Structure of PDB 6zoj Chain I Binding Site BS01

Receptor Information

>6zoj Chain I (length=205) Species: 9606 (Homo sapiens)

GISRDNWHKRRKTGGKRKPYHKKRKYELGRPAANTKIGPRRIHTVRVRGG
NKKYRALRLDVGNFSWGSECCTRKTRIIDVVYNASNNELVRTKTLVKNCI
VLIDSTPYRQWYESHYALPLGRKKGAKLTPEEEEILNKKRSKKIQKKYDE
RKKNAKISSLLEEQFQQGKLLACIASRPGQCGRADGYVLEGKELEFYLRK
IKARK

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 I3 R5 D6 N7 H9 K10 R12 T14 K19 Y21 K23 K24 R25 K26 Y27 L29 R31 A33 A34 R41 R42 H44 T45 R47 R49 G50 K53 K54 Y55 R56 L58 N64 S66 T73 R74 S86 K98 N99 K143 K144 I145 R178 Q181 R184 D186
• Binding residue (residue number reindexed from 1): G1 I2 R4 D5 N6 H8 K9 R11 T13 K18 Y20 K22 K23 R24 K25 Y26 L28 R30 A32 A33 R40 R41 H43 T44 R46 R48 G49 K52 K53 Y54 R55 L57 N63 S65 T72 R73 S85 K97 N98 K142 K143 I144 R177 Q180 R183 D185

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:0006412 translation
• GO:0042274 ribosomal small subunit biogenesis

Cellular Component

• GO:0005634 nucleus
• GO:0005654 nucleoplasm
• GO:0005730 nucleolus
• GO:0005737 cytoplasm
• GO:0005783 endoplasmic reticulum
• 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:0070062 extracellular exosome
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:6zoj, PDBe:6zoj, PDBj:6zoj
• PDBsum: 6zoj
• PubMed: 32908316
• UniProt: P62241|RS8_HUMAN Small ribosomal subunit protein eS8 (Gene Name=RPS8)