Structure of PDB 8c8z Chain N Binding Site BS01

Receptor Information

>8c8z Chain N (length=120) Species: 562 (Escherichia coli)

MRHRKSGRQLNRNSSHRQAMFRNMAGSLVRHEIIKTTLPKAKELRRVVEP
LITLAKTDSVANRRLAFARTRDNEIVAKLFNELGPRFASRAGGYTRILKC
GFRAGDNAPMAYIELVDRSE

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): M1 R2 H3 R4 K5 S6 R8 Q9 L10 N11 S14 H16 M20 N23 S27 H31 I34 K35 T36 P39 K40 K42 E49 T53 R63 R64 F67 A68 R71 N73 E74 A91 G92 G93 R96 K99 R103 G105 D106 N107
• Binding residue (residue number reindexed from 1): M1 R2 H3 R4 K5 S6 R8 Q9 L10 N11 S14 H16 M20 N23 S27 H31 I34 K35 T36 P39 K40 K42 E49 T53 R63 R64 F67 A68 R71 N73 E74 A91 G92 G93 R96 K99 R103 G105 D106 N107

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome
• GO:0005515 protein 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: P0AG44|RL17_ECOLI Large ribosomal subunit protein bL17 (Gene Name=rplQ)