaugaaccggcgaguuacgauuugaugcaagguuaa
gcaguaaauguggagccguagcgaaagcgagucugaauagggcguuuagu
auuuggucguagacccgaaaccaggugaucuacccuuggucagguugaag
uucagguaacacugaauggaggaccgaaccgacuuacguugaaaagugag
cggaugaacugaggguagcggagaaauuccaaucgaaccuggagauagcu
gguucucuccgaaauagcuuuagggcuagccucaagugaugauuauugga
gguagagcacuguuuggacgaggggccguuaccgaauucagacaaacucc
gaaugccaauuaauuuaacuugggagucagaacaugggugauaagguccg
uguucgaaagggaaacagcccagaccaccagcuaaggucccaaaauauau
guuaaguggaaaaggauguggcguugcccagacaacuaggauguuggcuu
agaagcagccaucauuuaaagagugcguaauagcucacuagucgagugac
acugcgccgaaaauguaccggggcuaaacauauuaccgaagcuguggauu
guccuuuggacaaugguaggagagcguucuaagggcguugaagcaugauc
guaaggacauguggagcgcuuagaagugagaaugccggugugaguagcga
aagacgggugagaaucccguccaccgauugacuaagguuuccagaggaag
gcucguccgcucuggguuagucggguccuaagcugaggccgacaggcgua
ggcgauggauaacagguugauauuccuguaccaccuauaaucguuuuaau
cgauggggggacgcaguaggauaggcgaagcgugcgauuggauugcacgu
cuaagcaguaaggcugaguauuaggcaaauccgguacucguuaaggcuga
gcugugauggggagaagacauugugucuucgagucguugauuucacacug
ccgagaaaagccucuagauagaaaauaggugcccguaccgcaaaccgaca
cagguagucaagaugagaauucuaaggugagcgagcgaacucucguuaag
gaacucggcaaaaugaccccguaacuucgggagaaggggugcucuuuagg
guuaacgcccagaagagccgcagugaauaggcccaagcgacuguuuauca
aaaacacaggucucugcuaaaccguaaggugauguauaggggcugacgcc
ugcccggugcuggaagguuaagaggagugguuagcuucugcgaagcuacg
aaucgaagccccaguaaacggcggccguaacuauaacgguccuaagguag
cgaaauuccuugucggguaaguuccgacccgcacgaaaggcguaacgauu
ugggcacugucucaacgagagacucggugaaaucauaguaccugugaaga
ugcagguuacccgcgacaggacggaaagaccccguggagcuuuacuguag
ccugauauugaaauucggcacagcuugcccuagcuguguuggcuuucuaa
cccgcaccacuuaucguggugggagacagugucaggcgggcaguuugacu
ggggcggucgccuccuaaaagguaacggaggcgcucaaagguucccucag
aaugguuggaaaucauucauagaguguaaaggcauaagggagcuugacug
cgagaccuacaagucgagcagggucgaaagacggacuuagugauccggug
guuccgcauggaagggccaucgcucaacggauaaaagcuaccccggggau
aacaggcuuaucucccccaagaguucacaucgacggggagguuuggcacc
ucgaugucggcucaucgcauccuggggcuguagucggucccaaggguugg
gcuguucgcccauuaaagcgguacgcgagcuggguucagaacgucgugag
acaguucggucccuauccgucgugggcguaggaaauuugagaggagcugu
ccuuaguacgagaggaccgggauggacauaccucugguguaccaguuguc
gugccaacggcauagcuggguagcuauguguggacgggauaagugcugaa
agcaucuaagcaugaagccccccucaagaugagauuucccaacuucgguu
auaagaucccucaaagaugaugagguuaauagguucgagguggaagcaug
gugacauguggagcugacgaauacuaaucgaucgaagacuuaau

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8p2f Cryo-EM structures of Staphylococcus aureus 70S ribosomes in complex with elongation factor G and fusidic acid
• Resolution: 2.44 Å
• Binding residue (original residue number in PDB): M1 R2 Q3 T4 M6 W16 T25 G27 R28 S31 S35 R38 K40 H48 Y54 T66 G67 K69 K73 Y75 Y76 R77 H78 S79 H81 P82 G83 I85 K86 R100 E103 S105 G108 M109 P111 T113 R114 L115 K121 P132 H133 A135 Q136 Q137 R144
• Binding residue (residue number reindexed from 1): M1 R2 Q3 T4 M6 W16 T25 G27 R28 S31 S35 R38 K40 H48 Y54 T66 G67 K69 K73 Y75 Y76 R77 H78 S79 H81 P82 G83 I85 K86 R100 E103 S105 G108 M109 P111 T113 R114 L115 K121 P132 H133 A135 Q136 Q137 R144

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:8p2f, PDBe:8p2f, PDBj:8p2f
• PDBsum: 8p2f
• PubMed: 38902339
• UniProt: Q2FW38|RL13_STAA8 Large ribosomal subunit protein uL13 (Gene Name=rplM)