Structure of PDB 7jqc Chain R Binding Site BS01

Receptor Information

>7jqc Chain R (length=142) Species: 9986 (Oryctolagus cuniculus)

GPLQSVQVFGRKKTATAVAHCKRGNGLIKVNGRPLEMIEPRTLQYKLLEP
VLLLGKERFAGVDIRVRVKGGGHVAQIYAIRQSISKALVAYYQKYVDEAS
KKEIKDILIQYDRTLLVADPRRCESKKFGGPGARARYQKSYR

Ligand information

>7jqc Chain A (length=1697)

uaccugguugauccugccaguagcauaugcuugucucaaagauuaagcca
ugcaugucuaaguacgcacggccgguacagugaaacugcgaauggcucau
uaaaucaguuaugguuccuuuggucgcucgacuuggauaacugugguaau
ucuagagcuaauacaugccgacgggcgcugacccccuucgcgggggggau
gcgugcauuuaucaguggugacucuagauaaccucgggccgaucgcacgc
ccggcggcgacgacccauucgaacgucugcccuaucaacuuucgauggua
gucgccgugccuaccauggugaccacgggugacggggaaucaggguucga
uuccggagagggagccugagaaacggcuaccacauccaaggaaggcagca
ggcgcgcaaauuacccacucccgacccggggagguagugacgaaaaauaa
caauacaggacucuuucgaggcccuguaauuggaaugaguccacuuuaaa
uccuuuaacgaggauccauuggagggcaagucuggugccagcagccgcgg
uaauuccagcuccaauagcguauauuaaaguugcugcaguuaaaaagcuc
guaguuggaucuugggagcggccguccccugcucggcgccggcccgaagc
guuuacuuugaaaaaauuagaguguucaaagcaggccgccuggauaccgc
agcuaggaauaauggaauaggaccgcgguucuauuuuguugguuuucgga
acugaggccaugauuaagagggacggccgggggcauucguauugcgccgc
uagaggugaaauucuuggaccggcgcaagacggaccagagcgaaagcauu
ugccaagaauguuuucauuaaucaagaacgaaagucggagguucgaagac
gaucagauaccgucguaguuccgaccauaaacgaugccgaccggcgaugc
ggcggcguuauucccaugacccgccgggcagcuuccgggaaaccaaaguc
uuuggguuccggggggaguaugguugcaaagcugaaacuuaaaggaauug
acggaagggcaccaccaggaguggagccugcggcuuaauuugacucaaca
cgggaaaccucacccggcccggacacggacaggauugacagauugauagc
ucuuucucgauuccgugggugguggugcauggccguucuuaguuggugga
gcgauuugucugguuaauuccgauaacgaacgagacucuggcaugcuaac
uaguuacgcgaccccggucggcguaacuucuuagagggacaaguggcguu
cagccacccgagauugagcaauaacaggucugugaugcccuuagaugucc
ggggcugcacgcgcgcuacacugacuggcucagcgugugccuacccuacg
ccggcaggcgcggguaacccguugaaccccauucgugauggggaucgggg
auugcaauuauuccccaugaacgaggaauucccaguaagugcgggucaua
agcuugcguugauuaagucccugcccuuuguacacaccgcccgucgcuac
uaccgauuggaugguuuagugaggcccucggaucggccccgccggggugc
ccuggcggagcgcugagaagacggucgaacuugacuaucuagaggaagua
aaagucguaacaagguuuccguaggugaaccugcggaaggaucauua

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7jqc Nonstructural Protein 1 of SARS-CoV-2 Is a Potent Pathogenicity Factor Redirecting Host Protein Synthesis Machinery toward Viral RNA.
• Resolution: 3.3 Å
• Binding residue (original residue number in PDB): Q11 V12 F13 K17 T18 V22 H24 K26 K33 N35 R71 K73 G75 G76 H77 V78 A79 P124 R125 R126 C127 E128 S129 K130 K131 F132 G136 A137 R138 R140 Y141 Q142 K143 R146
• Binding residue (residue number reindexed from 1): Q7 V8 F9 K13 T14 V18 H20 K22 K29 N31 R67 K69 G71 G72 H73 V74 A75 P120 R121 R122 C123 E124 S125 K126 K127 F128 G132 A133 R134 R136 Y137 Q138 K139 R142

Gene Ontology

Molecular Function

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

Biological Process

• GO:0000462 maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
• 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:0005730 nucleolus
• GO:0005737 cytoplasm
• GO:0005840 ribosome
• 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:7jqc, PDBe:7jqc, PDBj:7jqc
• PDBsum: 7jqc
• PubMed: 33188728
• UniProt: G1SGX4|RS16_RABIT Small ribosomal subunit protein uS9 (Gene Name=RPS16)