Structure of PDB 8c93 Chain E Binding Site BS01

Receptor Information

>8c93 Chain E (length=186) Species: 562 (Escherichia coli)

MELVLKDAQSALTVSETTFGRDFNEALVHQVVVAYAAGARQGTRAQKTRA
EVTGSGSIKSPIWRSGGVTFAARPQDHSQKVNKKMYRGALKSILSELVRQ
DRLIVVEKFSVEAPKTKLLAQKLKDMALEDVLIITGELDENLFLAARNLH
KVDVRDATGIDPVSLIAFDKVVMTADAVKQVEEMLA

Ligand information

>8c93 Chain A (length=1740)

gguuaagcgacuaagcguacacgguggaugcccuggcagucagaggcgau
gaaggacgugcuaaucugcgauaagcgucgguaaggugauaugaaccguu
auaaccggcgauuuccgaauggggaaacccaguguguuucgacacacuau
cauuaacugaauccauagguuaaugaggcgaaccgggggaacugaaacau
cuaaguaccccgaggaaaagaaaucaaccgagauucccccaguagcggcg
agcgaacggggagcagcccagagccugaaucaguguguguguuaguggaa
gcgucuggaaaggcgcgcgauacagggugacagccccguacacaaaaaug
cacaugcugugagcucgaugaguagggcgggacacgugguauccugucug
aauauggggggaccauccuccaaggcuaaauacuccugacugaccgauag
ugaaccaguaccgugagggaaaggcgaaaagaaccccggcgaggggagug
aaaaagaaccugaaaccguguacguacaagcagugggagcacgcuuaggc
gugugacugcguaccuuuuguauaaugggucagcgacuuauauucuguag
caagguuaaccgaauaggggagccgaagggaaaccgagugcguuaaguug
caggguauagacccgaaacccggugaccgggagauagcugguucuccccg
aaagcuauuuagguagcgccucgugaauucaucuccggggguagagcacc
aaacugcgaauaccggagaauguuaucacgggagacacacggcgggugcu
aacguccgucgugaagagggaaacaacccagaccgccagcuaagguccca
aagucaugguuaagugggaaacgcggaagauguaacggggcuaaaccaug
caccgaagcugcggcagcgacgcuuaugcguuguuggguaggggagcguu
cuguaagccugcgaaggugugcugugaggcaugcuggagguaucagaagu
gcgaaugcugacauaaguaacgauaaagcgggugaaaagcccgcucgccg
gaagaccaaggguuccuguccaacguuaaucggggcagggugagucgacc
ccuaaggcgaggccgaaaggcguagucgaugggaaacagguuaauauucc
uguacuugguguuacugcgaaggggggacggagaaggcuauguuggccgg
gcgacgguugucccgguuuaagcguguaggcugguuuuccaggcaaaucc
ggaaaaucaaggcugaggcgugaugacgaggcacuacggugcugaagcaa
caaaugcccugcuuccaggaaaagccucuaagcaucagguaacaucaaau
cguaccccaaaccgacacagguggucagguagagaauaccaaggcgcuug
agaaauugaacucgcugugaagaugcaguguacccgcggcaagacggccu
aucugccgugggcgcuggagaacugaggggggcugcuccuaguacgagag
gaccggaguggacgcaucacugguguucggguugucaugccaauggcacu
gcccgguagcuaaaugcggaagagauaagugcugaaagcaucuaagcacg
aaacuugccccgagaugaguucucccugacccuuuaaggguccugaagga
acguugaagacgacgacguugauaggccggguguguaagcgcagcgaugc
guugagcuaaccgguacuaaugaaccgugaggcuuaaccu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8c93 Cryo-EM captures early ribosome assembly in action.
• Resolution: 4.17 Å
• Binding residue (original residue number in PDB): A26 H29 Q30 Y35 A36 A39 R40 Q41 T43 R44 K47 T48 R49 A50 T53 G54 S55 I77 W78 R79 S80 V83 F85 Q90 Q94 K95 N97 K98 K99 M100 Y101 K130 T131 K132 L159 R162 N163 H165 T173
• Binding residue (residue number reindexed from 1): A26 H29 Q30 Y35 A36 A39 R40 Q41 T43 R44 K47 T48 R49 A50 T53 G54 S55 I62 W63 R64 S65 V68 F70 Q75 Q79 K80 N82 K83 K84 M85 Y86 K115 T116 K117 L144 R147 N148 H150 T158

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

External links

• PDB: RCSB:8c93, PDBe:8c93, PDBj:8c93
• PDBsum: 8c93
• PubMed: 36797249
• UniProt: P60723|RL4_ECOLI Large ribosomal subunit protein uL4 (Gene Name=rplD)