Structure of PDB 8c8z Chain J Binding Site BS01

Receptor Information

>8c8z Chain J (length=142) Species: 562 (Escherichia coli)

MKTFTAKPETVKRDWYVVDATGKTLGRLATELARRLRGKHKAEYTPHVDT
GDYIIVLNADKVAVTGNKRTDKVYYHHTGHIGGIKQATFEEMIARRPERV
IEIAVKGMLPKGPLGRAMFRKLKVYAGNEHNHAAQQPQVLDI

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): K2 T3 K7 E9 W15 L25 G26 R27 T30 R37 K39 H47 Y53 T65 K68 Y75 H77 T78 H80 K85 R96 E102 G107 M108 P110 K111 P113 L114 R116 R120 H132 A134 Q135 Q136
• Binding residue (residue number reindexed from 1): K2 T3 K7 E9 W15 L25 G26 R27 T30 R37 K39 H47 Y53 T65 K68 Y75 H77 T78 H80 K85 R96 E102 G107 M108 P110 K111 P113 L114 R116 R120 H132 A134 Q135 Q136

Gene Ontology

Molecular Function

• GO:0003729 mRNA binding
• GO:0003735 structural constituent of ribosome
• GO:0008270 zinc ion binding
• GO:0048027 mRNA 5'-UTR binding
• GO:0070180 large ribosomal subunit rRNA binding

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006412 translation
• GO:0017148 negative regulation of 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: P0AA10|RL13_ECOLI Large ribosomal subunit protein uL13 (Gene Name=rplM)