Structure of PDB 6xu8 Chain CN Binding Site BS02

Receptor Information

>6xu8 Chain CN (length=203) Species: 7227 (Drosophila melanogaster)

GAYRYMQELYRKKQSDVMRYLLRIRVWQYRQLTKLHRSPRPTRPDKARRL
GYRAKQGFVIYRIRVRRGGRKRPVPKGCTYGKPKSHGVNQLKPYRGLQSI
AEERVGRRLGGLRVLNSYWIAQDASYKYFEVILIDTHHSAIRRDPKINWI
CKHVHKHRELRGLTSAGKSSRGIGKGYRYSQTIGGSRRAAWKRKNREHMH
RKR

Ligand information

>6xu8 Chain A5 (length=3703)

uuauauacaaccucaacucauaugggacuacccccugaauuuaagcauau
uaauuaggggaggaaaagaaacuaacaaggauuuucuuaguagcggcgag
cgaaaagaaaacaguucagcacuaagucacuuugucuauauggcaaaugu
gagaugcaguguauggagcgucaauauucuaguaugagaaauuaacgauu
uaaguccuucuuaaaugaggccauuuacccauagagggugccaggcccgu
auaacguuaaugauuacuagaugauguuuccaaagagucguguugcuuga
uagugcagcacuaagugggugguaaacuccaucuaaaacuaaauauaacc
augagaccgauaguaaacaaguaccgugagggaaaguugaaaagaacucu
gaauagagaguuaaacaguacgugaaacugcuuagagguuaagcccgaug
aaccugaauauccguuauggaaaauucaucauuaaaauuguaauauuuaa
auaauauuaugagaauagugugcauuuuuuccauauaaggacauuguaau
cuauuagcauauaccaaauuuaucauaaaauauaacuuauaguuuauucc
aauuaaauugcuugcauuuuaacacagaauaaauguuauuaauuugauaa
agugcugauagauuuauaugauuacagugcguuaauuuuucggaauuaua
uaauggcauaauuaucauugauuuuuguguuuauuauaugcacuuguaug
auuaacaaugcgaaagauucaggauaccuucgggacccgucuugaaacac
ggaccaaggagucuaacauaugugcaaguuauugggauauaaaccuaaua
gcguaauuaacuugacuaauaaugggauuaguuuuuuagcuauuuauagc
uaauuaacacaaucccggggcguucuauauaguuauguauaauguauauu
uauauuauuuaugccucuaacuggaacguaccuugagcauauaugcugug
acccgaaagauggugaacuauacuugaucagguugaagucaggggaaacc
cugauggaagaccgaaacaguucugacgugcaaaucgauugucagaauug
aguauaggggcgaaagaccaaucgaaccaucuaguagcugguuccuuccg
aaguuucccucaggauagcuggugcauauauuauauaaaauaaucuuauc
ugguaaagcgaaugauuagaggccuuagggucgaaacgaucuuaaccuau
ucucaaacuuuaaauggguaagaaccuuaacuuucuugauaugaagauca
agguuaugauauaaaugucccagugggccacuuuugguaagcagaacugg
cgcugugggaugaaccaaacguaauguuacgugcccaaauuaacaacuca
ugcagauaccaugaaaggcguugguugcuuaaaacagcaggacggugauc
auggaagucgaaauccgcuaaggaguguguaacaacucaccugccgaagc
aacuagcccuuaaaauggauggcgcuuaaguuguauaccuauacauuacc
gcuaaaguagaugauuuauauuacuugugauauaaauuuugaaacuuuag
ugaguaggaagguacaaugguaugcguagaaguguuuggcguaagccugc
auggagcugccauugguacagaucuugguggauaguagcaaauaaucgaa
ugagagccuuggaggacugaaguggagaaggguuucgugugaacaguggu
ugaucacgaguuagucgguccuaaguucaaggcgaaagcgaaaauuuuca
aguaaaacauaauuuugaacgaaagggaauacgguuccaauuccguaacc
uguugaguauccguuuguuauuaaauaugggccucgugcucauccuggca
acaggaacgaccauaaagaagccgucgagagauaucggaagaguuuucuu
uucuguuuuauagccguacuaccauggaagucuuucgcagagagauaugg
uagaugggcuagaagagcaugacauauacuguugugucgauauuuucucc
ucggaccuugaaaauuuaugguggggacacgcaaacuucucaacaggccg
uaccaauauccgcagcuggucuccaaggugaagagucucuagucgauaga
auaauguagguaagggaagucggcaaauuagauccguaacuucgggauaa
ggauuggcucugaagauugagauagucggccuugauugggaaacuggaac
uuucuugcuaaauuauaacgauuaucaauuaacaaucaauucagaacugg
cacggacuuggggaauccgacugucuaauuaaaacaaagcauugugaugg
cccuagcggguguugacacaaugugauuucugcccagugcucugaauguc
aaagugaagaaauucaaguaagcgcgggucaacggcgggaguaacuauga
cucucuuaagguagccaaaugccucgucaucuaauuagugacgcgcauga
auggauuaacgagauuccuacugucccuaucuacuaucuagcgaaaccac
agccaagggaacgggcuuggaauaauuagcggggaaagaagacccuuuug
agcuugacucuaaucuggcaguguaaggagacauaagagguguagaauaa
gugggagauauuagaccucgguuugguaucgucaaugaaauaccacuacu
cuuauuguuuccuuacuuacuugauuaaauggaacguguaucauuuccua
gauuggguuuugaugcaagcuucuugaucaaaguaucacgaguuuguuau
auaaucgcaaacaaauuugguauaacuccaauuacucagguaugauccaa
uucaaggacauugccagguagggaguuugacuggggcgguacaucucuca
aauaauaacggaggugucccaaggccagcucagugcggacagaaaccaca
cauagagcaaaagggcaaaugcugacuugaucucgguguucaguacacac
agggacagcaaaagcucggccuaucgauccuuuugguuuaaagaguuuuu
aacaagaggugucagaaaaguuaccauagggauaacuggcuuguggcggc
caagcguucauagcgacgucgcuuuuugauccuucgaugucggcucuucc
uaucauugugaagcaaaauucaccaagcguuggauuguucacccaugcaa
gggaacgugagcuggguuuagaccgucgugagacagguuaguuuuacccu
acuaaugacaaaacguuguugcgacagcauuccugcguaguacgagagga
acccgcagguacggaccaauggcacaauacuuguucgagcgaacaguggu
augacgcuacguccguuggauuaugccugaacgccucuaaggucguaucc
gugcuggacugcaaugauaaauaaggggcaauuugcauuguauggcuucu
aaaccauuuaaaguuuauaauuuacuuuauaaacgacaauggaugugaug
ccaauguaauuuguaacauaguaaauugggaggaucuucgaucaccugau
gccgcgcuaguuacauauaaaagcauuauuuaauacaaugacaaagccua
gaaucaauuguaaacgacuuuuguaacaggcaagguguuguaagugguug
agcagcugccauacugcgauccacugaagcuuauccuuugcuugaugauu
cga

