Structure of PDB 6d9j Chain Z Binding Site BS01

Receptor Information

>6d9j Chain Z (length=135) Species: 9986 (Oryctolagus cuniculus)

GKFMKPGKVVLVLAGRYSGRKAVIVKNIDDGTSDRPYSHALVAGIDRYPR
KVTAAMGKKKIAKRSKIKSFVKVYNYNHLMPTRYSVDIPLDKTVVNKDVF
RDPALKRKARREAKVKFEERYKTGKNKWFFQKLRF

Ligand information

>6d9j Chain 5 (length=3594)

cgcgaccucagaucagacguggcgacccgcugaauuuaagcauauuaguc
agcggaggaaaagaaacuaaccaggauucccucaguaacggcgagugaac
agggaagagcccagcgccgaauccccgccccgcggcggggcgcgggaaau
guggcguacggaagacccacuccccggcgccggggggcccaaguccuucu
gaucgaggcccagcccguggacggugugaggccgguagcggcccccggcg
cgccgggcccgggucuucccggagucggguugcuugggaaugcagcccaa
agcgggugguaaacuccaucuaaggcuaaauaccggcacgagaccgauag
ucaacaaguaccguaagggaaaguugaaaagaacuuugaagagagaguuc
aagagggcgugaaaccguuaagagguaaacgggugggguccgcgcagucc
gcccggaggauucaacccggcggcggguccggccgugccggcggggcgga
ucucccgcucccgucggcgggggaccgccccccggccggcgaccggccgc
cgccgggcgcauuuccaccgcggcggugcgccgcgaccggcuccgggacg
gcugggaaggcccggcggggaagguggcccgggggccccggguguuacag
cccgccccggcagcagcagcucgccgaaucccggggccgagggagcgaga
cccgugcgccgcgcucuccccccucgggggggccgggccaccccucccac
ggcgcgaccgcuggggcggacuguccagugcgccccgggcgggucgcgcc
gucgggcccggggggccacgcgucccccgcgagcgcacggggucggcggc
gaugucggcuacccacccgacccgucuugaaacacggaccaaggagucua
acacgugcgcgagucgggggcuacgaaagccgccguggcgcaaugaaggu
gaaggccggcgccgccggccgaggugggaucccgaggccuuccaguccgc
cgagggcgcaccaccggcccgucucgcccgccgcgccggggagguggagc
acgagcgcacguguuaggacccgaaagauggugaacuaugccugggcagg
gcgaagccagaggaaacucugguggagguccguagcgguccugacgugcg
aaucggucguccgaccuggguauaggggcgaaagacuaaucgaaccaucu
aguagcugguucccuccaaaguuucccucaggauagcuggcgcucuccgc
aguuuuauccgguaaagcgaaugauuagaggucuuggggccgaaacgauc
ucaaccuauucucaaacuuuaaauggguaagaagcccggcucgcuggugu
ggagccgggcguggaaugcgagugccuagugggccacuuuugguaagcag
aacuggcgcugcgggaugaaccgaacgccggguuaaggcgcccgaugccg
acgcucaucagaccccagaaaagguguugguugauauagacagcaggaug
guggccauggaagucggaauccgcuaaggaguguguaacaacucaccugc
cgaaucaacuagcccugaaaauggauggcgcuggagcgucgggcccauac
ccggccgucgcuggcagucggcagagcgagaaagagaguggcgcggacgc
uacgccgcgacgaguaggagggccgcugcggugagccuugaagccuaggg
cgcgggcccggguggagccgccgcaggugcagaucuuggugguaguagca
aauauucaaacgagaacuuugaaggccgaaguggagaaggguuccaugug
aacagcaguugaacaugggucagucgguccugagagaugggcgagcgccg
uuccgaagggacgggcgauggccuccguugcccucagccgaucgaaaggg
agucggguucagauccccgaauccggaguggcggagaugggcgccgcgag
gcguccagugcgguaacgcgaccgaucccggagaagccggcgggagcccc
ggggagaguucucuuuucuuugugaagggcagggcgcccuggaauggguu
cgccccgagagaggggcccgugccuuggaaagcgucgcgguuccggcggc
guccggugagcucucgcuggcccuugaaaauccgggggagaggguguaaa
ucucgcgccgggccguacccauauccgcagcaggucuccaaggugaacag
ccucuggcauguuggaacaauguagguaagggaagucggcaagccggauc
cguaacuucgggauaaggauuggcucuaagggcuggcagccgacuuagaa
cuggugcggaccaggggaauccgacuguuuaauuaaaacaaagcaucgcg
aaggcccgcggcggguguugacgcgaugugauuucugcccagugcucuga
augucaaagugaagaaauucaaugaagcgcggguaaacggcgggaguaac
uaugacucucuuaagguagccaaaugccucgucaucuaauuagugacgcg
caugaauggaugaacgagauucccacugucccuaccuacuauccagcgaa
accacagccaagggaacgggcuuggcggaaucagcggggaaagaagaccc
uguugagcuugacucuagucuggcacggugaagagacaugagagguguag
aauaagugggaggcccgggccgccggugaauaccacuacucugaucguuu
uuucacugacccggugaggcgggggggcgagccgggcucucgcuucuggc
gccaagcgcccggccggccgggcgcgacccgcuccggggacagugccagg
uggggaguuugacuggggcgguacaccugucaaacgguaacgcagguguc
cuaaggcgagcucagggaggacagaaaccucccguggagcagaagggcaa
aagcucgcuugaucuugauuuucaguacgaauacagaccgugaaagcggg
gccucacgauccuucugaccuuuuggguuuuaagcaggaggugucagaaa
aguuaccacagggauaacuggcuuguggcggccaagcguucauagcgacg
ucgcuuuuugauccuucgaugucggcucuuccuaucauugugaagcagaa
uucaccaagcguuggauuguucacccacuaauagggaacgugagcugggu
uuagaccgucgugagacagguuaguuuuacccuacugaugauguguuguu
gccaugguaauccugcucaguacgagaggaaccgcagguucagacauuug
guguaugugcuuggcugaggagccaauggggcgaagcuaccaucuguggg
auuaugacugaacgccucuaagucagaaucccgcccaggcggaacgauag
cgccggagccucgguuggccucggauagccggucccccgccgggguccgg
ugcggagagcccuucgucccgggaaacggggcggccggaaagggggccgc
ccucucgcccgucacgcaccgcacguucguggggaaccuggcgcuaaacc
auucguagacgaccugcuucugggucgggguuucguacguagcagagcag
cugcugcgaucuauugaaagucagcccucgacacaaggguuugu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6d9j Dual tRNA mimicry in the Cricket Paralysis Virus IRES uncovers an unexpected similarity with the Hepatitis C Virus IRES.
• Resolution: 3.2 Å
• Binding residue (original residue number in PDB): R17 Y38 R51 A55 K61 K64 K67 K73 Y75 N76 H79 K107 R108 R112 K115 K133 R135
• Binding residue (residue number reindexed from 1): R16 Y37 R50 A54 K60 K63 K66 K72 Y74 N75 H78 K106 R107 R111 K114 K132 R134

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome

Biological Process

• GO:0006364 rRNA processing
• GO:0006412 translation

Cellular Component

• 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:0022625 cytosolic large ribosomal subunit
• GO:0022626 cytosolic ribosome
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:6d9j, PDBe:6d9j, PDBj:6d9j
• PDBsum: 6d9j
• PubMed: 29856316
• UniProt: G1TXF6|RL27_RABIT Large ribosomal subunit protein eL27 (Gene Name=RPL27)