Structure of PDB 6vwl Chain i Binding Site BS01

Receptor Information

>6vwl Chain i (length=98) Species: 562 (Escherichia coli)

RIRIRLKAFDHRLIDQATAEIVETAKRTGAQVRGPIPLPTRKERFTVLIS
PHVNKDARDQYEIRTHLRLVDIVEPTEKTVDALMRLDLAAGVDVQISL

Ligand information

>6vwl Chain 1 (length=1521)

ugaagaguuugaucauggcucagauugaacgcuggcggcaggccuaacac
augcaagucgaacgguaacaggaagcuuugcugacgaguggcggacgggu
gaguaaugucugggaaacugccugauggagggggauaacuacuggaaacg
guagcuaauaccgcauaacgucgcaagaccaaagagggggaccuucgggc
cucuugccaucggaugugcccagaugggauuagcuaguaggugggguaac
ggcucaccuaggcgacgaucccuagcuggucugagaggaugaccagccac
acuggaacugagacacgguccagacuccuacgggaggcagcaguggggaa
uauugcacaaugggcgcaagccugaugcagccaugccgcguguaugaaga
aggccuucggguuguaaaguacuuucagcggggaggaagggaguaaaguu
aauaccuuugcucauugacguuacccgcagaagaagcaccggcuaacucc
gugccagcagccgcgguaauacggagggugcaagcguuaaucggaauuac
ugggcguaaagcgcacgcaggcgguuuguuaagucagaugugaaaucccc
gggcucaaccugggaacugcaucugauacuggcaagcuugagucucguag
agggggguagaauuccagguguagcggugaaaugcguagagaucuggagg
aauaccgguggcgaaggcggcccccuggacgaagacugacgcucaggugc
gaaagcguggggagcaaacaggauuagauacccugguaguccacgccgua
aacgaugucgacuuggagguugugccgcguggcuuccggagcuaacgcgu
uaagucgaccgccuggggaguacggccgcaagguuaaaacucaaaugaau
ugacgggggcccgcacaagcgguggagcaugugguuuaauucgaugcaac
gcgaagaaccuuaccuggucuugacauccacggaaguuuucagagaugag
aaugugccuucgggaaccgugagacaggugcugcauggcugucgucagcu
cguguugugaaauguuggguuaagucccgcaacgagcgcaacccuuaucc
uuuguugccagcgguccggccgggaacucaaaggagacugccagugauaa
acuggaggaagguggggaugacgucaagucaucauggcccuuacgaccag
ggcuacacacgugcuacaauggcgcauacaaagagaagcgaccucgcgag
agcaagcggaccucauaaagugcgucguaguccggauuggagucugcaac
ucgacuccaugaagucggaaucgcuaguaaucguggaucagaaugccacg
gugaauacguucccgggccuuguacacaccgcccgucacaccaugggagu
ggguugcaaaagaaguagguagcuuaaccuucgggagggcgcuuaccacu
uugugauucaugacuggggugaagucguaacaagguaaccguagggaaac
cugcgguuggaucaccuccuu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6vwl mRNA stem-loops can pause the ribosome by hindering A-site tRNA binding.
• Resolution: 3.1 Å
• Binding residue (original residue number in PDB): R7 R9 R37 G38 I40 P41 L42 P43 T44 R45 K46 E47 T50 I53 P55 H56 N58 K59 R62 Q64 R68 H70 R72
• Binding residue (residue number reindexed from 1): R3 R5 R33 G34 I36 P37 L38 P39 T40 R41 K42 E43 T46 I49 P51 H52 N54 K55 R58 Q60 R64 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:6vwl, PDBe:6vwl, PDBj:6vwl
• PDBsum: 6vwl
• PubMed: 32427100
• UniProt: P0A7R5|RS10_ECOLI Small ribosomal subunit protein uS10 (Gene Name=rpsJ)