Structure of PDB 6zoj Chain R Binding Site BS01

Receptor Information

>6zoj Chain R (length=132) Species: 9606 (Homo sapiens)

GRVRTKTVKKAARVIIEKYYTRLGNDFHTNKRVCEEIAIIPSKKLRNKIA
GYVTHLMKRIQRGPVRGISIKLQEEERERRDNYVPEVSALDQEIIEVDPD
TKEMLKLLDFGSLSNLQVTQPTVGMNFKTPRG

Ligand information

>6zoj Chain 2 (length=1704)

uaccugguugauccugccaguagcauaugcuugucucaaagauuaagcca
ugcaugucuaaguacgcacggccgguacagugaaacugcgaauggcucau
uaaaucaguuaugguuccuuuggucgcucguacuuggauaacugugguaa
uucuagagcuaauacaugccgacgggcgcugacccccuucgcggggggga
ugcgugcauuuaucaguggugacucuagauaaccucgggccgaucgcacg
ccccccguggcggcgacgacccauucgaacgucugcccuaucaacuuucg
augguagucgccgugccuaccauggugaccacgggugacggggaaucagg
guucgauuccggagagggagccugagaaacggcuaccacauccaaggaag
gcagcaggcgcgcaaauuacccacucccgacccggggagguagugacgaa
aaauaacaauacaggacucuuucgaggcccuguaauuggaaugaguccac
uuuaaauccuuuaacgaggauccauuggagggcaagucuggugccagcag
ccgcgguaauuccagcuccaauagcguauauuaaaguugcugcaguuaaa
aagcucguaguuggaucucucucggccgaagcguuuacuuugaaaaaauu
agaguguucaaagcaggcccgagccgccuggauaccgcagcuaggaauaa
uggaauaggaccgcgguucuauuuuguugguuuucggaacugaggccaug
auuaagagggacggccgggggcauucguauugcgccgcuagaggugaaau
ucuuggaccggcgcaagacggaccagagcgaaagcauuugccaagaaugu
uuucauuaaucaagaacgaaagucggagguucgaagacgaucagauaccg
ucguaguuccgaccauaaacgaugccgaccggcgaugcggcggcguuauu
cccaugacccgccgggcagcuuccgggaaaccaaagucuuuggguuccgg
ggggaguaugguugcaaagcugaaacuuaaaggaauugacggaagggcac
caccaggaguggagccugcggcuuaauuugacucaacacgggaaaccuca
cccggcccggacacggacaggauugacagauugauagcucuuucucgauu
ccgugggugguggugcauggccguucuuaguugguggagcgauuugucug
guuaauuccgauaacgaacgagacucuggcaugcuaacuaguuacgcgac
ccccgagcggucggcgucccccaacuucuuagagggacaaguggcguuca
gccacccgagauugagcaauaacaggucugugaugcccuuagauguccgg
ggcugcacgcgcgcuacacugacuggcucagcgugugccuacccuacgcc
ggcaggcgcggguaacccguugaaccccauucgugauggggaucggggau
ugcaauuauuccccaugaacgaggaauucccaguaagugcgggucauaag
cuugcguugauuaagucccugcccuuuguacacaccgcccgucgcuacua
ccgauuggaugguuuagugaggcccucggaucggccccgccggggucggc
ccacggcccuggcggagcgcugagaagacggucgaacuugacuaucuaga
ggaaguaaaagucguaacaagguuuccguaggugaaccugcggaaggauc
auua

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6zoj SARS-CoV-2 Nsp1 binds the ribosomal mRNA channel to inhibit translation.
• Resolution: 2.8 Å
• Binding residue (original residue number in PDB): G2 R3 V4 R5 T6 K7 F28 K32 S43 K44 K45 N48 K49 G52 H56 K59 R60 R67 V124 M126 K129 R132
• Binding residue (residue number reindexed from 1): G1 R2 V3 R4 T5 K6 F27 K31 S42 K43 K44 N47 K48 G51 H55 K58 R59 R66 V123 M125 K128 R131

Gene Ontology

Molecular Function

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

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006364 rRNA processing
• GO:0006412 translation
• GO:0006413 translational initiation
• GO:0034101 erythrocyte homeostasis
• 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:0016020 membrane
• GO:0022626 cytosolic ribosome
• GO:0022627 cytosolic small ribosomal subunit
• GO:0032040 small-subunit processome
• GO:0045202 synapse
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:6zoj, PDBe:6zoj, PDBj:6zoj
• PDBsum: 6zoj
• PubMed: 32908316
• UniProt: P08708|RS17_HUMAN Small ribosomal subunit protein eS17 (Gene Name=RPS17)