Structure of PDB 6zmt Chain S Binding Site BS01

Receptor Information

>6zmt Chain S (length=130) Species: 9606 (Homo sapiens)

GRVRTKTVKKAARVIIEKYYTRLGNDFHTNKRVCEEIAIIPSKKLRNKIA
GYVTHLMKRIQRGPVRGISIKLQEEERERRYVPEVSALDQEIIEVDPDTK
EMLKLLDFGSLSNLQVTQPTVGMNFKTPRG

Ligand information

>6zmt Chain 2 (length=1569)

uaccugguugauccugccaguagcauaugcuugucucaaagauuaagcca
ugcaugucuaaguacgcacggccgguacagugaaacugcgaauggcucau
uaaaucaguuaugguuccuuuggucgcucguacuuggauaacugugguaa
uucuagagcuaauacaugccgacgggcgcugacccccuucgcggggggga
ugcgugcauuuaucaguggugacucuagauaaccucgggccgaucgcacg
ccggcggcgacgacccauucgaacgucugcccuaucaacuuucgauggua
gucgccgugccuaccauggugaccacgggugacggggaaucaggguucga
uuccggagagggagccugagaaacggcuaccacauccaaggaaggcagca
ggcgcgcaaauuacccacucccgacccggggagguagugacgaaaaauaa
caauacaggacucuuucgaggcccuguaauuggaaugaguccacuuuaaa
uccuuuaacgaggauccauuggagggcaagucuggugccagcagccgcgg
uaauuccagcuccaauagcguauauuaaaguugcugcaguuaaaaagcuc
guaguuggaucucucucggccgaagcguuuacuuugaaaaaauuagagug
uucaaagcaggccgccuggauaccgcagcuaggaauaauggaauaggacc
gcgguucuauuuuguugguuuucggaacugaggccaugauuaagagggac
ggccgggggcauucguauugcgccgcuagaggugaaauucuuggaccggc
gcaagacggaccagagcgaaagcauuugccaagaauguuuucauuaauca
agaacgaaagucaccauaaacgaugccgaccggcgaugcggcggcguuau
ucccaugacccgccgggcagcuuccgggaaaccaaagucuuuggguuccg
gggggaguaugguugcaaagcugaaacuuaaaggaauugacggaagggca
ccaccaggaguggagccugcggcuuaauuugacucaacacgggaaaccuc
acccggcccggacacggacaggauugacagauugauagcucuuucucgau
uccgugggugguggugcauggccguucuuaguugguggagcgauuugucu
gguuaauuccgauaacgaacgagacucuggcaugcuaacuaguuacgcga
ccggucggcguaacuucuuagagggacaaguggcguucagccacccgaga
uugagcaauaacaggucugugaugcccuuagauguccggggcugcacgcg
cgcuacacugacuggcucagcguguccuacgccggcaggcgcggguaacc
cguugaaccccauucgugauggggaucggggauugcaauuauuccccaug
aacgaggaauucccaguaagugcgggucauaagcuugcguugauuaaguc
ccugcccuuuguacacuacuaccgauuggaugguuuagugaggcccucgg
aucggccccgccggggugcccuggcggagcgcugagaagacggucgaacu
ugacuaucuagaggaagua

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6zmt Structural basis for translational shutdown and immune evasion by the Nsp1 protein of SARS-CoV-2.
• Resolution: 3.0 Å
• Binding residue (original residue number in PDB): G2 R3 V4 R5 T6 K7 K10 K11 R14 F28 K32 S43 K44 N48 K49 H56 R60 R67 V124 M126 F128 K129 R132
• Binding residue (residue number reindexed from 1): G1 R2 V3 R4 T5 K6 K9 K10 R13 F27 K31 S42 K43 N47 K48 H55 R59 R66 V121 M123 F125 K126 R129

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:6zmt, PDBe:6zmt, PDBj:6zmt
• PDBsum: 6zmt
• PubMed: 32680882
• UniProt: P08708|RS17_HUMAN Small ribosomal subunit protein eS17 (Gene Name=RPS17)