Structure of PDB 3j78 Chain L9 Binding Site BS01

Receptor Information

>3j78 Chain L9 (length=191) Species: 4932 (Saccharomyces cerevisiae)

MKYIQTEQQIEVPEGVTVSIKSRIVKVVGPRGTLTKNLKHIDVTFTKVNN
QLIKVAVHNGGRKHVAALRTVKSLVDNMITGVTKGYKYKMRYVYAHFPIN
VNIVEKDGAKFIEVRNFLGDKKIRNVPVRDGVTIEFSTNVKDEIVLSGNS
VEDVSQNAADLQQICRVRNKDIRKFLDGIYVSHKGFITEDL

Ligand information

>3j78 Chain 2S (length=3302)

uugaccucaaaucagguaggaguacccgcugaacuuaagcauaucaauaa
gcggaggaaaagaaaccaaccgggauugccuuaguaacggcgagugaagc
ggcaaaagcucaaauuugaaaucugguaccuucggugcccgaguuguaau
uuggagagggcaacuuuggggccguuccuugucuauguuccuuggaacag
gacgucauagagggugagaaucccguguggcgaggagugcgguucuuugu
aaagugccuucgaagagucgaguuguuugggaaugcagcucuaagugggu
gguaaauuccaucuaaagcuaaauauuggcgagagaccgauagcgaacaa
guacagugauggaaagaugaaaagaacuuugaaaagagagugaaaaagua
cgugaaauuguugaaagggaagggcauuugaucagacaugguguuuugua
uuucacuggccagcaucaguuuugguggcaggauaaauccauaggaaugu
agcuugccucgguaaguauuauagccugugggaauacugccagcugggac
ugaggacugcgacguaagucaaggaugcuggcauaaugguuauaugccgc
ccgucuugaaacacggaccaaggagucuaacgucuaugcgaguguuuggg
uguaaaacccauacgcguaaugaaagugaacguagguuggggccucgcaa
gaggugcacaaucgaccgauccugaugucuucggauggauuugaguaaga
gcauagcuguugggacccgaaagauggugaacuaugccugaauaggguga
agccagaggaaacucugguggaggcucguagcgguucugacgugcaaauc
gaucgucgaauuuggguauaggggcgaaagacuaaucgaaccaucuagua
gcugguuccugccgaaguuucccucaggauagcagaagcucguaucaguu
uuaugagguaaagcgaaugauuagagguuccggggucgaaaugaccuuga
ccuauucucaaacuuuaaauauguaagaaguccuuguuacuuaauugaac
guggacauuugaaugaagagcuuuuagugggccauuuuugguaagcagaa
cuggcgaugcgggaugaaccgaacguagaguuaaggugccggaauacacg
cucaucagacaccacaaaagguguuaguucaucuagacagccggacggug
gccauggaagucggaauccgcuaaggaguguguaacaacucaccggccga
augaacuagcccugaaaauggauggcgcucaagcguguuaccuauacucu
accgucaggguugauaugaugcccugacgaguaggcaggcguggagguca
gugacgaagccuagaccguaaggucgggucgaacggccucuagugcagau
cuuggugguaguagcaaauauucaaaugagaacuuugaagacugaagugg
ggaaagguuccacgucaacagcaguuggacguggguuagucgauccuaag
agauggggaagcuccguuucaaaggccugauuuuaugcaggccaccaucg
aaagggaauccgguuaagauuccggaaccuggauauggauucuucacggu
aacguaacugaauguggagacgucggcgcgagcccugggaggaguuaucu
uuucuucuuaacagcuuaucaccccggaauugguuuauccggagaugggg
ucuuauggcuggaagaggccagcaccuuugcuggcuccggugcgcuugug
acggcccgugaaaauccacaggaaggaauaguuuucaugccaggucguac
ugauaaccgcagcaggucuccaaggugaacagccucuaguugauagaaua
auguagauaagggaagucggcaaaauagauccguaacuucgggauaagga
uuggcucuaagggucggguagugagggccuuggucagacgcagcgggccu
uguuguagacggccuugguaggucucuuguagaccgucgcuugcuacaac
gaucaacuuagaacugguacggacaaggggaaucugacugucuaauuaaa
acauagcauugcgauggucagaaagugauguugacgcaaugugauuucug
cccagugcucugaaugucaaagugaagaaauucaaccaagcgcggguaaa
cggcgggaguaacuaugacucucuuaagguagccaaaugccucgucaucu
aauuagugacgcgcaugaauggauuaacgagauucccacugucccuaucu
acuaucuagcgaaaccacagccaagggaacgggcuuggcagaaucagcgg
ggaaagaagacccuguugagcuugacucuaguuugacauugugaagagac
auagaggguguagaauaagugggagcuucggcgccagugaaauaccacua
ccuuuauaguuucuuuacuuauucaaugaagcggagcuggaauucauuuu
ccacguucuagcauucaaggucccauucggggcugauccggguugaagac
auugucagguggggaguuuggcuggggcggcacaucuguuaaacgauaac
gcagauguccuaaggggggcucauggagaacagaaaucuccaguagaaca
aaaggguaaaagcccccuugauuuugauuuucagugugaauacaaaccau
gaaaguguggccuaucgauccuuuagucccucggaauuugaggcuagagg
ugccagaaaaguuaccacagggauaacuggcuuguggcagucaagcguuc
auagcgacauugcuuuuugauucuucgaugucggcucuuccuaucauacc
gaagcagaauucgguaagcguuggauuguucacccacuaauagggaacgu
gagcuggguuuagaccgucgugagacagguuaguuuuacccuacugauga
auguuaccgcaauaguaauugaacuuaguacgagaggaacaguucauucg
gauaauugguuuuugcggcugucugaucaggcauugccgcgaagcuacca
uccgcuggauuauggcugaacgccucuaagucagaauccaugcuagaacg
cggugauuucuuugcuccacacaauauagauggauacgaauaaggcgucc
uuguggcgucgcugaaccauagcaggcuagcaacggugcacuuggcggaa
aggccuugggugcuugcuggcgaauugcaaugucauuuugcguggggaua
aaucauuuguauacgacuuagauguacaacgggguauuguaagcaguaga
guagccuuguuguuacgaucugcugagauuaagccuuuguugucugauuu
gu

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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: 3j78 Structures of Yeast 80S Ribosome-tRNA Complexes in the Rotated and Nonrotated Conformations.
• Resolution: 6.3 Å
• Binding residue (original residue number in PDB): S19 K21 S22 R23 K26 D42 V43 T44 R62 K63 A66 R69 T70 S73 H96 F97 D120 K121 K122 R129 V151 Q156 D160 Q163 R166 R168 D171 R173
• Binding residue (residue number reindexed from 1): S19 K21 S22 R23 K26 D42 V43 T44 R62 K63 A66 R69 T70 S73 H96 F97 D120 K121 K122 R129 V151 Q156 D160 Q163 R166 R168 D171 R173

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome
• GO:0019843 rRNA binding

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006412 translation

Cellular Component

• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0022625 cytosolic large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:3j78, PDBe:3j78, PDBj:3j78
• PDBsum: 3j78
• PubMed: 25043550
• UniProt: P05738|RL9A_YEAST Large ribosomal subunit protein uL6A (Gene Name=RPL9A)