Structure of PDB 3jbu Chain J Binding Site BS01

Receptor Information

>3jbu Chain J (length=98) Species: 83333 (Escherichia coli K-12)

RIRIRLKAFDHRLIDQATAEIVETAKRTGAQVRGPIPLPTRKERFTVLIS
PHVNKDARDQYEIRTHLRLVDIVEPTEKTVDALMRLDLAAGVDVQISL

Ligand information

>3jbu Chain A (length=1530)

ugaagaguuugaucauggcucagauugaacgcuggcggcaggccuaacac
augcaagucgaacgguaacaggaagaagcuugcuucuuugcugacgagug
gcggacgggugaguaaugucugggaaacugccugauggagggggauaacu
acuggaaacgguagcuaauaccgcauaacgucgcaagaccaaagaggggg
accuucgggccucuugccaucggaugugcccagaugggauuagcuaguag
gugggguaacggcucaccuaggcgacgaucccuagcuggucugagaggau
gaccagccacacuggaacugagacacgguccagacuccuacgggaggcag
caguggggaauauugcacaaugggcgcaagccugaugcagccaugccgcg
uguaugaagaaggccuucggguuguaaaguacuuucagcggggaggaagg
gaguaaaguuaauaccuuugcucauugacguuacccgcagaagaagcacc
ggcuaacuccgugccagcagccgcgguaauacggagggugcaagcguuaa
ucggaauuacugggcguaaagcgcacgcaggcgguuuguuaagucagaug
ugaaauccccgggcucaaccugggaacugcaucugauacuggcaagcuug
agucucguagagggggguagaauuccagguguagcggugaaaugcguaga
gaucuggaggaauaccgguggcgaaggcggcccccuggacgaagacugac
gcucaggugcgaaagcguggggagcaaacaggauuagauacccugguagu
ccacgccguaaacgaugucgacuuggagguugugcccuugaggcguggcu
uccggagcuaacgcguuaagucgaccgccuggggaguacggccgcaaggu
uaaaacucaaaugaauugacgggggcccgcacaagcgguggagcaugugg
uuuaauucgaugcaacgcgaagaaccuuaccuggucuugacauccacgga
aguuuucagagaugagaaugugccuucgggaaccgugagacaggugcugc
auggcugucgucagcucguguugugaaauguuggguuaagucccgcaacg
agcgcaacccuuauccuuuguugccagcgguccggccgggaacucaaagg
agacugccagugauaaacuggaggaagguggggaugacgucaagucauca
uggcccuuacgaccagggcuacacacgugcuacaauggcgcauacaaaga
gaagcgaccucgcgagagcaagcggaccucauaaagugcgucguaguccg
gauuggagucugcaacucgacuccaugaagucggaaucgcuaguaaucgu
ggaucagaaugccacggugaauacguucccgggccuuguacacaccgccc
gucacaccaugggaguggguugcaaaagaaguagguagcuuaaccuucgg
gagggcgcuuaccacuuugugauucaugacuggggugaagucguaacaag
guaaccguaggggaaccugcgguuggauca

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3jbu Mechanisms of ribosome stalling by SecM at multiple elongation steps
• Resolution: 3.64 Å
• Binding residue (original residue number in PDB): R7 R9 R16 R37 G38 P39 P41 L42 P43 T44 R45 K46 I53 P55 H56 V57 N58 K59 R62 L73
• Binding residue (residue number reindexed from 1): R3 R5 R12 R33 G34 P35 P37 L38 P39 T40 R41 K42 I49 P51 H52 V53 N54 K55 R58 L69

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:3jbu, PDBe:3jbu, PDBj:3jbu
• PDBsum: 3jbu
• PubMed: 26670735
• UniProt: P0A7R5|RS10_ECOLI Small ribosomal subunit protein uS10 (Gene Name=rpsJ)