Structure of PDB 8c8z Chain 0 Binding Site BS01

Receptor Information

>8c8z Chain 0 (length=56) Species: 562 (Escherichia coli)

AVQQNKPTRSKRGMRRSHDALTAVTSLSVDKTSGEKHLRHHITADGYYRG
RKVIAK

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): A1 V2 Q3 Q4 N5 K6 T8 R9 S10 K11 R12 G13 M14 R15 R16 S17 H18 S28 V29 R39 H40 Y48 R49
• Binding residue (residue number reindexed from 1): A1 V2 Q3 Q4 N5 K6 T8 R9 S10 K11 R12 G13 M14 R15 R16 S17 H18 S28 V29 R39 H40 Y48 R49

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome
• GO:0005515 protein binding

Biological Process

• GO:0000027 ribosomal large subunit assembly
• GO:0000302 response to reactive oxygen species
• GO:0002181 cytoplasmic translation
• GO:0006412 translation
• GO:0009314 response to radiation

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:8c8z, PDBe:8c8z, PDBj:8c8z
• PDBsum: 8c8z
• PubMed: 36797249
• UniProt: P0A7N4|RL32_ECOLI Large ribosomal subunit protein bL32 (Gene Name=rpmF)