Structure of PDB 6q97 Chain o Binding Site BS01

Receptor Information

>6q97 Chain o (length=99) Species: 562 (Escherichia coli)

RIRIRLKAFDHRLIDQATAEIVETAKRTGAQVRGPIPLPTRKERFTVLIS
PHVNKDARDQYEIRTHLRLVDIVEPTEKTVDALMRLDLAAGVDVQISLG

Ligand information

>6q97 Chain 2 (length=1534)

aaauugaagaguuugaucauggcucagauugaacgcuggcggcaggccua
acacaugcaagucgaacgguaacaggaagaagcuugcuucuuugcugacg
aguggcggacgggugaguaaugucugggaaacugccugauggagggggau
aacuacuggaaacgguagcuaauaccgcauaacgucgcaagaccaaagag
ggggaccuucgggccucuugccaucggaugugcccagaugggauuagcua
guaggugggguaacggcucaccuaggcgacgaucccuagcuggucugaga
ggaugaccagccacacuggaacugagacacgguccagacuccuacgggag
gcagcaguggggaauauugcacaaugggcgcaagccugaugcagccaugc
cgcguguaugaagaaggccuucggguuguaaaguacuuucagcggggagg
aagggaguaaaguuaauaccuuugcucauugacguuacccgcagaagaag
caccggcuaacuccgugccagcagccgcgguaauacggagggugcaagcg
uuaaucggaauuacugggcguaaagcgcacgcaggcgguuuguuaaguca
gaugugaaauccccgggcucaaccugggaacugcaucugauacuggcaag
cuugagucucguagagggggguagaauuccagguguagcggugaaaugcg
uagagaucuggaggaauaccgguggcgaaggcggcccccuggacgaagac
ugacgcucaggugcgaaagcguggggagcaaacaggauuagauacccugg
uaguccacgccguaaacgaugucgacuuggagguugugcccuugaggcgu
ggcuuccggagcuaacgcguuaagucgaccgccuggggaguacggccgca
agguuaaaacucaaaugaauugacgggggcccgcacaagcgguggagcau
gugguuuaauucgaugcaacgcgaagaaccuuaccuggucuugacaucca
cggaaguuuucagagaugagaaugugccuucgggaaccgugagacaggug
cugcauggcugucgucagcucguguugugaaauguuggguuaagucccgc
aacgagcgcaacccuuauccuuuguugccagcgguccggccgggaacuca
aaggagacugccagugauaaacuggaggaagguggggaugacgucaaguc
aucauggcccuuacgaccagggcuacacacgugcuacaauggcgcauaca
aagagaagcgaccucgcgagagcaagcggaccucauaaagugcgucguag
uccggauuggagucugcaacucgacuccaugaagucggaaucgcuaguaa
ucguggaucagaaugccacggugaauacguucccgggccuuguacacacc
gcccgucacaccaugggaguggguugcaaaagaaguagguagcuuaaccu
ucgggagggcgcuuaccacuuugugauucaugacuggggugaagucguaa
caagguaaccguaggggaaccugcgguuggauca

........<<<<....((((.>>>>.<<<<.<<<<<..<<<<<<<<....
.<<<.<<<..<<<..<<.<...<<<.<<<<........>>.>>.>>>.>.
.>>>>>......<<.......<<<<<<<..<<...<<<<<<<.<.<<..<
..<<<<<......>>>>>.....>>>.>.....<<<....>>>....<<<
<<<..<......>>>>>>>.>>>>>>>..>>.>>>>>>><<<....<<<.
..<<<<<<.........>>>>>>.>>>......>>>..<<<<<<<<....
>>>>...>>>>.>>.<<<<.<<.........>>>>>>.<<<<....>>>>
...>>>>>>.........<<<...<<<<<....>>>>.>>>>..>>.>>>
>>>..<<<<......<<<<<..>>>>>.....>>>>...<.<<<<<....
..<.<<<<.<<<.......>.>>>>>>.>........>>>>>....>..<
<<<<(((...<<<<<.....<<.)))>>.......>>>>>>>>>>..>>>
>>>>>>..........<<<((.....<<<<...<<<.<<<<<<<.<<<<<
<<<<<......<<<<<<.....>>>>>>....>>>>>>>>..>>>>>>>>
>...<<<<<<<<...<<<<<<<....<<<<<<<<...<<<......>>>.
.....>>>>>>>.>..........<<....>>.>>>>>>>..>>>>.>>>
>...>>>...>>>>....<<<<<<...<<...<<<<.........>>>>.
..>>>>>>>>..........<<<<<<.<<<<<<<<<<<<<.....>>>>>
>>>>>>>>..<<..))>>.....>>>>>>.>>>.<<<......<<<....
..>>>....>>>..))))...<<<<.<<<<<<..<<.<<<<<<..<<<<<
<<<<<......<<........>>..........<<<<<<<......<..<
<<<.....<<<<....>>>>................>>>>...>.<<<.<
<<..<<<<<<.......<<<<<<<<<....>>>..<<<<......>>>>.
.>>>>>>.....<<<<.<<<<<<....<<..<<<.....>>>>>.....>
>>>>>......<<<<.....>>>>.........>>>>.........>>..
.>>>>>>>>>>...>>>>>>>...>>.>>>>>>>>.....<<<<<<<...
..<<<..<<...<<<....>>>...>>....>>>.....>>>>>>>....
..<....<<<<<<<........>>>>>>>....>.....>>>>>>....<
<<<<<<.........>>>>>>>......>>....>>>>>>>>>.>.....
<..<<.<.<<<<.<<<..<<<<<<<<<<<<....<<<<<<.<<<<..<<.
...>>.>>>>>>>>>>...>>>>>>>>>>>>..>>.>>>>>..>.>>...
>.....<<<<<<<<<....>>>>>>>>>......

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6q97 How a circularized tmRNA moves through the ribosome.
• Resolution: 3.9 Å
• Binding residue (original residue number in PDB): R9 R37 G38 P39 P41 L42 P43 T44 R45 I53 S54 P55 H56 V57 N58 K59 H70 R72
• Binding residue (residue number reindexed from 1): R5 R33 G34 P35 P37 L38 P39 T40 R41 I49 S50 P51 H52 V53 N54 K55 H66 R68

Gene Ontology

Molecular Function

• GO:0000049 tRNA binding
• GO:0001072 transcription antitermination factor activity, RNA binding
• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0005515 protein binding

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006412 translation
• GO:0031564 transcription antitermination
• GO:0032784 regulation of DNA-templated transcription elongation
• GO:0042254 ribosome biogenesis

Cellular Component

• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0008023 transcription elongation factor complex
• GO:0015935 small ribosomal subunit
• GO:0022627 cytosolic small ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:6q97, PDBe:6q97, PDBj:6q97
• PDBsum: 6q97
• PubMed: 30765567
• UniProt: P0A7R5|RS10_ECOLI Small ribosomal subunit protein uS10 (Gene Name=rpsJ)