Structure of PDB 6zmt Chain R Binding Site BS01

Receptor Information

>6zmt Chain R (length=139) Species: 9606 (Homo sapiens)

QSVQVFGRKKTATAVAHCKRGNGLIKVNGRPLEMIEPRTLQYKLLEPVLL
LGKERFAGVDIRVRVKGGGHVAQIYAIRQSISKALVAYYQKYVDEASKKE
IKDILIQYDRTLLVADPRRCESKKFGGPGARARYQKSYR

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): Q11 V12 F13 R15 K16 K17 T18 H24 K33 R37 E43 R69 R71 G74 G75 G76 H77 V78 A79 Q80 R117 R125 R126 C127 E128 S129 K130 K131 F132 G136 A137 R138 A139 R140 Y141 Q142 K143 S144 R146
• Binding residue (residue number reindexed from 1): Q4 V5 F6 R8 K9 K10 T11 H17 K26 R30 E36 R62 R64 G67 G68 G69 H70 V71 A72 Q73 R110 R118 R119 C120 E121 S122 K123 K124 F125 G129 A130 R131 A132 R133 Y134 Q135 K136 S137 R139

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:6zmt, PDBe:6zmt, PDBj:6zmt
• PDBsum: 6zmt
• PubMed: 32680882
• UniProt: P62249|RS16_HUMAN Small ribosomal subunit protein uS9 (Gene Name=RPS16)