Structure of PDB 8c8z Chain U Binding Site BS01

Receptor Information

>8c8z Chain U (length=102) Species: 562 (Escherichia coli)

AAKIRRDDEVIVLTGKDKGKRGKVKNVLSSGKVIVEGINLVKKHQKPVPA
LNQPGGIVEKEAAIQVSNVAIFNAATGKADRVGFRFEDGKKVRFFKSNSE
TI

Ligand information

>8c8z Chain A (length=2205)

gguuaagcgacuaagcguacacgguggaugcccuggcagucagaggcgau
gaaggacgugcuaaucugcgauaagcgucgguaaggugauaugaaccguu
auaaccggcgauuuccgaauggggaaacccaguguguuucgacacacuau
cauuaacugaauccauagguuaaugaggcgaaccgggggaacugaaacau
cuaaguaccccgaggaaaagaaaucaaccgagauucccccaguagcggcg
agcgaacggggagcagcccagagccugaaucaguguguguguuaguggaa
gcgucuggaaaggcgcgcgauacagggugacagccccguacacaaaaaug
cacaugcugugagcucgaugaguagggcgggacacgugguauccugucug
aauauggggggaccauccuccaaggcuaaauacuccugacugaccgauag
ugaaccaguaccgugagggaaaggcgaaaagaaccccggcgaggggagug
aaaaagaaccugaaaccguguacguacaagcagugggagcacgcuuaggc
gugugacugcguaccuuuuguauaaugggucagcgacuuauauucuguag
caagguuaaccgaauaggggagccgaagggaaaccgagucuuaacugggc
guuaaguugcaggguauagacccgaaacccggugaucaccgggagauagc
ugguucuccccgaaagcuauuuagguagcgccucgugaauucaucuccgg
ggguagagcacuguuucggcaagcaacccgaugcaaacugcgaauaccgg
agaauguuaucacgggagacacacggcgggugcuaacguccgucgugaag
agggaaacaacccagaccgccagcuaaggucccaaagucaugguuaagug
ggaaacgaugugggaaggcgucggccugcgcggaagauguaacggggcua
aaccaugcaccgaagcugcggcagcgacgcuuaugcguuguuggguaggg
gagcguucuguaagccugcgaaggugugcugugaggcaugcuggagguau
cagaagugcgaaugcugacauaaguaacgauaaagcgggugaaaagcccg
cucgccggaagaccaaggguuccuguccaacguuaaucggggcaggguga
gucgaccccuaaggcgaggccgaaaggcguagucgaugggaaacagguua
auauuccuguacuugguguuacugcgaaggggggacggagaaggcuaugu
uggccgggcgacgguugucccgguuuaagcguguaggcugguuuuccagg
caaauccggaaaaucaaggcugaggcgugaugacgaggcacuacggugcu
gaagcaacaaaugcccugcuuccaggaaaagccucuaagcaucagguaac
aucaaaucguaccccaaaccgacacagguggucagguagagaauaccaag
gcgcuugagagaacucgggugaaggaacuaggcaaaauggugccgcugau
auguaggugaggucccucgcggauggagcugaaaucagucgaagauacca
gagacucagugaaauugaacucgcugugaagaugcaguguacccgcggca
agacggaaagaccccgugaaccuuuacuauagcuugacacugaacauugu
uugauguucuaacguugacccguaauccggguugcggacagugucuggug
gguaguuugacuggggcggucuccuccuaaagaguaacggaggagcacga
agguuggcuaauccuggucggacaucaggagguuagugcaauggcauaag
ccagcuugacugcgagcgugacggcgcgagcaggugcgaaagcaggucau
agugauccggugguucugaauggaagggccaucgcucaacggauaaaagg
uacuccggggucccuaucugccgugggcgcuggagaacugaggggggcug
cuccuaguacgagaggaccggaguggacgcaucacugguguucggguugu
caugccaauggcacugcccgguagcuaaaugcggaagagauaagugcuga
aagcaucuaagcacgaaacuugccccgagaugaguucucccugacccuuu
aaggguccugaaggaacguugaagacgacgacguugauaggccgggugug
uaagcgcagcgaugcguugagcuaaccgguacuaaugaaccgugaggcuu
aaccu

