Structure of PDB 8c90 Chain W Binding Site BS01

Receptor Information

>8c90 Chain W (length=70) Species: 562 (Escherichia coli)

SEAKRLGVKRFGGESVLAGSIIVRQRGTKFHAGANVGCGRDHTLFAKADG
KVKFEVKGPKNRKFISIEAE

Ligand information

>8c90 Chain A (length=2100)

gguuaagcgacuaagcguacacgguggaugcccuggcagucagaggcgau
gaaggacgugcuaaucugcgauaagcgucgguaaggugauaugaaccguu
auaaccggcgauuuccgaauggggaaacccaguguguuucgacacacuau
cauuaacugaauccauagguuaaugaggcgaaccgggggaacugaaacau
cuaaguaccccgaggaaaagaaaucaaccgagauucccccaguagcggcg
agcgaacggggagcagcccagagccugaaucaguguguguguuaguggaa
gcgucuggaaaggcgcgcgauacagggugacagccccguacacaaaaaug
cacaugcugugagcucgaugaguagggcgggacacgugguauccugucug
aauauggggggaccauccuccaaggcuaaauacuccugacugaccgauag
ugaaccaguaccgugagggaaaggcgaaaagaaccccggcgaggggagug
aaaaagaaccugaaaccguguacguacaagcagugggagcacgcuuaggc
gugugacugcguaccuuuuguauaaugggucagcgacuuauauucuguag
caagguuaaccgaauaggggagccgaagggaaaccgagucuuaacugggc
guuaaguugcaggguauagacccgaaacccggugaucaccgggagauagc
ugguucuccccgaaagcuauuuagguagcgccucgugaauucaucuccgg
ggguagagcacuguuucggcaacccgaugcaaacugcgaauaccggagaa
uguuaucacgggagacacacggcgggugcuaacguccgucgugaagaggg
aaacaacccagaccgccagcuaaggucccaaagucaugguuaagugggaa
acgaugugggaaggcgucggccugcgcggaagauguaacggggcuaaacc
augcaccgaagcugcggcagcgacgcuuaugcguuguuggguaggggagc
guucuguaagccugcgaaggugugcugugaggcaugcuggagguaucaga
agugcgaaugcugacauaaguaacgauaaagcgggugaaaagcccgcucg
ccggaagaccaaggguuccuguccaacguuaaucggggcagggugagucg
accccuaaggcgaggccgaaaggcguagucgaugggaaacagguuaauau
uccuguacuugguguuacugcgaaggggggacggagaaggcuauguuggc
cgggcgacgguugucccgguuuaagcguguaggcugguuuuccaggcaaa
uccggaaaaucaaggcugaggcgugaugacgaggcacuacggugcugaag
caacaaaugcccugcuuccaggaaaagccucuaagcaucagguaacauca
aaucguaccccaaaccgacacagguggucagguagagaauaccaaggcgc
uugagagaacucgggugaaggaacuaggcaaaauggugccggcacgcuga
uauguaggugaggucccucgcggauggagcugaaaucagucgaagauacc
agcuggcgccaggcugucuccacccgagacucagugaaauugaacucgcu
gugaagaugcaguguacccgcggcaagacggaaaguccuccuaaagagua
acggaggagcacgaagguuggcuaauccuggucggacaucaggagguuag
ugcaauggcauaagccagcuugacugcgagcgugacggcgcgagcaggug
cgaaagcaggucauagugauccggugguucugaauggaagggccaucgcu
caacgucccuaucugccgugggcgcuggagaacugaggggggcugcuccu
aguacgagaggaccggaguggacgcaucacugguguucggguugucaugc
caauggcacugcccgguagcuaaaugcggaagagauaagugcugaaagca
ucuaagcacgaaacuugccccgagaugaguucucccugacccuuuaaggg
uccugaaggaacguugaagacgacgacguugauaggccggguguguaagc
gcagcgaugcguugagcuaaccgguacuaaugaaccgugaggcuuaaccu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8c90 Cryo-EM captures early ribosome assembly in action.
• Resolution: 3.15 Å
• Binding residue (original residue number in PDB): S12 E13 A14 R16 R21 F22 G23 E25 A29 G30 I32 R35 R37 G38 T39 K40 G50 R51 D52 H53 F56 K71 R73 K74
• Binding residue (residue number reindexed from 1): S1 E2 A3 R5 R10 F11 G12 E14 A18 G19 I21 R24 R26 G27 T28 K29 G39 R40 D41 H42 F45 K60 R62 K63

Gene Ontology

Molecular Function

• GO:0000049 tRNA binding
• GO:0003735 structural constituent of ribosome
• GO:0005515 protein binding
• GO:0019843 rRNA binding
• GO:0043022 ribosome binding

Biological Process

• GO:0000027 ribosomal large subunit assembly
• GO:0001558 regulation of cell growth
• GO:0002181 cytoplasmic translation
• GO:0006412 translation
• GO:0042256 cytosolic ribosome assembly
• GO:0090070 positive regulation of ribosome biogenesis
• GO:1902626 assembly of large subunit precursor of preribosome

Cellular Component

• GO:0005737 cytoplasm
• GO:0005840 ribosome
• GO:0022625 cytosolic large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8c90, PDBe:8c90, PDBj:8c90
• PDBsum: 8c90
• PubMed: 36797249
• UniProt: P0A7L8|RL27_ECOLI Large ribosomal subunit protein bL27 (Gene Name=rpmA)