Structure of PDB 8yoo Chain SN Binding Site BS02

Receptor Information

>8yoo Chain SN (length=150) Species: 9606 (Homo sapiens)

GRMHAPGKGLSQSALPYRRSVPTWLKLTSDDVKEQIYKLAKKGLTPSQIG
VILRDSHGVAQVRFVTGNKILRILKSKGLAPDLPEDLYHLIKKAVAVRKH
LERNRKDKDAKFRLILIESRIHRLARYYKTKRVLPPNWKYESSTASALVA

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): G2 R3 M4 H5 P7 G8 K9 G10 L11 S12 Q13 S14 A15 P17 R20 P47 S48 G51 R55 A61 Q62 R64 K70 I71 L72 R73 D87 H90 L91 K94 V98 H101 N105 K107 D108 K109 K112 F113 R114 I116 L117 S120 R121 R124 Y128 K132
• Binding residue (residue number reindexed from 1): G1 R2 M3 H4 P6 G7 K8 G9 L10 S11 Q12 S13 A14 P16 R19 P46 S47 G50 R54 A60 Q61 R63 K69 I70 L71 R72 D86 H89 L90 K93 V97 H100 N104 K106 D107 K108 K111 F112 R113 I115 L116 S119 R120 R123 Y127 K131

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003729 mRNA binding
• GO:0003735 structural constituent of ribosome
• GO:0005515 protein binding
• GO:0048027 mRNA 5'-UTR binding
• GO:0070181 small ribosomal subunit rRNA binding

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006412 translation
• GO:0033119 negative regulation of RNA splicing
• 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:0016020 membrane
• GO:0022626 cytosolic ribosome
• GO:0022627 cytosolic small ribosomal subunit
• GO:0032040 small-subunit processome
• GO:0070062 extracellular exosome
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8yoo, PDBe:8yoo, PDBj:8yoo
• PDBsum: 8yoo
• PubMed: 38942792
• UniProt: P62277|RS13_HUMAN Small ribosomal subunit protein uS15 (Gene Name=RPS13)