<<<<<<<<......<<<<<<<<<<<....{[[..[[<<<<<<<[[<<...
...<<<<<<....(((.>>>.....<<<<<<<..<<<)))....>>>...
...>>>>>>>...>>>....<<<....>>><<<<<<<....>>>>>>>.<
<<<<<<<<.........>>>>>>>>>.>>...<<<<<<.....<......
>......>>>>>.>.........<<....>>..<<<<<<.....<<....
.>>....>>>>>>..(((..<<<<......<<<<<<<<<<<<<.<<<...
<<<<<......>>>>>((......<<<.....))>>>...>>>...>>>>
>>>>>>>>>...>>>>........<<<<<<<<.........>>>>>>>>.
.....<<<<<..<<<<>>>>>..)))......]].>>>>>>>.]].....
..........<<....>>....]].........<<<<.....>>>>....
.........}....>>>>>>>>>>>.......<<<<..<<<<<......>
>>>>..>>>>...<.<........>.>.<<<<<<....<<<<<<<<<<<<
<..<<<...<<.....>>...>>>...<<....>>..<<<<.....>>>>
.....>>>>>>>>>>>>>..<<.<..<<<<<<<....>>>>>>...>..>
.>>..<<<<<<....<<<........>>>.<<<<<<<<...<<<<<<<.<
<....<<<...<<<.<<<<........>>>>.>>>..>>.>.....>>>>
>>.>>>...>>>>>>>.>...<<<<<<<<<<......>>>>>>>>>>...
.<<<......>>>...<<<<.<<<...<<<(((.....<<<<<<......
.....<<..<<<<<..<<..>>..>>>>>.>>...........)))....
.>>>>>>.>>>...>>>>>>><<<<<<<<<....>>>>>>>>>....>>>
>>><.<<<<<...<<<......<<<<<<<<....>>>>>>>>...>>>..
>>>>>..>.....>>>>>><......<<.....<<<<<<.......>>>>
>><<<<....<<<<<.<<...<<<<<<...<<.....>>.>>>>>>....
((<<<.<<<...<<<..<<<<....>>>.>.>>>...>>>..<<<<<...
.....>>>>>))<<<<<<<<<<<.....<<<<....<<<<..<<<..<<<
<<<<<<<<....(((...>>>>>><<..<<<<...<<<<<<<<<<<<.<<
.....>>>>>>>>>>..>>>>...>>>>...>><..<<<<<....>>>>>
...>>>>>>...>>>...>>>>.........>>>>.........>>>>>>
>>>>>.>>>..>>.....<<......>>>>>>>.<<<<.....>>>>..>
>>>..<<<<....<<.............................<<<<<<
.....<<<...<<<<.....>>>>...>>>...>>>>>>...........
.>>.>>>>>>.....>.....<<<<<........>>>>>..<<<<<<<<.
(((.[[......<<<<.[[<<<<...<<<<.<<<.<<<<<.<<<<<<<..
..>>>>>>>...<<<.<<<<<<.....>>>>>>>>>....>>>>>.>>>.
.>>>>...<...........><<<<<<...........>>>>>>..<<..
.<<<<<<<...<<<<<<.......>>>>>>.....<<...(((>>....>
>>>>>>...<<<<..<<<<....>>>>..>>>>.<<<....>>>.>>)))
.......<<<<<<<.((..>>>>..))>>>>>>>.............>>>
>..]]>>>>...]]..)))>>>>>>>>....<<<<<<<...<<<<..<<<
<<<<...............>>>>>>>.<<<<<...<<<<...<<<<<<<<
<<<))).>>>>>>..>>>>>...>>>>.>>>>>...<<<....<<<<...
..........>>>>....>>>.>>>>.......>>>>>>>..<<<<<...
..>>>>><....<<..<<<<<.......>>>>>....<<<<<<<<..<<.
...<<<<<....>>>>>...>>...>>>>>.>>>.....>>..>..>>>>
>>>>.

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8c8z Cryo-EM captures early ribosome assembly in action.
• Resolution: 3.12 Å
• Binding residue (original residue number in PDB): K3 R5 R6 G15 K16 V27 V41 K43 H44 K46 P47 G56 I57 S67 R81 F84 F86 K90 K91 K96
• Binding residue (residue number reindexed from 1): K3 R5 R6 G15 K16 V27 V41 K43 H44 K46 P47 G56 I57 S67 R81 F84 F86 K90 K91 K96

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0005515 protein binding
• GO:0019843 rRNA binding
• GO:0070180 large ribosomal subunit rRNA binding

Biological Process

• GO:0000027 ribosomal large subunit assembly
• 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:8c8z, PDBe:8c8z, PDBj:8c8z
• PDBsum: 8c8z
• PubMed: 36797249
• UniProt: P60624|RL24_ECOLI Large ribosomal subunit protein uL24 (Gene Name=rplX)