Structure of PDB 8ury Chain J Binding Site BS01

Receptor Information
>8ury Chain J (length=205) Species: 562 (Escherichia coli) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ARYLGPKLKLSRREGTDLFLKSGVRAIDTKCKIEQAPGQHGARKPRLSDY
GVQLREKQKVRRIYGVLERQFRNYYKEAARLKGNTGENLLALLEGRLDNV
VYRMGFGATRAEARQLVSHKAIMVNGRVVNIASYQVSPNDVVSIREKAKK
QSRVKAALELAEQREKPTWLEVDAGKMEGTFKRKPERSDLSADINEHLIV
ELYSK
Ligand information
>8ury Chain D (length=1524) [Search RNA sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
aaauugaagaguuugaucauggcucagauugaacgcuggcggcaggccua
acacaugcaagucgaacgguaacaggaagaagcuugcuucuuugcugacg
aguggcggacgggugaguaaugucugggaaacugccugauggagggggau
aacuacuggaaacgguagcuaauaccgcauaacgucgcaagaccaaagag
ggggaccuucgggccucuugccaucggaugugcccagaugggauuagcua
guaggugggguaacggcucaccuaggcgacgaucccuagcuggucugaga
ggaugaccagccacacuggaacugagacacgguccagacuccuacgggag
gcagcaguggggaauauugcacaaugggcgcaagccugaugcagccaugc
cgcguguaugaagaaggccuucggguuguaaaguacuuucagcggggagg
aagggaguaaaguuaauaccuuugcucauugacguuacccgcagaagaag
caccggcuaacuccggccagcagcccgguaauacggagggugcaagcguu
aaucggaauuacugggcguaaagcgcacgcaggcgguuuguuaagucaga
ugugaaauccccgggcucaaccugggaacugcaucugauacuggcaagcu
ugagucucguagagggggguagaauuccagguguagcggugaaaugcgua
gagaucuggaggaauaccgguggcgaaggcggcccccuggacgaagacug
acgcucaggugcgaaagcguggggagcaaacaggauuagauacccuggua
guccacgccguaaacgaugucgacuuggagguugugcccuugaggcgugg
cuuccggagcuaacgcguuaagucgaccgccuggggaguacggccgcaag
guuaaaacucaaaugaauugacgggggcccgcacaagcgguggagcaugu
gguuuaauucgauaacgcgaagaaccuuaccuggucuugacauccacgga
aguuuucagagaugagaaugugccuucgggaaccgugagacaggugcugc
auggcugucgucagcucguguugugaaauguuggguuaagucccgcaacg
agcgcaacccuuauccuuuguugccagcgguccggccgggaacucaaagg
agacugccagugauaaacuggaggaagguggggaugacgucaagucauca
ugcccuuacgaccagggcuacacacgugcuacaauggcgcauacaaagag
aagcgaccucgcgagagcaagcggaccucauaaagugcgucguaguccgg
auuggagucugcaacucgacuccaugaagucggaaucgcuaguaaucgug
gaucagaaugccacggugaauacguucccgggccuuguacacaccgccgu
acaccaugggaguggguugcaaaagaaguagguagcuuaaccuucgggag
ggcgcuuaccacuuugugauucaugacuggggugaagucgaacaagguaa
ccguaggggccugcgguuggauca
........<<<<..[.((((.>>>>.<<<<.<<<<<..<<<<<<<<....
.<<<.<<<..<<<..<<.<<..<<<<<<<<<......>>>>>>.>>>>>.
.>>>>>......<<.......<<<<<<<..<<...<<<<<<<.<.<<...
..<<<<<......>>>>>......>>.>.....<<<....>>>....<<<
<<<..<<....>>>>>>>>.>>>>>>>..>>.>>>>>>><<<....<<<.
.<<<<<<<.........>>>>>>>>>>......>>>..<<<<<<<<....
>>>>...>>>>.>>.<<<<<.<.........>>>>>>.<<<<....>>>>
...>>>>>>.........<<<....<<<<....>>>>..>>>..>>.>>>
>>>..<<<<......<<<<....>>>>.....>>>>..<<.<<<<<....
..<.<<<<<<<<.......>>>>>>>>.>........>>>>>....>>.<
<<<<(((...<<<<<.......)))........>>>>>>>>>>..>>>>>
>>>>..........<<<((.....<<<<...<<<.<<<<<<<.<<<<<<<
<<<......<<<<<<.....>>>>>>....>>>>>>>>..>>>>>>>>>.
