Structure of PDB 8c8y Chain E Binding Site BS01

Receptor Information
>8c8y Chain E (length=192) Species: 562 (Escherichia coli) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MELVLKDAQSALTVSETTFGRDFNEALVHQVVVAYAAGARQGTRAQKTRA
EVTGSGKKPWSGSIKSPIWRSGGVTFAARPQDHSQKVNKKMYRGALKSIL
SELVRQDRLIVVEKFSVEAPKTKLLAQKLKDMALEDVLIITGELDENLFL
AARNLHKVDVRDATGIDPVSLIAFDKVVMTADAVKQVEEMLA
Ligand information
>8c8y Chain A (length=2548) [Search RNA sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
gguuaagcgacuaagcguacacgguggaugcccuggcagucagaggcgau
gaaggacgugcuaaucugcgauaagcgucgguaaggugauaugaaccguu
auaaccggcgauuuccgaauggggaaacccaguguguuucgacacacuau
cauuaacugaauccauagguuaaugaggcgaaccgggggaacugaucuaa
guaccccgaggaaaagaaaucaaccgagauucccccaguagcggcgagcg
aacggggagcagcccagagccugaaucaguguguguguuaguggaagcgu
cuggaaaggcgcgcgauacagggugacagccccguacacaaaaaugcaca
ugcugugagcucgaugaguagggcgggacacgugguauccugucugaaua
uggggggaccauccuccaaggcuaaauacuccugacugaccgauagugaa
ccaguaccgugagggaaaggcgaaaagaaccccggcgaggggagugaaaa
agaaccugaaaccguguacguacaagcagugggagcacgcuuaggcgugu
gacugcguaccuuuuguauaaugggucagcgacuuauauucuguagcaag
guuaaccgaauaggggagccgaagggaaaccgagucuuaacugggcguua
aguugcaggguauagacccgaaacccggugaucuagccaugggcagguug
aagguuggguaacacuaacuggaggaccgaaccgacuaauguugaaaaau
uagcggaugacuuguggcugggggugaaaggccaaucaaaccgggagaua
gcugguucuccccgaaagcuauuuagguagcgccucgugaauucaucucc
ggggguagagcacuguuucggccgaugcaaacugcgaauaccggagaaug
uuaucacgggagacacacggcgggugcuaacguccgucgugaagagggaa
acaacccagaccgccagcuaaggucccaaagucaugguuaagugggaaac
gaugugggaaggcgucggccugcgcggaagauguaacggggcuaaaccau
gcaccgaagcugcggcagcgacgcuuaugcguuguuggguaggggagcgu
ucuguaagccugcgaaggugugcugugaggcaugcuggagguaucagaag
ugcgaaugcugacauaaguaacgauaaagcgggugaaaagcccgcucgcc
ggaagaccaaggguuccuguccaacguuaaucggggcagggugagucgac
cccuaaggcgaggccgaaaggcguagucgaugggaaacagguuaauauuc
cuguacuugguguuacugcgaaggggggacggagaaggcuauguuggccg
ggcgacgguugucccgguuuaagcguguaggcugguuuuccaggcaaauc
cggaaaaucaaggcugaggcgugaugacgaggcacuacggugcugaagca
acaaaugcccugcuuccaggaaaagccucuaagcaucagguaacaucaaa
ucguaccccaaaccgacacagguggucagguagagaauaccaaggcgcuu
gagagaacucgggugaaggaacuaggcaaaauggugccguaacuucggga
gaaggcacgcugauauguaggugaggucccucgcggauggagcugaaauc
agucgaagauaccagcuggcugcaacuguuuauuaaaaacacagcacugu
gcaaacacgaaaguggacguauacggugugacgccugcccgguguaaacg
gcggccgacgguccuaagguagcgaauggcguaaugauggccaggcuguc
uccacccgagacucagugaaauugaacucgcugugaagaugcaguguacc
cgcggcaagacggaaagaccccgugaaccuuuacuauagcuugacacuga
acauugagccuugauguguaggauaggugggaggcuuugaaguguggacg
ccagucugcauggagccgaccuugaaauaccacccuuuaauguuugaugu
ucuaacguugacccguaauccggguugcggacagugucugguggguaguu
ugacuggggcggucuccuccuaaagaguaacggaggagcacgaagguugg
cuaauccuggucggacaucaggagguuagugcaauggcauaagccagcuu
gacugcgagcgugacggcgcgagcaggugcgaaagcaggucauagugauc
cggugguucugaauggaagggccaucgcucaacggauaaaagguacuccg
gggucccuaucugccgugggcgcuggagaacugaggggggcugcuccuag
uacgagaggaccggaguggacgcaucacugguguucggguugucaugcca
auggcacugcccgguagcuaaaugcggaagagauaagugcugaaagcauc
uaagcacgaaacuugccccgagaugaguucucccugacccuuuaaggguc
cugaaggaacguugaagacgacgacguugauaggccggguguguaagcgc
agcgaugcguugagcuaaccgguacuaaugaaccgugaggcuuaaccu
<<<<<<<<......<<<<<<<<<<<....{[[..[[<<<<<<<[[<<...
...<<<<<<....(((.>>>.....<<<<<<<..<<<)))....>>>...
...>>>>>>>...>>>....<<<....>>><<<<<<<....>>>>>>>.<
<<<<<<<<.........>>>>>>>>>.>>...<<<<<<.....<..>...
