Structure of PDB 3j78 Chain L1 Binding Site BS01

Receptor Information

>3j78 Chain L1 (length=204) Species: 4932 (Saccharomyces cerevisiae)

VKELLKYSNETKKRNFLETVELQVGLKNYDPQRDKRFSGSLKLPNCPRPN
MSICIFGDAFDVDRAKSCGVDAMSVDDLKKLNKNKKLIKKLSKKYNAFIA
SEVLIKQVPRLLGPQLSKAGKFPTPVSHNDDLYGKVTDVRSTIKFQLKKV
LCLAVAVGNVEMEEDVLVNQILMSVNFFVSLLKKNWQNVGSLVVKSSMGP
AFRL

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

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

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): L29 E30 V32 E33 Q35 K39 K102 G125 Q158 V162 C164 N197 V205 K207 S209 M210
• Binding residue (residue number reindexed from 1): L17 E18 V20 E21 Q23 K27 K90 G113 Q146 V150 C152 N185 V193 K195 S197 M198

Gene Ontology

Molecular Function

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

Biological Process

• GO:0000055 ribosomal large subunit export from nucleus
• GO:0002181 cytoplasmic translation
• GO:0006412 translation
• GO:0042254 ribosome biogenesis

Cellular Component

• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0015934 large ribosomal subunit
• GO:0022625 cytosolic large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:3j78, PDBe:3j78, PDBj:3j78
• PDBsum: 3j78
• PubMed: 25043550
• UniProt: P0CX43|RL1A_YEAST Large ribosomal subunit protein uL1A (Gene Name=RPL1A)