Structure of PDB 6zmi Chain SX Binding Site BS01

Receptor Information

>6zmi Chain SX (length=141) Species: 9606 (Homo sapiens)

GKCRGLRTARKLRSHRRDQKWHDKQYKKAHLGTALKANPFGGASHAKGIV
LEKVGVEAKQPNSAIRKCVRVQLIKNGKKITAFVPNDGCLNFIEENDEVL
VAGFGRKGHAVGDIPGVRFKVVKVANVSLLALYKGKKERPR

Ligand information

>6zmi Chain S2 (length=1740)

uaccugguugauccugccaguagcauaugcuugucucaaagauuaagcca
ugcaugucugaguacgcacggccgguacagugaaacugcgaauggcucau
uaaaucaguuaugguuccuuuggucgcucgcuccucuccuacuuggauaa
cugugguaauucuagagcuaauacaugccgacgggcgcugacccccuucg
cgggggggaugcgugcauuuaucaguggugacucuagauaaccucgggcc
gaucgcacgccccccguggcggcgacgacccauucgaacgucugcccuau
caacuuucgaugguagucgccgugccuaccauggugaccacgggugacgg
ggaaucaggguucgauuccggagagggagccugagaaacggcuaccacau
ccaaggaaggcagcaggcgcgcaaauuacccacucccgacccggggaggu
agugacgaaaaauaacaauacaggacucuuucgaggcccuguaauuggaa
ugaguccacuuuaaauccuuuaacgaggauccauuggagggcaagucugg
ugccagcagccgcgguaauuccagcuccaauagcguauauuaaaguugcu
gcaguuaaaaagcucguaguuggaucuugggagcgggcguccccgcccuc
ucggccggggcccgaagcguuuacuuugaaaaaauuagaguguucaaagc
aggcccgagccgccuggauaccgcagcuaggaauaauggaauaggaccgc
gguucuauuuuguugguuuucggaacugaggccaugauuaagagggacgg
ccgggggcauucguauugcgccgcuagaggugaaauucuuggaccggcgc
aagacggaccagagcgaaagcauuugccaagaauguuuucauuaaucaag
aacgaaagucggagguucgaagacgaucagauaccgucguaguuccgacc
auaaacgaugccgaccggcgaugcggcggcguuauucccaugacccgccg
ggcagcuuccgggaaaccaaagucuuuggguuccggggggaguaugguug
caaagcugaaacuuaaaggaauugacggaagggcaccaccaggaguggag
ccugcggcuuaauuugacucaacacgggaaaccucacccggcccggacac
ggacaggauugacagauugauagcucuuucucgauuccgugggugguggu
gcauggccguucuuaguugguggagcgauuugucugguuaauuccgauaa
cgaacgagacucuggcaugcuaacuaguuacgcgacccccgagcggucgg
cgucccccaacuucuuagagggacaaguggcguucagccacccgagauug
agcaauaacaggucugugaugcccuuagauguccggggcugcacgcgcgc
uacacugacuggcucagcgugugccuacccuacgccggcaggcgcgggua
acccguugaaccccauucgugauggggaucggggauugcaauuauucccc
augaacgaggaauucccaguaagugcgggucauaagcuugcguugauuaa
gucccugcccuuuguacacaccgcccgucgcuacuaccgauuggaugguu
uagugaggcccucggaucggccccgccggggucggcccacggcccuggcg
gagcgcugagaagacggucgaacuugacuaucuagaggaaguaaaagucg
uaacaagguuuccguaggugaaccugcggaaggaucauua

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6zmi Structural basis for translational shutdown and immune evasion by the Nsp1 protein of SARS-CoV-2.
• Resolution: 2.6 Å
• Binding residue (original residue number in PDB): G2 K3 C4 R5 G6 R8 T9 R11 K12 H16 R17 R18 Q20 K21 W22 H23 D24 K25 K28 L36 K37 A44 S45 H46 K48 K60 N63 S64 A65 I66 R67 K68 K76 N87 D88 G104 G106 R107 K108 H110 G113 D114 R119 K121 K124 S129 K138
• Binding residue (residue number reindexed from 1): G1 K2 C3 R4 G5 R7 T8 R10 K11 H15 R16 R17 Q19 K20 W21 H22 D23 K24 K27 L35 K36 A43 S44 H45 K47 K59 N62 S63 A64 I65 R66 K67 K75 N86 D87 G103 G105 R106 K107 H109 G112 D113 R118 K120 K123 S128 K137

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:0034063 stress granule assembly
• GO:0042274 ribosomal small subunit biogenesis
• GO:1990145 maintenance of translational fidelity

Cellular Component

• GO:0005634 nucleus
• GO:0005654 nucleoplasm
• GO:0005730 nucleolus
• GO:0005737 cytoplasm
• GO:0005783 endoplasmic reticulum
• GO:0005791 rough endoplasmic reticulum
• GO:0005829 cytosol
• GO:0005840 ribosome
• 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:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:6zmi, PDBe:6zmi, PDBj:6zmi
• PDBsum: 6zmi
• PubMed: 32680882
• UniProt: P62266|RS23_HUMAN Small ribosomal subunit protein uS12 (Gene Name=RPS23)