Structure of PDB 8ppk Chain Q Binding Site BS01

Receptor Information

>8ppk Chain Q (length=142) Species: 9606 (Homo sapiens)

GPLQSVQVFGRKKTATAVAHCKRGNGLIKVNGRPLEMIEPRTLQYKLLEP
VLLLGKERFAGVDIRVRVKGGGHVAQIYAIRQSISKALVAYYQKYVDEAS
KKEIKDILIQYDRTLLVADPRRCESKKFGGPGARARYQKSYR

Ligand information

>8ppk Chain 2 (length=1771)

uaccugguugauccugccaguagcauaugcuugucucaaagauuaagcca
ugcaugucuaaguacgcacggccgguacagugaaacugcgaauggcucau
uaaaucaguuaugguuccuuuggucgcucguacuuggauaacugugguaa
uucuagagcuaauacaugccgacgggcgcugacccccuucgcggggggga
ugcgugcauuuaucagaucaaaaccaacccggugccggcggcuuugguga
cucuagauaaccucgggccgaucgcacgccccccguggcggcgacgaccc
auucgaacgucugcccuaucaacuuucgaugguagucgccgugccuacca
uggugaccacgggugacggggaaucaggguucgauuccggagagggagcc
ugagaaacggcuaccacauccaaggaaggcagcaggcgcgcaaauuaccc
acucccgacccggggagguagugacgaaaaauaacaauacaggacucuuu
cgaggcccuguaauuggaaugaguccacuuuaaauccuuuaacgaggauc
cauuggagggcaagucuggugccagcagccgcgguaauuccagcuccaau
agcguauauuaaaguugcugcaguuaaaaagcucguaguuggaucuuggg
agcgggcggccguccccgccccgccucucggcgccccggggcccgaagcg
uuuacuuugaaaaaauuagaguguucaaagcaggcccgagccgccuggau
accgcagcuaggaauaauggaauaggaccgcgguucuauuuuguugguuu
ucggaacugaggccaugauuaagagggacggccgggggcauucguauugc
gccgcuagaggugaaauucuuggaccggcgcaagacggaccagagcgaaa
gcauuugccaagaauguuuucauuaaucaagaacgaaagucggagguucg
aagacgaucagauaccgucguaguuccgaccauaaacgaugccgaccggc
gaugcggcggcguuauucccaugacccgccgggcagcuuccgggaaacca
aagucuuuggguuccggggggaguaugguugcaaagcugaaacuuaaagg
aauugacggaagggcaccaccaggaguggagccugcggcuuaauuugacu
caacacgggaaaccucacccggcccggacacggacaggauugacagauug
auagcucuuucucgauuccgugggugguggugcauggccguucuuaguug
guggagcgauuugucugguuaauuccgauaacgaacgagacucuggcaug
cuaacuaguuacgcgacccccgagcggucggcgucccccaacuucuuaga
gggacaaguggcguucagccacccgagauugagcaauaacaggucuguga
ugcccuuagauguccggggcugcacgcgcgcuacacugacuggcucagcg
ugugccuacccuacgccggcaggcgcggguaacccguugaaccccauucg
ugauggggaucggggauugcaauuauuccccaugaacgaggaauucccag
uaagugcgggucauaagcuugcguugauuaagucccugcccuuuguacac
accgcccgucgcuacuaccgauuggaugguuuagugaggcccucggaucg
gccccgccggggucggcccacggcccuggcggagcgcugagaagacgguc
gaacuugacuaucuagaggaaguaaaagucguaacaagguuuccguaggu
gaaccugcggaaggaucauua

