Structure of PDB 8c8x Chain S Binding Site BS01

Receptor Information

>8c8x Chain S (length=110) Species: 562 (Escherichia coli)

METIAKHRHARSSAQKVRLVADLIRGKKVSQALDILTYTNKKAAVLVKKV
LESAIANAEHNDGADIDDLKVTKIFVDEGPSMKRIMPRAKGRADRILKRT
SHITVVVSDR

Ligand information

>8c8x Chain A (length=2705)

gguuaagcgacuaagcguacacgguggaugcccuggcagucagaggcgau
gaaggacgugcuaaucugcgauaagcgucgguaaggugauaugaaccguu
auaaccggcgauuuccgaauggggaaacccaguguguuucgacacacuau
cauuaacugaauccauagguuaaugaggcgaaccgggggaacugaaacau
cuaaguaccccgaggaaaagaaaucaaccgagauucccccaguagcggcg
agcgaacggggagcagcccagagccugaaucaguguguguguuaguggaa
gcgucuggaaaggcgcgcgauacagggugacagccccguacacaaaaaug
cacaugcugugagcucgaugaguagggcgggacacgugguauccugucug
aauauggggggaccauccuccaaggcuaaauacuccugacugaccgauag
ugaaccaguaccgugagggaaaggcgaaaagaaccccggcgaggggagug
aaaaagaaccugaaaccguguacguacaagcagugggagcacgcuuaggc
gugugacugcguaccuuuuguauaaugggucagcgacuuauauucuguag
caagguuaaccgaauaggggagccgaagggaaaccgagucuuaacugggc
guuaaguugcaggguauagacccgaaacccggugaucuagccaugggcag
guugaagguuggguaacacuaacuggaggaccgaaccgacuaauguugaa
aaauuagcggaugacuuguggcugggggugaaaggccaaucaaaccggga
gauagcugguucuccccgaaagcuauuuagguagcgccucgugaauucau
cuccggggguagagcacuguuucggcaagggggucaucccgacuuaccaa
cccgaugcaaacugcgaauaccggagaauguuaucacgggagacacacgg
cgggugcuaacguccgucgugaagagggaaacaacccagaccgccagcua
aggucccaaagucaugguuaagugggaaacgaugugggaaggcccgucgg
ccugcgcggaagauguaacggggcuaaaccaugcaccgaagcugcggcag
cgacgcuuaugcguuguuggguaggggagcguucuguaagccugcgaagg
ugugcugugaggcaugcuggagguaucagaagugcgaaugcugacauaag
uaacgauaaagcgggugaaaagcccgcucgccggaagaccaaggguuccu
guccaacguuaaucggggcagggugagucgaccccuaaggcgaggccgaa
aggcguagucgaugggaaacagguuaauauuccuguacuugguguuacug
cgaaggggggacggagaaggcuauguuggccgggcgacgguugucccggu
uuaagcguguaggcugguuuuccaggcaaauccggaaaaucaaggcugag
gcgugaugacgaggcacuacggugcugaagcaacaaaugcccugcuucca
ggaaaagccucuaagcaucagguaacaucaaaucguaccccaaaccgaca
cagguggucagguagagaauaccaaggcgcuugagagaacucgggugaag
gaacuaggcaaaauggugccguaacuucgggagaaggcacgcugauaugu
aggugaggucccucgcggauggagcugaaaucagucgaagauaccagcug
gcugcaacuguuuauuaaaaacacagcacugugcaaacacgaaaguggac
guauacggugugacgccugcccggugccggaagguuaauugaugggguua
gcgcaagcgaagcucuugaucgaagccccgguaaacggcggccguaacua
uaacgguccuaagguagcgaaauuccccugcacgaauggcguaaugaugg
ccaggcugucuccacccgagacucagugaaauugaacucgcugugaagau
gcaguguacccgcggcaagacggaaagaccccgugaaccuuuacuauagc
uugacacugaacauugagccuugauguguaggauaggugggaggcuuuga
aguguggacgccagucugcauggagccgaccuugaaauaccacccuuuaa
uguuugauguucuaacguugacccguaauccggguugcggacagugucug
guggguaguuugacuggggcggucuccuccuaaagaguaacggaggagca
cgaagguuggcuaauccuggucggacaucaggagguuagugcaauggcau
aagccagcuugacugcgagcgugacggcgcgagcaggugcgaaagcaggu
cauagugauccggugguucugaauggaagggccaucgcucaacggauaaa
agguacuccggggaggcugauaccgcccaagaguucauaucgacggcggu
guuuggcacgucccuaucugccgugggcgcuggagaacugaggggggcug
cuccuaguacgagaggaccggaguggacgcaucacugguguucggguugu
caugccaauggcacugcccgguagcuaaaugcggaagagauaagugcuga
aagcaucuaagcacgaaacuugccccgagaugaguucucccugacccuuu
aaggguccugaaggaacguugaagacgacgacguugauaggccgggugug
uaagcgcagcgaugcguugagcuaaccgguacuaaugaaccgugaggcuu
aaccu

