Structure of PDB 6zme Chain LX Binding Site BS01

Receptor Information

>6zme Chain LX (length=120) Species: 9606 (Homo sapiens)

KKKIRTSPTFRRPKTLRLRRQPKYPRKSAPRRNKLDHYAIIKFPLTTESA
MKKIEDNNTLVFIVDVKANKHQIKQAVKKLYDIDVAKVNTLIRPDGEKKA
YVRLAPDYDALDVANKIGII

Ligand information

>6zme Chain L5 (length=3773)

cgcgaccucagaucagacguggcgacccgcugaauuuaagcauauuaguc
agcggaggagaagaaacuaaccaggauucccucaguaacggcgagugaac
agggaagagcccagcgccgaauccccgccccgcggcggggcgcgggacau
guggcguacggaagacccgcuccccggcgccgcucguggggggcccaagu
ccuucugaucgaggcccagcccguggacggugugaggccgguagcggccc
ccggcgcgccgggcccgggucuucccggagucggguugcuugggaaugca
gcccaaagcgggugguaaacuccaucuaaggcuaaauaccggcacgagac
cgauagucaacaaguaccguaagggaaaguugaaaagaacuuugaagaga
gaguucaagagggcgugaaaccguuaagagguaaacgggugggguccgcg
caguccgcccggaggauucaacccggcggcggguccggccgugucggcgg
cccggcggaucuuucccgcgcgggggaccgucccccgaccggcgaccggc
cgccgccgggcgcauuuccaccgcggcggugcgccgcgaccggcuccggg
acggcugggaaggcccggcggggaagguggcucgggggcccccgaguguu
acagcccccccggcagcagcacucgccgaaucccggggccgagggagcga
gacccgucgccgcgcucuccccccucccggcgcgccggggggggccgggc
caccccucccacggcgcgaccgcucggggcggacuguccccagugcgccc
cgggcgggucgcgccgucgggcccgggggaggccacgcgcgcgucccccg
aagagggggacggcggagcgagcgcacggggucggcggcgacgucggcua
cccacccgacccgucuugaaacacggaccaaggagucuaacacgugcgcg
agucgggggcucgcacgaaagccgccguggcgcaaugaaggugaaggccg
gcgcgcucgccggccgaggugggaucccgaggccucuccaguccgccgag
ggcgcaccaccggcccgucucgcccgccgcgccggggagguggagcacga
gcgcacguguuaggacccgaaagauggugaacuaugccugggcagggcga
agccagaggaaacucugguggagguccguagcgguccugacgugcaaauc
ggucguccgaccuggguauaggggcgaaagacuaaucgaaccaucuagua
gcugguucccuccgaaguuucccucaggauagcuggcgcucucgcagacc
cgacgcccgccacgcaguuuuauccgguaaagcgaaugauuagaggucuu
ggggccgaaacgaucucaaccuauucucaaacuuuaaauggguaagaagc
ccggcucgcuggcguggagccgggcguggaaugcgagugccuagugggcc
acuuuugguaagcagaacuggcgcugcgggaugaaccgaacgccggguua
aggcgcccgaugccgacgcucaucagaccccagaaaagguguugguugau
auagacagcaggacgguggccauggaagucggaauccgcuaaggagugug
uaacaacucaccugccgaaucaacuagcccugaaaauggauggcgcugga
gcgucgggcccauacccggccgucgccggcagucgagaguggacgggagc
ggcgggccggagccccgcggacgcuacgccgcgacgaguaggagggccgc
