Structure of PDB 8c95 Chain J Binding Site BS01

Receptor Information

>8c95 Chain J (length=142) Species: 562 (Escherichia coli)

MKTFTAKPETVKRDWYVVDATGKTLGRLATELARRLRGKHKAEYTPHVDT
GDYIIVLNADKVAVTGNKRTDKVYYHHTGHIGGIKQATFEEMIARRPERV
IEIAVKGMLPKGPLGRAMFRKLKVYAGNEHNHAAQQPQVLDI

Ligand information

>8c95 Chain A (length=1220)

gguuaagcgacuaagcguacacgguggaugcccuggcagucagaggcgau
gaaggacgugcuaaucugcgauaagcgucgguaaggugauaugaaccguu
auaaccggcgauuuccgaauggggaaacccaguguguuucgacacacuau
cauuaacugaauccauagguuaaugaggcgaaccgggggaacugaaacau
cuaaguaccccgaggaaaagaaaucaaccgagauucccccaguagcggcg
agcgaacggggagcagcccagagccugaaucaguguguguguuaguggaa
gcgucuggaaaggcgcgcgauacagggugacagccccguacacaaaaaug
cacaugcugugagcucgaugaguagggcgggacacgugguauccugucug
aauauggggggaccauccuccaaggcuaaauacuccugacugaccgauag
ugaaccaguaccgugagggaaaggcgaaaagaaccccggcgaggggagug
aaaaagaaccugaaaccguguacguacaagcagugggagcacgcuuaggc
gugugacugcguaccuuuuguauaaugggucagcgacuuauauucuguag
caagguuaaccgaauaggggagccgaagggaaaccgagucuuaacugggc
guuaaguugcaggguauagacccgaaacccggugaccgggagauagcugg
uucuccccgaaagcuauuuagguagcgccucgugaauucaucuccggggg
uagagcagcaaacugcgaauaccggagaauguuaucacgggagacacacg
gcgggugcuaacguccgucgugaagagggaaacaacccagaccgccagcu
aaggucccaaagucaugguuaagucggggcuaaaccaugcaccgaagcug
cggcagcgacgcuuaugcguuguuggguaggggagcguucuguaagccug
cgaaggugugcugugaggcaugcuggagguaucagaagugcgaaugcuga
cauaaguaacagacucagugaaauugaacucgcugugugcaguguccucc
uaaagaguaacggaggagcacgaagguuggcuaauccuggucggacauca
ggagguuagugcaauggcauaagccagcuugacugcgagcgugacggcgc
gagcaggugcgaaagcaggucauagugauccggugguucugaauggaagg
gccaucgcuaggcuuaaccu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8c95 Cryo-EM captures early ribosome assembly in action.
• Resolution: 4.92 Å
• Binding residue (original residue number in PDB): M1 K2 K7 T24 L25 G26 R27 T30 R37 K39 H47 T65 K68 K72 A104 G107 M108 P110 K111 P113 L114 R116 N131 H132 A134 Q135 Q136
• Binding residue (residue number reindexed from 1): M1 K2 K7 T24 L25 G26 R27 T30 R37 K39 H47 T65 K68 K72 A104 G107 M108 P110 K111 P113 L114 R116 N131 H132 A134 Q135 Q136

Gene Ontology

Molecular Function

• GO:0003729 mRNA binding
• GO:0003735 structural constituent of ribosome
• GO:0008270 zinc ion binding
• GO:0048027 mRNA 5'-UTR binding
• GO:0070180 large ribosomal subunit rRNA binding

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006412 translation
• GO:0017148 negative regulation of translation

Cellular Component

• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0022625 cytosolic large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8c95, PDBe:8c95, PDBj:8c95
• PDBsum: 8c95
• PubMed: 36797249
• UniProt: P0AA10|RL13_ECOLI Large ribosomal subunit protein uL13 (Gene Name=rplM)