Structure of PDB 8c96 Chain E Binding Site BS01

Receptor Information
>8c96 Chain E (length=187) Species: 562 (Escherichia coli) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MELVLKDAQSALTVSETTFGRDFNEALVHQVVVAYAAGARQGTRAQKTRA
EVTGSSGSIKSPIWRSGGVTFAARPQDHSQKVNKKMYRGALKSILSELVR
QDRLIVVEKFSVEAPKTKLLAQKLKDMALEDVLIITGELDENLFLAARNL
HKVDVRDATGIDPVSLIAFDKVVMTADAVKQVEEMLA
Ligand information
>8c96 Chain A (length=1475) [Search RNA sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
gguuaagcgacuaagcguacacgguggaugcccuggcagucagaggcgau
gaaggacgugcuaaucugcgauaagcgucgguaaggugauaugaaccguu
auaaccggcgauuuccgaauggggaaacccaguguguuucgacacacuau
cauuaacugaauccauagguuaaugaggcgaaccgggggaacugaaacau
cuaaguaccccgaggaaaagaaaucaaccgagauucccccaguagcggcg
agcgaacggggagcagcccagagccugaaucaguguguguguuaguggaa
gcgucuggaaaggcgcgcgauacagggugacagccccguacacaaaaaug
cacaugcugugagcucgaugaguagggcgggacacgugguauccugucug
aauauggggggaccauccuccaaggcuaaauacuccugacugaccgauag
ugaaccaguaccgugagggaaaggcgaaaagaaccccggcgaggggagug
aaaaagaaccugaaaccguguacguacaagcagugggagcacgcuuaggc
gugugacugcguaccuuuuguauaaugggucagcgacuuauauucuguag
caagguuaaccgaauaggggagccgaagggaaaccgagucuuaacugggc
guuaaguugcaggguauagacccgaaacccggugaccgggagauagcugg
uucuccccgaaagcuauuuagguagcgccucgugaauucaucuccggggg
uagaugcgaauaccggagaauguuaucacgggagacacacggcgggugcu
aacguccgucgugaagagggaaacaacccagaccgccagcuaagguccca
aagucaugguuaagugggaaacgcggaagauguaacggggcuaaaccaug
caccgaagcugcggcagcgacgcuuaugcguuguuggguaggggagcguu
cuguaagccugcgaaggugugcugugaggcaugcuggagguaucagaagu
gcgaaugcugacauaaguaacgauaaagcgggugaaaagcccgcucgccg
gaagaccaaggcgacgguugggucagguagagaauaccaaggcgcuugag
agaacucgggugaaggaaaggcugucuccacccgagacucagugaaauug
aacucgcugugaagaugcaguguacccgcggcaagaucugccgugggcgc
uggagaacugaggggggcugcuccuaguacgagaggaccggaguggacgc
aucacugguguucggguugucaugccaauggcacugcccgguagcuaaau
gcggaagagauaagugcugaaagcaucuaagcacgaaacuugccccgaga
ugaguucucccugacccuuuaaggguccugaaggaacguugaagacgacg
acguugauaggccggguguguaagcgcagcgaugcguugagcuaaccggu
acuaaugaaccgugaggcuuaaccu
<<<<<<<<......<<<<<<<<<<<....<<<..<<<<<<<<<<<<<...
...<<<<<<....(((.>>>.....<<<<<<<..<<<)))....>>>...
...>>>>>>>...>>>....<<<....>>><<<<<<<....>>>>>>>.<
<<<<<<<<.........>>>>>>>>>.>>....<<<<<.....<<....>
>......>>>>>...........<<....>>..<<<<<<.....<<....
.>>....>>>>>>..<<<..<<<<......<<<<<<<<<<<<<.<<<...
<<<<<......>>>>>((......<<<.....))>>>...>>>...>>>>
>>>>>>>>>...>>>>........<<<.<<<<.........>>>>.>>>.
.....<<<<<......>>>>>..>>>......>>.>>>>>>>.>>.....
..........<<....>>....>>.........<<<<.....>>>>....
.........>....>>>>>>>>>>>.......<<<<..<<<<<......>
>>>>..>>>>...<.<........>.>.<<<<<<....<<<<<<<<<<<<
<..<<<...<<.....>>...>>>....<<...>>..<<<<.....>>>>
.....>>>>>>>>>>>>>..<<.<...<<<<<<.>>>>>>......>.>>
..<<<<<<....<<<<<....>>>>>..<<<<<<<...<<<<<<<<<...
..<...>.....>>>>>>.>>>...>>>>>>>.....<<<<<<<<<<...
...>>>>>>>>>>....<<<......>>>...<<<<.<<<...<<<(((.
....<<<<<<...........<..>...........))).....>>>>>>
.>>>...>>>>>>><<<<<<<<<....>>>>>>>>>....>>>>>><<<<
<<<...<<<......<<<<<<<<....>>>>>>>>...>>>..>>>>>.>
>.....>>>>>><......<<.....<<<<<<.......>>>>>><<<<.
...<<<<........((...>>>>.<<<<.....>>>>..>>>>..<<<<
....<<<<<<<<................>>>>>>>>.>>>>>>.....>.
....<<<<<........>>>>>..<<<<<<<<.<<..>>>>>>>>>>...
.<<<<<<<...<<<<..<<<<<<.................>>>>>>.<<<
<<...<<<<...<<<<<<<<<<<.)).>>>>>>..>>>>>...>>>>.>>
>>>...<<<....<<<<<...........>>>>>....>>>.>>>>....
...>>>>>>>..<<<<<.....>>>>>.....<<..<<<<<.......>>
>>>....<<<<<<<<..<<....<<<<<....>>>>>...>>...>>>>>
.>>>.....>>.....>>>>>>>>.
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB8c96 Cryo-EM captures early ribosome assembly in action.
Resolution4.43 Å
Binding residue
(original residue number in PDB)		Y35 A36 R40 Q41 T43 R44 A45 Q46 K47 R49 T53 G54 S70 I77 W78 R79 S80 V83 F85 Q90 Q94 K95 N97 K99 K130 T131 K132 R162 N163 H165 T173
Binding residue
(residue number reindexed from 1)		Y35 A36 R40 Q41 T43 R44 A45 Q46 K47 R49 T53 G54 S56 I63 W64 R65 S66 V69 F71 Q76 Q80 K81 N83 K85 K116 T117 K118 R148 N149 H151 T159
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0001070 RNA-binding transcription regulator activity
GO:0003677 DNA binding
GO:0003735 structural constituent of ribosome
GO:0005515 protein binding
GO:0019843 rRNA binding
GO:0030371 translation repressor activity
GO:0048027 mRNA 5'-UTR binding
GO:0060698 endoribonuclease inhibitor activity
Biological Process
GO:0002181 cytoplasmic translation
GO:0006353 DNA-templated transcription termination
GO:0006412 translation
GO:0006417 regulation of translation
GO:0017148 negative regulation of translation
GO:0031555 transcriptional attenuation
GO:0042255 ribosome assembly
GO:0045892 negative regulation of DNA-templated transcription
GO:0046677 response to antibiotic
GO:2000766 negative regulation of cytoplasmic translation
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0005840 ribosome
GO:0015934 large ribosomal subunit
GO:0022625 cytosolic large ribosomal subunit
GO:1990904 ribonucleoprotein complex

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:8c96, PDBe:8c96, PDBj:8c96
PDBsum8c96
PubMed36797249
UniProtP60723|RL4_ECOLI Large ribosomal subunit protein uL4 (Gene Name=rplD)

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