...>>>>>.>.........<<....>>..<<<<<<.....<<.....>>.
...>>>>>>..(((..<<<<......<<<<<<<<<<<<<.<<<...<<<<
<......>>>>>((......<<<.....))>>>...>>>...>>>>>>>>
>>>>>...>>>>........<<<<<<<<.........>>>>>>>>.....
.<<<<<..<<<<>>>>>..)))......]].>>>>>>>.]].........
......<<....>>....]].........<<<<.....>>>>........
.....}....>>>>>>>>>>>.......<<<<..<<<<<......>>>>>
..>>>>...<.<........>.>.<<<<<<....<<<<<<<<<<<<<..<
<<...<<.....>>...>>>...<<....>>..<<<<.....>>>>....
.>>>>>>>>>>>>>..<<.<..<<<<<<<.....<<<<<<<<<..<<<..
..<<<<<<......>>>>>>.....>>>...<<<.<<<<<........>>
>>>>>>....>>>>>>>>>...<<<.....>>>......>>>>>>...>.
.>.>>..<<<<<<....<<<<<....>>>>>.<<<<<<<<...<<<<<<<
<<.....<<<...<<<.<<<..>>>.>>>..>>.>.....>>>>>>.>>>
...>>>>>>>.>...<<<<<<<<<<......>>>>>>>>>>....<<<..
....>>>...<<<<.<<<...<<<(((.....<<<<<<...........<
<..<<<<<..<<..>>..>>>>>.>>...........))).....>>>>>
>.>>>...>>>>>>><<<<<..<<....>>..>>>>>....>>>>>><.<
<<<<...<<<......<<<<<<<<....>>>>>>>>...>>>..>>>>>.
.>.....>>>>>><......<<.....<<<<<<.......>>>>>><<<<
....<<<<<.<<...<<<<<<...<<.....>>.>>>>>>....((<<<.
<<<...<<<...<<<....>>>...>>>...>>>..<<<<<........>
>>>>))<<<<<<<<<<<<<...<<<<....<<<<..<<<..<<<<<<<<<
<<....(((...>>>>>><<..<<<<...<<<<<<<<<<<<.<<.....>
>>>>>>>>>..>>>>...>>>>...>><..<<<<<....>>>>>...>>>
>>>...>>>...>>>>.........>>>>...>>....>>>>>>>>>>>.
>>>..>>.....<<......>>>>>>>.<<<<.....>>>>..>>>>..<
<<<....<<<<<<<<.<<...............<<<<<....<<..>>..
...>>>>><<<<<<.....<<<...<<<<.....>>>>...>>>...>>>
>>>............<<<<<<<<<..<<<.........>>>..<<<<<<<
.....<<<....>>>.......>>>>>>>.<<<<<.<<<..<<....>>>
>>.<<<<.>>>>...............>>>>>..>>.>>>>>>>.....>
>.>>>>>>>>.>>>>>>.....>.....<<<<<........>>>>>..<<
<<<<<<.(((.[[......<<<<.[[<<<<...<<<<.<<<.<<<<<.<<
<<<<<<.<..<<<............<<<<<...<<.......<<<..<..
....>..>>>....>>.............>>>>>...>>>..>>.>>>>>
>>...<<<.<<<<<<.....>>>>>>>>>....>>>>>.>>>..>>>>..
.<<<.......>>><<<<<<...........>>>>>>..<<...<<<<<<
<...<<<<<<.......>>>>>>.....<....(((.>....>>>>>>>.
..<<<<..<<<<....>>>>..>>>>.<<<....>>>.>>))).......
<<<<<<<.((..>>>>..))>>>>>>>.............>>>>..]]>>
>>...]]..)))>>>>>>>>....<<<<<<<...<<<<..<<<<<<<...
............>>>>>>>.<<<<<...<<<<...<<<<<<<<<<<))).
>>>>>>..>>>>>...>>>>.>>>>>...<<<....<<<<<.........
..>>>>>....>>>.>>>>.......>>>>>>>..<<<<<.....>>>>>
<....<<..<<<<<.......>>>>>....<<<<<<<<..<<....<<<<
<....>>>>>...>>...>>>>>.>>>.....>>..>..>>>>>>>>.
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB8c8y Cryo-EM captures early ribosome assembly in action.
Resolution3.03 Å
Binding residue
(original residue number in PDB)		N24 H29 Q30 Y35 A36 A39 R40 Q41 T43 R44 A45 Q46 K47 T48 R49 T53 G54 S55 K57 G71 S75 I77 W78 R79 S80 T84 F85 Q94 K95 N97 K98 K99 M100 Y101 T131 K132 L159 R162 N163 H165 T173
Binding residue
(residue number reindexed from 1)		N24 H29 Q30 Y35 A36 A39 R40 Q41 T43 R44 A45 Q46 K47 T48 R49 T53 G54 S55 K57 G62 S66 I68 W69 R70 S71 T75 F76 Q85 K86 N88 K89 K90 M91 Y92 T122 K123 L150 R153 N154 H156 T164
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
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:8c8y, PDBe:8c8y, PDBj:8c8y
PDBsum8c8y
PubMed36797249
UniProtP60723|RL4_ECOLI Large ribosomal subunit protein uL4 (Gene Name=rplD)

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