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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: 6xu8 Ribosome heterogeneity in Drosophila melanogaster gonads through paralog-switching.
• Resolution: 3.0 Å
• Binding residue (original residue number in PDB): G2 Y4 R5 Q8 R12 K14 Q15 R24 W28 T34 K35 H37 P40 K47 R49 R50 L51 R54 A55 Q57 R67 R68 G69 G70 R71 K72 R73 P74 P76 K77 Y81 G82 K83 K85 H87 N90 Q91 L92 K93 P94 Y95 R96 G97 L98 E104 R105 R108 Y119 W120 D124 A125 H138 S140 A141 R143 R144 K147 W150 H154 V155 K157 H158 R162 G163 S166 K169 S170 S171 R172 I174 K176 G177 Y178 R179 S181 Q182 I184 G185 S187 R188 R189 W192 K193 R194 K195 R197 H199 M200 H201 R202 K203 R204
• Binding residue (residue number reindexed from 1): G1 Y3 R4 Q7 R11 K13 Q14 R23 W27 T33 K34 H36 P39 K46 R48 R49 L50 R53 A54 Q56 R66 R67 G68 G69 R70 K71 R72 P73 P75 K76 Y80 G81 K82 K84 H86 N89 Q90 L91 K92 P93 Y94 R95 G96 L97 E103 R104 R107 Y118 W119 D123 A124 H137 S139 A140 R142 R143 K146 W149 H153 V154 K156 H157 R161 G162 S165 K168 S169 S170 R171 I173 K175 G176 Y177 R178 S180 Q181 I183 G184 S186 R187 R188 W191 K192 R193 K194 R196 H198 M199 H200 R201 K202 R203

Gene Ontology

Molecular Function

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

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006412 translation

Cellular Component

• GO:0005840 ribosome
• GO:0022625 cytosolic large ribosomal subunit
• GO:0022626 cytosolic ribosome
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:6xu8, PDBe:6xu8, PDBj:6xu8
• PDBsum: 6xu8
• PubMed: 34283226
• UniProt: O17445|RL15_DROME Large ribosomal subunit protein eL15 (Gene Name=RpL15)