Structure of PDB 8c8y Chain O Binding Site BS01

Receptor Information

>8c8y Chain O (length=116) Species: 562 (Escherichia coli)

DKKSARIRRATRARRKLQELGATRLVVHRTPRHIYAQVIAPNGSEVLVAA
STVEKAIAEQLKYTGNKDAAAAVGKAVAERALEKGIKDVSFDRSGFQYHG
RVQALADAAREAGLQF

Ligand information

>8c8y Chain A (length=2548)

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

Structure summary

• PDB: 8c8y Cryo-EM captures early ribosome assembly in action.
• Resolution: 3.03 Å
• Binding residue (original residue number in PDB): R9 R10 T12 R13 R16 K17 S91 F92 R94 Q98 Y99 R111 F117
• Binding residue (residue number reindexed from 1): R8 R9 T11 R12 R15 K16 S90 F91 R93 Q97 Y98 R110 F116

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome
• GO:0008097 5S rRNA binding
• GO:0019843 rRNA binding

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006412 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:8c8y, PDBe:8c8y, PDBj:8c8y
• PDBsum: 8c8y
• PubMed: 36797249
• UniProt: P0C018|RL18_ECOLI Large ribosomal subunit protein uL18 (Gene Name=rplR)