Structure of PDB 6d90 Chain C Binding Site BS01

Receptor Information

>6d90 Chain C (length=362) Species: 9986 (Oryctolagus cuniculus)

ACARPLISVYSEKGESSGKNVTLPAVFKAPIRPDIVNFVHTNLRKNNRQP
YAVSELAGHQTSAESWGTGRAVARIPRVRGGGTHRSGQGAFGNMCRGGRM
FAPTKTWRRWHRRVNTTQKRYAICSALAASALPALVMSKGHRIEEVPELP
LVVEDKVEGYKKTKEAVLLLKKLKAWNDIKKVYASQRMRAGKGKMRNRRR
IQRRGPCVIYNEDNGIVKAFRNIPGITLLNVTKLNILKLAPGGHVGRFCI
WTESAFRKLDDLYGTWRKAASLKSNYNLPMHKMLNTDLSRILKSPEIQRA
LRAPRKKIHRRVLKKNPLKNLRIMLKLNPYAKTMRRNTILRQARNHKLRV
ERAAAALAAKSD

Ligand information

>6d90 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

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6d90 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): A2 A4 R5 R33 F39 R45 K46 N48 R49 Q50 Y52 V54 S55 A58 H60 T62 S63 T69 G70 A72 V73 A74 R75 I76 P77 R80 T84 R86 Q89 N94 M95 R97 R100 M101 F102 K106 W108 R109 R110 R114 N116 T117 Q119 R121 K140 T164 K165 K172 N178 K181 K182 Y184 R188 R190 A191 K193 K195 M196 R197 R199 R204 R205 K219 R222 N223 P242 G243 H245 R268 K269 K274 S275 H282 R291 R303 P305 R306 K307 K308 I309 H310 R311 R312 K316 N321 L322 R323 L326 K327 K333 M335 R336 I340 R342 Q343 N346 H347 R350 R353
• Binding residue (residue number reindexed from 1): A1 A3 R4 R32 F38 R44 K45 N47 R48 Q49 Y51 V53 S54 A57 H59 T61 S62 T68 G69 A71 V72 A73 R74 I75 P76 R79 T83 R85 Q88 N93 M94 R96 R99 M100 F101 K105 W107 R108 R109 R113 N115 T116 Q118 R120 K139 T163 K164 K171 N177 K180 K181 Y183 R187 R189 A190 K192 K194 M195 R196 R198 R203 R204 K218 R221 N222 P241 G242 H244 R267 K268 K273 S274 H281 R290 R302 P304 R305 K306 K307 I308 H309 R310 R311 K315 N320 L321 R322 L325 K326 K332 M334 R335 I339 R341 Q342 N345 H346 R349 R352

Gene Ontology

Molecular Function

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

Biological Process

• GO:0006412 translation

Cellular Component

• GO:0005737 cytoplasm
• GO:0005840 ribosome
• GO:0022625 cytosolic large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:6d90, PDBe:6d90, PDBj:6d90
• PDBsum: 6d90
• PubMed: 29856316
• UniProt: G1SVW5|RL4_RABIT Large ribosomal subunit protein uL4 (Gene Name=RPL4)