Structure of PDB 8c97 Chain U Binding Site BS01

Receptor Information

>8c97 Chain U (length=102) Species: 562 (Escherichia coli)

AAKIRRDDEVIVLTGKDKGKRGKVKNVLSSGKVIVEGINLVKKHQKPVPA
LNQPGGIVEKEAAIQVSNVAIFNAATGKADRVGFRFEDGKKVRFFKSNSE
TI

Ligand information

>8c97 Chain A (length=1292)

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

Structure summary

• PDB: 8c97 Cryo-EM captures early ribosome assembly in action.
• Resolution: 4.07 Å
• Binding residue (original residue number in PDB): K3 R5 R6 T14 G15 K16 V27 S29 K42 K43 H44 K46 P47 G56 I57 Q65 S67 N68 R81 G83 F84 F86 K91 K96
• Binding residue (residue number reindexed from 1): K3 R5 R6 T14 G15 K16 V27 S29 K42 K43 H44 K46 P47 G56 I57 Q65 S67 N68 R81 G83 F84 F86 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:8c97, PDBe:8c97, PDBj:8c97
• PDBsum: 8c97
• PubMed: 36797249
• UniProt: P60624|RL24_ECOLI Large ribosomal subunit protein uL24 (Gene Name=rplX)