Structure of PDB 6zmt Chain O Binding Site BS01

Receptor Information

>6zmt Chain O (length=123) Species: 9606 (Homo sapiens)

GVMDVNTALQEVLKTALIHDGLARGIREAAKALDKRQAHLCVLASNCDEP
MYVKLVEALCAEHQINLIKVDDNKKLGEWVGLCKIDREGKPRKVVGCSCV
VVKDYGKESQAKDVIEEYFKCKK

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): R33 R36 E37 D57 K83 R96 R101 K102 V104 C106
• Binding residue (residue number reindexed from 1): R24 R27 E28 D48 K74 R87 R92 K93 V95 C97

Gene Ontology

Molecular Function

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

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006412 translation
• GO:0042274 ribosomal small subunit biogenesis
• GO:0090263 positive regulation of canonical Wnt signaling pathway
• GO:1990145 maintenance of translational fidelity

Cellular Component

• GO:0005634 nucleus
• GO:0005654 nucleoplasm
• GO:0005730 nucleolus
• GO:0005737 cytoplasm
• GO:0005794 Golgi apparatus
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0016020 membrane
• GO:0022626 cytosolic ribosome
• GO:0022627 cytosolic small ribosomal subunit
• GO:0032040 small-subunit processome
• GO:0043231 intracellular membrane-bounded organelle
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:6zmt, PDBe:6zmt, PDBj:6zmt
• PDBsum: 6zmt
• PubMed: 32680882
• UniProt: P25398|RS12_HUMAN Small ribosomal subunit protein eS12 (Gene Name=RPS12)