ugcggugagccuugaagccuagggcgcgggcccggguggagccgccgcag
gugcagaucuuggugguaguagcaaauauucaaacgagaacuuugaaggc
cgaaguggagaaggguuccaugugaacagcaguugaacaugggucagucg
guccugagagaugggcgagcgccguuccgaagggacgggcgauggccucc
guugcccucggccgaucgaaagggagucggguucagauccccgaauccgg
aguggcggagaugggcgccgcgaggcguccagugcgguaacgcgaccgau
cccggagaagccggcgggagccccggggagaguucucuuuucuuugugaa
gggcagggcgcccuggaauggguucgccccgagagaggggcccgugccuu
ggaaagcgucgcgguuccggcggcguccggugagcucucgcuggcccuug
aaaauccgggggagaggguguaaaucucgcgccgggccguacccauaucc
gcagcaggucuccaaggugaacagccucuggcauguuggaacaauguagg
uaagggaagucggcaagccggauccguaacuucgggauaaggauuggcuc
uaagggcugggucggucgcggccggcgccuagcagccgacuuagaacugg
ugcggaccaggggaauccgacuguuuaauuaaaacaaagcaucgcgaagg
cccgcggcggguguugacgcgaugugauuucugcccagugcucugaaugu
caaagugaagaaauucaaugaagcgcggguaaacggcgggaguaacuaug
acucucuuaagguagccaaaugccucgucaucuaauuagugacgcgcaug
aauggaugaacgagauucccacugucccuaccuacuauccagcgaaacca
cagccaagggaacgggcuuggcggaaucagcggggaaagaagacccuguu
gagcuugacucuagucuggcacggugaagagacaugagagguguagaaua
agugggaggcccccggcgcccccccgguguccccgcgaggggcccggggc
gggguccgccggcccugcgggccgccggugaaauaccacuacucugaucg
uuuuuucacugacccggugaggcgggggggcgagccccgaggggcucucg
cuucuggcgccaagcgcccggccgcgcgccggccgggcgcgacccgcucc
ggggacagugccagguggggaguuugacuggggcgguacaccugucaaac
gguaacgcagguguccuaaggcgagcucagggaggacagaaaccucccgu
ggagcagaagggcaaaagcucgcuugaucuugauuuucaguacgaauaca
gaccgugaaagcggggccucacgauccuucugaccuuuuggguuuuaagc
aggaggugucagaaaaguuaccacagggauaacuggcuuguggcggccaa
gcguucauagcgacgucgcuuuuugauccuucgaugucggcucuuccuau
cauugugaagcagaauucaccaagcguuggauuguucacccacuaauagg
gaacgugagcuggguuuagaccgucgugagacagguuaguuuuacccuac
ugaugauguguuguugccaugguaauccugcucaguacgagaggaaccgc
agguucagacauuugguguaugugcuuggcugaggagccaauggggcgaa
gcuaccaucugugggauuaugacugaacgccucuaagucagaaucccgcc
caggcggaacgauacggcagcgccgcggagccucgguuggccucggauag
ccggucccccgccgggguccggugcggagugcccuucguccugggaaacg
gggcgcggcuggaaaggcggccgcccccucgcccgucacgcaccgcacgu
ucguggggaaccuggcgcuaaaccauucguagacgaccugcuucuggguc
gggguuucguacguagcagagcagcucccucgcugcgaucuauugaaagu
cagcccucgacacaaggguuugu

