Structure of PDB 3j77 Chain 75 Binding Site BS01

Receptor Information

>3j77 Chain 75 (length=121) Species: 4932 (Saccharomyces cerevisiae)

KALKVRTSATFRLPKTLKLARAPKYASKAVPHYNRLDSYKVIEQPITSET
AMKKVEDGNILVFQVSMKANKYQIKKAVKELYEVDVLKVNTLVRPNGTKK
AYVRLTADYDALDIANRIGYI

Ligand information

>3j77 Chain 2S (length=3287)

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
uguuguagacggccuugguagucgcuugcuacaacgaucaacuuagaacu
gguacggacaaggggaaucugacugucuaauuaaaacauagcauugcgau
ggucagaaagugauguugacgcaaugugauuucugcccagugcucugaau
gucaaagugaagaaauucaaccaagcgcggguaaacggcgggaguaacua
ugacucucuuaagguagccaaaugccucgucaucuaauuagugacgcgca
ugaauggauuaacgagauucccacugucccuaucuacuaucuagcgaaac
cacagccaagggaacgggcuuggcagaaucagcggggaaagaagacccug
uugagcuugacucuaguuugacauugugaagagacauagaggguguagaa
uaagugggagcuucggcgccagugaaauaccacuaccuuuauaguuucuu
uacuuauucaaugaagcggagcuggaauucauuuuccacguucuagcauu
caaggucccauucggggcugauccggguugaagacauugucaggugggga
guuuggcuggggcggcacaucuguuaaacgauaacgcagauguccuaagg
ggggcucauggagaacagaaaucuccaguagaacaaaaggguaaaagccc
ccuugauuuugauuuucagugugaauacaaaccaugaaaguguggccuau
cgauccuuuagucccucggaauuugaggcuagaggugccagaaaaguuac
cacagggauaacuggcuuguggcagucaagcguucauagcgacauugcuu
uuugauucuucgaugucggcucuuccuaucauaccgaagcagaauucggu
aagcguuggauuguucacccacuaauagggaacgugagcuggguuuagac
cgucgugagacagguuaguuuuacccuacugaugaauguuaccgcaauag
uaauugaacuuaguacgagaggaacaguucauucggauaauugguuuuug
cggcugucugaucaggcauugccgcgaagcuaccauccgcuggauuaugg
cugaacgccucuaagucagaauccaugcuagaacgcggugauuucuuugc
uccacacaauauagauggauacgaauaaggcguccuuguggcgucgcuga
accauagcaggcuagcaacggugcacuuggcggaaaggccuugggugcuu
gcuggcgaauugcaaugucauuuugcguggggauaaaucauuuguauacg
acuuagauguacaacgggguauuguaagcaguagaguagccuuguuguua
cgaucugcugagauuaagccuuuguugucugauuugu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3j77 Structures of Yeast 80S Ribosome-tRNA Complexes in the Rotated and Nonrotated Conformations.
• Resolution: 6.2 Å
• Binding residue (original residue number in PDB): K22 A30 R33 L34 L38 R42 A43 P44 K45 Y46 T71 K75 N91 K92 Y93 K109 N111 T112 L113 Y123 R125
• Binding residue (residue number reindexed from 1): K1 A9 R12 L13 L17 R21 A22 P23 K24 Y25 T50 K54 N70 K71 Y72 K88 N90 T91 L92 Y102 R104

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0005515 protein binding
• GO:0019843 rRNA binding

Biological Process

• GO:0000027 ribosomal large subunit assembly
• 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:0030687 preribosome, large subunit precursor
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:3j77, PDBe:3j77, PDBj:3j77
• PDBsum: 3j77
• PubMed: 25043550
• UniProt: P04456|RL25_YEAST Large ribosomal subunit protein uL23 (Gene Name=RPL25)