..<<<<<<<<...<<<<<<<....<<<<<<<<...<<<......>>>...
...>>>>>>>>...........<<....>>.>>>>>>>..>>>>.>>>>.
..>>>...>>>>....<<<<<<...<<...<<<<.<.....>.>>>>...
>>>>>>>>..........<<<<<<.<<<<<<<<<<<<<.....>>>>>>>
>>>>>>..<<..))>>.....>>>>>>.>>>.<<<......<<<<....>
>>>....>>>..)))).]<<<<<.<<<<<<<.<<.<<<<<<..<<<<<<<
<<<......<<......>>..........<<<<<<<......<<<<<<<.
.<<<<<<<....>>>>>>>...<......>..>>>>>.>>.<<<.<....
<<<<<<.......<<<<<<<<<....>>>..<<<<......>>>>..>>>
>>>.....<<<<.<<<<<<<...<<..<<<.....>>>>>....>>>>>>
>.....<<<<<.....>>>>>........>>>>.........>>>...>>
>.>>>>...>>>>>>>...>>.>>>>>>>>.....<<<<<<<.....<<<
..<<...<<<....>>>...>>....>>>.....>>>>>>>......<..
..<<<<<<<........>>>>>>>....>.....>>>>>>....<<<<<<
<.........>>>>>>>......>>...>>>>>>>>>>.>>......<<.
.<<<<.<<<..<<<<<<<<<<<<....<<<<<<.<<<<..<<<..>>>.>
>>>>>>>>>...>>>>>>>>>>>>..>>>.>>>>....>>........<<
<<<<<<<..>>>>>>>>>......
Receptor-Ligand Complex Structure
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PDB8ury Structural basis of RfaH-mediated transcription-translation coupling
Resolution3.1 Å
Binding residue
(original residue number in PDB)		A2 R3 L5 P7 K8 L9 K10 R13 R14 K22 S23 R26 K31 C32 K33 Q36 G39 Q40 H41 R44 Y51 L55 R56 K58 Q59 R62 R63 E69 R70 Q71 R81 T110 E113 R115 Q116 S119 H120 K121 R128 V130 N131 I132 S134 Y135 Q152 E202 S205 K206
Binding residue
(residue number reindexed from 1)		A1 R2 L4 P6 K7 L8 K9 R12 R13 K21 S22 R25 K30 C31 K32 Q35 G38 Q39 H40 R43 Y50 L54 R55 K57 Q58 R61 R62 E68 R69 Q70 R80 T109 E112 R114 Q115 S118 H119 K120 R127 V129 N130 I131 S133 Y134 Q151 E201 S204 K205
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0000900 mRNA regulatory element binding translation repressor activity
GO:0003735 structural constituent of ribosome
GO:0005515 protein binding
GO:0019843 rRNA binding
GO:0048027 mRNA 5'-UTR binding
Biological Process
GO:0000028 ribosomal small subunit assembly
GO:0002181 cytoplasmic translation
GO:0006353 DNA-templated transcription termination
GO:0006412 translation
GO:0006417 regulation of translation
GO:0031564 transcription antitermination
GO:0042254 ribosome biogenesis
GO:0042274 ribosomal small subunit biogenesis
GO:0045947 negative regulation of translational initiation
GO:0046677 response to antibiotic
GO:1990145 maintenance of translational fidelity
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0005840 ribosome
GO:0015935 small ribosomal subunit
GO:0022627 cytosolic small ribosomal subunit
GO:1990904 ribonucleoprotein complex

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:8ury, PDBe:8ury, PDBj:8ury
PDBsum8ury
PubMed39117885
UniProtP0A7V8|RS4_ECOLI Small ribosomal subunit protein uS4 (Gene Name=rpsD)

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