<<<<<<<<......<<<<<<<<<<......<<..<<<<<<<<<<<<<...
...<<<<<<....(((.>>>.....<<<<<<<..<<<)))....>>>...
...>>>>>>>...>>>....<<<....>>><<<<<<<....>>>>>>>.<
<<<<<<<<.........>>>>>>>>>.>>...<<<<<<.....<......
>......>>>>>.>.........<<....>>..<<<<<<.....<<....
.>>....>>>>>>..<<<..<<<<......<<<<<<<<<<<<<.<<<...
<<<<<......>>>>>((......<<<.....))>>>...>>>...>>>>
>>>>>>>>>...>>>>........<<<<<<<<.........>>>>>>>>.
.....<<<<<..((((>>>>>..>>>......>>.>>>>>>>.>>.....
..........<<....>>....>>.........<<<<.....>>>>....
...............>>>>>>>>>>.......<<<<..<<<<<......>
>>>>..>>>>...<.<........>.>.<<<<<<....<<<<<<<<<<<<
<..<<<...<<.....>>...>>>...<<....>>..<<<.......>>>
.....>>>>>>>>>>>>>..<<.<..<<<<<<<.....<<<<<<<<<..<
<<....<<<<<<......>>>>>>.....>>>...<<..<<<<<......
..>>>>>.>>....>>>>>>>>>...<<<.....>>>......>>>>>>.
..>..>.>>..<<<<<<....<<<<<....>>>>>.<<<<<<<<...<<<
<<<<<<......<<...<<<.<<<<...<<<<<<.......>>>>.>>..
.>>>>.>>>..>>.......>>>>>>.>>>...>>>>>>>.>...<<<<<
<<<<<......>>>>>>>>>>....<<<......>>>...<<<<.<<<..
.<<<(((.....<<<<<<...........<<..<<<<<..<<....>>..
>>>>>.>>...........))).....>>>>>>.>>>...>>>>>>><<<
<<<<<<....>>>>>>>>>....>>>>>><<<<<<<...<<<......<<
<<<<<<....>>>>>>>>...>>>..>>>>>.>>.....>>>>>>.....
..<<.....<<<<<<.......>>>>>><<<<....<<<<<.<<...<<<
<<<...<<.....>>.>>>>>>....((<<<.<<.<..<<<...<<<...
.>>>...>>>...>>>..<<<<<........>>>>>))<<<<<<<<<<<<
<...<<<<....<<<<..<<<..<<<<<<<<<<<....[[[...>>>>>>
<<..<<<<...<<<<<<<<<<<<.<<.....>>>>>>>>>>..>>>>...
>>>>...>><..<<<<<....>>>>>...>>>>>>...>>>...>>>>..
.......>>>>...>>....>>>>>>>>>>>.>>>..>>.....<<....
..>>>>>>>.<<<<.....>>>>..>>>>..<<<<....<<<<<<<<.<<
...............<<<<<...............>>>>><<<<<<....
.<<<...<<<<.....>>>>...>>>...>>>>>>............<<<
<<<<<<..<<<.........>>>..<<<<<<<.....<<<....>>>...
....>>>>>>>.<<<<<.<<<..<<<<<<<..<<<........<<<<<..
<<....>>...>>>>>........>>>>>>>>..>>>>>.<<<<......
...>>>>.........<...............>....>>>>>..>>.>>>
>>>>.....>>.>>>>>>>>.>>>>>>...........<<<<<.......
.>>>>>..<<<<<<<<.<<<.<<<....<<<<<.<<<<<<..<<<<<.<<
<.<<<<<.<<<<<<<<<<<.<<<............<<<<<...<<.....
.<<<<..<<....>>..>>>>...>>.............>>>>>...>>>
.>>>>>>>>>>>...<<<.<<<<<<.....>>>>>>>>>....>>>>>.>
>>..>>>>>..<<<<.....>>>><<<<<<...........>>>>>>..<
<...<<<<<<<...<<<<<<.......>>>>>>.....<<...(((>>..
..>>>>>>>...<<<<..<<<<....>>>>..>>>>.<<<....>>>.>>
))).......<<<<<<<.<<..))))..>>>>>>>>>.............
>>>>..>>>>>>>..<<.......<<<.................>>>...
.....>>...>>>...>>>>>>>>>>>....<<<<<<<...<<<<...<<
<<<<.....<....>....>>>>>>..<<<<....<<<<...<<<<.<<<
<<<]]].>>>>>>...>>>>...>>>>..>>>>...<<<.<...<<<<..
.........>>>>....>>>>.>>>>.......>>>>>>>..<<<<<...
..>>>>><....<<..<<<<<.......>>>>>....<<<<<<<<..<<.
...<<<<<....>>>>>...>>...>>>>>.>>>.....>>..>..>>>>
>>>>.

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8c8x Cryo-EM captures early ribosome assembly in action.
• Resolution: 3.93 Å
• Binding residue (original residue number in PDB): I4 K6 H7 R8 H9 R11 S13 Q15 K16 R18 R25 K41 K42 K49 E52 A56 N57 N61 D77 E78 G79 P80 R84 P87 R88 A89 K90 G91 R92 A93 D94 I96 L97 K98 R99 H102
• Binding residue (residue number reindexed from 1): I4 K6 H7 R8 H9 R11 S13 Q15 K16 R18 R25 K41 K42 K49 E52 A56 N57 N61 D77 E78 G79 P80 R84 P87 R88 A89 K90 G91 R92 A93 D94 I96 L97 K98 R99 H102

Gene Ontology

Molecular Function

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

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006412 translation
• GO:0042255 ribosome assembly
• GO:0042256 cytosolic ribosome assembly
• GO:0046677 response to antibiotic
• GO:1902626 assembly of large subunit precursor of preribosome

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:8c8x, PDBe:8c8x, PDBj:8c8x
• PDBsum: 8c8x
• PubMed: 36797249
• UniProt: P61175|RL22_ECOLI Large ribosomal subunit protein uL22 (Gene Name=rplV)