...<<<<<...[[[[>>>>>[[[.((((((.....{{.........[[[.
[[[..<<....<<....<<..........>>...>>.>>......{{...
.....[[[......{{....[[[{..........<<.....<<.<<<...
..>>>.>>......>>.........<<<<...<<<<<<....>>>>>>..
.>>>>[[..(((((.....<<<<<<<<<<<<<..>>>>.......<....
..>..)))))......]]...<<<<.<<<<......>>>>>>>>..}.]]
]...}}....]]].<<<....<<<....<<<<<<<.........>>>>>>
>>>>......>>>...<<<.<<<<....>>>>....>>>.}}.<<.<<<.
.........>>>.>>.<.<<....>>.>...]]]]]].........<<<.
...<<<<...>>>>..>>>......}}.......<<<<<<<<<.<<<...
.>>>..>>>>>>.>>>......<<..<...........>..>>.......
..<<<<<((......<<<<.....<<..))>>.......>>>>.>>>>>.
.)))))).]]]............{{.......{{...[[[.[[....<<<
.<.<<<<<..>>>>>.>.>>>.<<...<<<..<<<<<>>>>>.>>>.>>.
.<<<<<<.<.......<<...<.......>.<<<<.......>>>>...>
>......>.>>>..>>>........{.[[.(((((((.....>>>>>>>>
>.))))))).]].}....]]....<<<<<<..<...<<<<..<<..<<<<
<<<<...<<<......>>>......>>>>>>>>..>>.......<<....
>>...>>>>..>..>>>.>>>...]]]...}}......<<<<<<<...<.
..<<<<.<.....>.>>>>...>>>>>>>>..........<<<.<<.<<<
..<.<<<<<<.<<<<<....>>>>>>>>>>>.>..>>>...<<..}}>>.
..>>.....>>>.....<<<......<<<<....>>>>....>>>..]]]
]..<<<<<.<<<<<<<..<<..<<<<<..<<<.<<<<........<<...
.....>>..........<<<<<......<<<<<<.......<<.<<<...
.....>>>.>>.....>>>>>>.<.<<.<<<..<<.<<<<<<....<<<.
<<<<<....>>>...<<<......>>>...>>.>>>....<<<...<...
<<<<..<<<<<<<<<<<<.......>>>>.>>>>.....>>>>..>>>>.
.>.....<<<<<.....>>>>>........>>>....>>>.>>>.....>
>>>>>>>......>>>>>......>>>>.>>>.....<<.<<<.......
.<.......<<<.<<<<....>>>>.>>>....>.........>>>.>>.
...........<<<<<..........>>>>>...........>>>>>...
..<<<<<<<<.......>>>>>>>>......>>...>>>>>>>>>>.>>.
......<<.<..<<<<.<<....<<<<<<<<.<<<..<<<<.<<...<<<
<<.<<<<<<<<<<<<.....>>>>>>>>>>>>...>>>>>...>>.>>>>
..>>>.>>>>>>>>...>>.>>>>...>.>>.........<<<<<<<<<.
...>>>>>>>>>.........

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8ppk Universal features of Nsp1-mediated translational shutdown by coronaviruses.
• Resolution: 2.98 Å
• Binding residue (original residue number in PDB): Q11 V12 F13 R15 K16 K17 T18 V22 H24 K33 R37 R69 K73 G74 G75 G76 H77 V78 A79 Q80 R117 V121 P124 R125 R126 C127 E128 S129 K130 K131 F132 R138 A139 R140 Y141 Q142 K143 S144 Y145 R146
• Binding residue (residue number reindexed from 1): Q7 V8 F9 R11 K12 K13 T14 V18 H20 K29 R33 R65 K69 G70 G71 G72 H73 V74 A75 Q76 R113 V117 P120 R121 R122 C123 E124 S125 K126 K127 F128 R134 A135 R136 Y137 Q138 K139 S140 Y141 R142

Gene Ontology

Molecular Function

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

Biological Process

• GO:0000462 maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
• GO:0002181 cytoplasmic translation
• GO:0006364 rRNA processing
• GO:0006412 translation
• GO:0042274 ribosomal small subunit biogenesis
• GO:1990830 cellular response to leukemia inhibitory factor

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:0045202 synapse
• GO:0070062 extracellular exosome
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8ppk, PDBe:8ppk, PDBj:8ppk
• PDBsum: 8ppk
• PubMed: 37802027
• UniProt: P62249|RS16_HUMAN Small ribosomal subunit protein uS9 (Gene Name=RPS16)