Structure of PDB 8c97 Chain E Binding Site BS01

Receptor Information
>8c97 Chain E (length=146) Species: 562 (Escherichia coli) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MELVLKDAQSALTVSETTFGRDFNEALVHQVVVAYAAGAKVNKKMYRGAL
KSILSELVRQDRLIVVEKFSVEAPKTKLLAQKLKDMALEDVLIITGELDE
NLFLAARNLHKVDVRDATGIDPVSLIAFDKVVMTADAVKQVEEMLA
Ligand information
>8c97 Chain A (length=1292) [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
aaaaagaaccugaaaccguguacguaacuuauauucuguagcaagguuaa
ccgaauaggggagccgaagggaaaccgagucuuaacugggcguuaaguug
caggguaugauaaagcgggugaaaagcccgcucgccggaagaccaagggu
uccuguccaacguuaaucggggcagggugagucgaccccuaaggcgaggc
cgaaaggcguagucgaugggaaacagguuaauauuccuguacuugguguu
acugcgaaggggggacggagaaggcuauguuggccgggcgacgguugucc
cgguuuaagcguguaggcugguuuuccaggcaaauccggaaaaucaaggc
ugaggcgugaugacgaggcacuacggugcugaagcaacaaaugcccugcu
uccaggaaaagccucuaagcaucagguaacaucaaaucguaccccaaacc
gacacagguggucagguagagaauaccaaggcgcucgcugauauguaggu
gaggucccucgcggauggagcugaaaucagucgaagacugcuggagaacu
gaggggggcugcuccuaguacgagaggaccggaguggacgcaucacuggu
guucggguugucaugccaauggcacugcccgguagcuaaaugcggaagag
auaaacuugccccgagaugaguucucccugacccuuuaaggguccugaag
gaacguugaagacgacgacguugauaggccggguguguaagcgcagcgau
gcguugagcuaaccgguacuaaugaaccgugaggcuuaaccu
<<<<<<<.......<<<<<<<<<<.....<<<..<<<<<<<<<<<<<...
...<<<<<<.[..(((.>>>.....<<<<<<<..<<<)))..].>>>...
...>>>>>>>...>>>....<<<....>>><<<<<<<....>>>>>>>.<
<<<<<<<<.........>>>>>>>>>.>>...<.<<<<.....<......
>......>>>>..>.........<<....>>...<<<<<.....<<....
.>>....>>>>>...<<<..<<<<......<<<<<<<<<<<<<.<<<...
<<<<<......>>>>>((......<<<.....))>>>...>>>...>>>>
>>>>>>>>>...>>>>........<<<.<<<<.........>>>>.>>>.
.....<<<<<......>>>>>..>>>......>>.>>>>>>>.>>.....
..........<<....>>....>>.........<.<<......>>>....
.........>.....>>>>>>>>>>.....<<<<<<<<<<<<..<<<...
<<.....>>...>>>...<<....>>..<<<.......>>>.....>>>>
>>>>>>>>.....<<<<<<.......>>>>>><<<<....<<<<<.<<..
.<<<<<<...<<.....>>.>>>>>>....((<<<.<<<...<<<...<<
<....>>>...>>>...>>>..<<<<<........>>>>>))<<<<<<<<
<<<.<...<<<.<...<<<<..<<<..<<<<<<<<<<<....(((...>>
>>>><<..<<<<...<<<<<<<<<<<<.<<.....>>>>>>>>>>..>>>
>...>>>>...>><..<<<<<....>>>>>...>>>>>>...>>>...>>
>>.........>>>>...>.....>>>>>>>>>>>.>>>..>>.....<<
......>>>>>>>.<<<<.....>>>>..>>>>...<<<<<<.....<<<
...<<.<<....>>>>...>>>...>>>>>>...........<<<<<<<.
..<<<<..<<<<<<<...............>>>>>>>.<<<<<...<<<<
...<<<<<<<<<<<))).>>>>>>..>>>>>...>>>>.>>>>>...<<<
.....>>>.>>>>.......>>>>>>>..<<<<<.....>>>>><....<
<..<<<<<.......>>>>>....<<<<<<<<..<<....<<<<<....>
>>>>...>>...>>>>>.>>>.....>>..>...>>>>>>>.
Receptor-Ligand Complex Structure
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PDB8c97 Cryo-EM captures early ribosome assembly in action.
Resolution4.07 Å
Binding residue
(original residue number in PDB)		N24 A26 L27 Q30 Y35 G38 A39 K95 N97 K98 K99 Y101 R102 K130 T131 K132 L159 A160 R162 N163 T173 M199
Binding residue
(residue number reindexed from 1)		N24 A26 L27 Q30 Y35 G38 A39 K40 N42 K43 K44 Y46 R47 K75 T76 K77 L104 A105 R107 N108 T118 M144
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

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Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:8c97, PDBe:8c97, PDBj:8c97
PDBsum8c97
PubMed36797249
UniProtP60723|RL4_ECOLI Large ribosomal subunit protein uL4 (Gene Name=rplD)

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