Structure of PDB 8yoo Chain SO Binding Site BS01

Receptor Information

>8yoo Chain SO (length=135) Species: 9606 (Homo sapiens)

LGPQVAEGENVFGVCHIFASFNDTFVHVTDLSGKETICRVTGGMKVKADR
DESSPYAAMLAAQDVAQRCKELGITALHIKLRATGGNRTKTPGPGAQSAL
RALARSGMKIGRIEDVTPIPSDSTRRKGGRRGRRL

Ligand information

>8yoo Chain S2 (length=1719)

uaccugguugauccugccaguagcauaugcuugucucaaagauuaagcca
ugcaugucuaaguacgcacggccgguacagugaaacugcgaauggcucau
uaaaucaguuaugguuccuuuggucgcucgcuccucucccacuuggauaa
cugugguaauucuagagcuaauacaugccgacgggcgcugacccccuucg
cgggggggaugcgugcauuuaucaguggugacucuagauaaccucgggcc
gaucgcacgccccccguggcggcgacgacccauucgaacgucugcccuau
caacuuucgaugguagucgccgugccuaccauggugaccacgggugacgg
ggaaucaggguucgauuccggagagggagccugagaaacggcuaccacau
ccaaggaaggcagcaggcgcgcaaauuacccacucccgacccggggaggu
agugacgaaaaauaacaauacaggacucuuucgaggcccuguaauuggaa
ugaguccacuuuaaauccuuccgcgaggauccauuggagggcaagucugg
ugccagcagccgcgguaauuccagcuccaauagcguauauuaaaguugcu
gcaguuaaaaagcucguaguuggaucuuggcucucggcgcccgaagcauu
uacuuugaaaaaauuagaguguucaaagcaggcccgagccgccuggauac
cgcagcuaggaauaauggaauaggaccgcgguucuauuuuguugguuuuc
ggaacugaggccaugauuaagagggacggccgggggcauucguauugcgc
cgcuagaggugaaauucuuggaccggcgcaagacggaccagagcgaaagc
auuugccaagaauguuuucauuaaucaagaacgaaagucggagguucgaa
gacgaucagauaccgucguaguuccgaccauaaacgaugccgacuggcga
ugcggcggcguuauucccaugacccgccgggcagcuuccgggaaaccaaa
gucuuuggguuccggggggaguaugguugcaaagcugaaacuuaaaggaa
uugacggaagggcaccaccaggaguggagccugcggcuuaauuugacuca
acacgggaaaccucacccggcccggacacggacaggauugacagauugau
agcucuuucucgauuccgugggugguggugcauggccguucuuaguuggu
ggagcgauuugucugguuaauuccgauaacgaacgagacucuggcaugcu
aacuaguuacgcgacccccgagcggucggcgucccccaacuucuuagagg
gacaaguggcguucagccacccgagauugagcaauaacaggucugugaug
cccuuagauguccggggcugcacgcgcgcuacacugacuggcucagcgug
ugccuacccuacgccggcaggcgcggguaacccguugaaccccauucgug
auggggaucggggauugcaauuauuccccaugaacgaggaauucccagua
agugcgggucauaagcuugcguugauuaagucccugcccuuuguacacac
cgcccgucgcuacuaccgauuggaugguuuagugaggcccucggaucggc
cccgccggggucggcccacggcccuggcggagcgcugagaagacggucga
acuugacuaucuagaggaaguaaaagucguaacaagguuuccguagguga
accugcggaaggaucauua

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8yoo Structural basis for differential inhibition of eukaryotic ribosomes by tigecycline.
• Resolution: 2.0 Å
• Binding residue (original residue number in PDB): H32 N38 D39 F41 H43 G49 K50 T52 R55 T57 G59 M60 A64 D65 R66 R98 R104 I135 P136 S137 D138 S139 T140 R141 K143 G144 G145 R146 R147 R149 R150
• Binding residue (residue number reindexed from 1): H16 N22 D23 F25 H27 G33 K34 T36 R39 T41 G43 M44 A48 D49 R50 R82 R88 I119 P120 S121 D122 S123 T124 R125 K127 G128 G129 R130 R131 R133 R134

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0005515 protein binding
• GO:0045182 translation regulator activity
• GO:0048027 mRNA 5'-UTR binding

Biological Process

• GO:0000028 ribosomal small subunit assembly
• GO:0000122 negative regulation of transcription by RNA polymerase II
• GO:0002181 cytoplasmic translation
• GO:0006412 translation
• GO:0006417 regulation of translation
• GO:0030218 erythrocyte differentiation
• GO:0030490 maturation of SSU-rRNA
• GO:0042274 ribosomal small subunit biogenesis

Cellular Component

• GO:0005634 nucleus
• GO:0005654 nucleoplasm
• GO:0005730 nucleolus
• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0005925 focal adhesion
• GO:0014069 postsynaptic density
• GO:0015935 small ribosomal subunit
• GO:0016020 membrane
• GO:0022626 cytosolic ribosome
• GO:0022627 cytosolic small ribosomal subunit
• GO:0032040 small-subunit processome
• GO:0045202 synapse
• GO:0070062 extracellular exosome
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8yoo, PDBe:8yoo, PDBj:8yoo
• PDBsum: 8yoo
• PubMed: 38942792
• UniProt: P62263|RS14_HUMAN Small ribosomal subunit protein uS11 (Gene Name=RPS14)