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................<<....>>...............<<<<....>>>
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>>>>>>>>>>......>>>.>>>.>>>>>...<<<<<<<<<<<<<<<<<<
<<<<<...<<..<<<.<<.<<<<......<<<<<<<<..>>>>>>>>...
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...........<<<<<<.<<<<<<<............>>>>>>>.<<<<<
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<<......>>>>>>>..<<<<<...<<<..<<<..(((...(((>>>..>
>>....>>>>>.<<<<<<<<<.<<<<......>>>>>>>>>>>.>>....
>>>>>>>>>>>>>..<<.<..<<<<<<<.....<<<<<<<<<..<<<...
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>>.>>>....>>>>>>>>>...<<.......>>......>>>>>>...>.
.>.>>..<<<<<<....<.<<<....>>>.><<.<<<<<<<.........
.............<<<.<<<<<<<<<...<<<....<<<..<.<<<....
<<.............>>..>>>.>..>>>..>.>>...>>>>>>>...<<
<<<<<<<.<......>>>>>>>>>>....>>>>>>>>>>>>..>>..<<<
<.<<<<<.....>>>>>.>>>>....<<<......>>>...<<<<<<<..
.<<<(((.......<<<<<.....<<..........<<<.<<<<<<<<<<
.......<<<<<.<<....<<.........>>....>>.........<<.
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>>>>>..>>>...>>>>>>><<<<<<.<<<..........)))...))).
..<.....>..................>>>>>>>>>....>>>>>>.<.<
<<<<<<<.<<......<<<<.<<<<....>>>>>>>>...>>>>>>>>>>
..>.....>>>>>><<<....<<.....<<<<<<.......>>>>>>.<<
<.....<<<<<.<<...<<<<<<...<<.....>>.>>>>>>....((<<
<<<<...<<....<<<....>>>..........<<.<<<<<...<...>.
..>>>>>>>......>>....>>>..<<<<<........>>>>>))<<<<
....<<<<<..<<<<<<<<....>>>>>>>>..<<<....>>>...<..<
<<<<<<...<<<<<<<<<<<<<<<<<<<<<<<..{{{..>>>>>>....<
<<<<.<<<<.<<<<.....<<<.....>>>.....>>>>>>>>..>>>>>
.....<<<<<<<.......>>>>>>>>>>>.>.>>>>>>>>>>>>.....
....>>>>>>>..>..........>>.>>>.>>>>.>>>..>>.....<<
......>>>>>>>.<<<<.....>>>>..>>>....<<<<.....<<<<<
<<.<<...............<<<<<....<....>.....>>>>><<.<<
<<<<<<<<<..<<..........>>.......>>>>>..>>>>>>.>>..
..........<<<<<<<<<..<<<.........>>>..<<<<<<<....<
<<<.....>>>>......>>>>>>>...<<..<<<..<<<<<<....<<<
.....<<<<....>>>>.....>>>.>>>>..>>>>>.<<<<<.......
>>>>>.........<...........<<<<<.......>>>>>.....>.
....>>....>>.>>>>>>>.....>>.>>>>>>>..>>>>>>...>>>.
...<<<<<........>>>>>....[[[[[..{{{.{{......[[[[.{
{[[[[..<<<<<.<<<<<<<<<.<<<<<<<<..<<...............
.....................<........................>...
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.>>>>>>>>...<<<<<.....<<<<........<........>......
.............<<<<<<<<<<.......>>>>>>>>>>..>>>>..>>
>>>....>>>>>>>>>..>>>>>...<<<.....>>>..<<<<<<.....
......>>>>>>..<<...<<<<<<<...<<<<<<.......>>>>>>..
...<<.[.(((>>....>>>>>>>...<<<..<<<<.......>>>>..>
>>.<<<....>>>.>>)))]......((((((..(((..>>>>>>.))))
)))))..........]]]]..}}]]]].......<<.<.<.<<<<<<...
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]]]].....<<<<<<.<..<<<..<.<<<<<.................>>
>>>.><<<<....<<<<....<<.<<<<<<.}}}..>>>>..>>.>>...
>>>>...>>>><<<<....<<<<<...........>>>>>....>>>>.>
>>...>.>>>>>>.....<<<<<<<.<<..<<<<....<<<........<
<<<<.<<<<....>>>>.>>>>>.......>>>...<<<..<<<<....<
<<<.<<<<<<<......>>>>>>>>>>>...>>>>..>>>..........
....>>>>..>>>>>>>>><<<<<.<.............>....<<.<<<
<<<<.<<.....<<<<....<<<<<......>>>>>...>>>>....>>.
...>>>>.>>>.>>..>>>>>..

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6zme 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): K37 P44 T45 R47 R48 K50 T51 R53 R56 Q57 K59 Y60 R62 T83 K89 N93 N105 K106 H107 K123 N125 T126 L127 I128 P130 K134 Y137 R139
• Binding residue (residue number reindexed from 1): K1 P8 T9 R11 R12 K14 T15 R17 R20 Q21 K23 Y24 R26 T47 K53 N57 N69 K70 H71 K87 N89 T90 L91 I92 P94 K98 Y101 R103

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0005515 protein binding
• GO:0019843 rRNA binding
• GO:0045296 cadherin binding
• GO:1904841 TORC2 complex binding

Biological Process

• GO:0000027 ribosomal large subunit assembly
• GO:0002181 cytoplasmic translation
• GO:0006412 translation

Cellular Component

• GO:0005634 nucleus
• GO:0005730 nucleolus
• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0022625 cytosolic large ribosomal subunit
• GO:0022626 cytosolic ribosome
• GO:0070062 extracellular exosome
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:6zme, PDBe:6zme, PDBj:6zme
• PDBsum: 6zme
• PubMed: 32680882
• UniProt: P62750|RL23A_HUMAN Large ribosomal subunit protein uL23 (Gene Name=RPL23A)