Structure of PDB 8yoo Chain SE Binding Site BS01

Receptor Information

>8yoo Chain SE (length=262) Species: 9606 (Homo sapiens)

ARGPKKHLKRVAAPKHWMLDKLTGVFAPRPSTGPHKLRECLPLIIFLRNR
LKYALTGDEVKKICMQRFIKIDGKVRTDITYPAGFMDVISIDKTGENFRL
IYDTKGRFAVHRITPEEAKYKLCKVRKIFVGTKGIPHLVTHDARTIRYPD
PLIKVNDTIQIDLETGKITDFIKFDTGNLCMVTGGANLGRIGVITNRERH
PGSFDVVHVKDANGNSFATRLSNIFVIGKGNKPWISLPRGKGIRLTIAEE
RDKRLAAKQSSG

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): A2 R3 G4 P5 K6 K7 H8 K10 R11 V12 K16 M19 D21 K22 L23 F27 A28 P29 R30 T33 G34 K37 R49 T57 G58 K62 K63 M66 K75 R77 K106 R108 K128 V131 G132 K134 V140 A144 T146 R148 K155 G186 A187 H201 G203 A219 R221 R240 I248
• Binding residue (residue number reindexed from 1): A1 R2 G3 P4 K5 K6 H7 K9 R10 V11 K15 M18 D20 K21 L22 F26 A27 P28 R29 T32 G33 K36 R48 T56 G57 K61 K62 M65 K74 R76 K105 R107 K127 V130 G131 K133 V139 A143 T145 R147 K154 G185 A186 H200 G202 A218 R220 R239 I247

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0005515 protein binding
• GO:0019843 rRNA binding

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006412 translation
• GO:0008284 positive regulation of cell population proliferation
• GO:0042274 ribosomal small subunit biogenesis
• GO:0045727 positive regulation of translation

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:0015935 small ribosomal subunit
• GO:0016020 membrane
• GO:0022626 cytosolic ribosome
• GO:0022627 cytosolic small ribosomal subunit
• GO:0032040 small-subunit processome
• GO:0036464 cytoplasmic ribonucleoprotein granule
• 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: P62701|RS4X_HUMAN Small ribosomal subunit protein eS4, X isoform (Gene Name=RPS4X)