Structure of PDB 4v8y Chain BJ Binding Site BS01

Receptor Information

>4v8y Chain BJ (length=169) Species: 4932 (Saccharomyces cerevisiae)

QNPMRDLKIEKLVLNISVGESGDRLTRASKVLEQLSGQTPVQSKARYTVR
TFGIRRNEKIAVHVTVRGPKAEEILERGLKVKEYQLRDRNFSATGNFGFG
IDEHIDLGIKYDPSIGIFGMDFYVVMNRPGARVTRRKRCKGTVGNSHKTT
KEDTVSWFKQKYDADVLDK

Ligand information

>4v8y Chain B5 (length=3147)

uugaccucaaaucagguaggaguacccgcugaacuuaagcauaucaauaa
gcggaggaaaagaaaccaaccgggauugccuuaguaacggcgagugaagc
ggcaaaagcucaaauuugaaaucugguaccuucggugcccgaguuguaau
uuggagagggcaacuuuggggccguuccuugucuauguuccuuggaacag
gacgucauagagggugagaaucccguguggcgaggagugcgguucuuugu
aaagugccuucgaagagucgaguuguuugggaaugcagcucuaagugggu
gguaaauuccaucuaaagcuaaauauuggcgagagaccgauagcgaacaa
guacagugauggaaagaugaaaagaacuuugaaaagagagugaaaaagua
cgugaaauuguugaaagggaagggcauuugaucagacauggcugggccag
caucaguuuugguggcaggauaaauccauaggaauguagcuugccucggu
aaguauuauagccugugggaauacugccagcugggacugaggacugcgac
guaagucaaggaugcuggcauaaugguuauaugccgcccgucuugaaaca
cggaccaaggagucuaacgucuaugcgaguguuuggguguaaaacccaua
cgcguaaugaaagugaacguagguuggggccucgcaagaggugcacaauc
gaccgauccugaugucuucggauggauuugaguaagagcauagcuguugg
gacccgaaagauggugaacuaugccugaauagggugaagccagaggaaac
ucugguggaggcucguagcgguucugacgugcaaaucgaucgucgaauuu
ggguauaggggcgaaagacuaaucgaaccaucuaguagcugguuccugcc
gaaguuucccucaggauagcagaagcucguaucaguuuuaugagguaaag
cgaaugauuagagguuccggggucgaaaugaccuugaccuauucucaaac
uuuaaauauguaagaaguccuuguuacuuaauugaacguggacauuugaa
ugaagagcuuuuagugggccauuuuugguaagcagaacuggcgaugcggg
augaaccgaacguagaguuaaggugccggaauacacgcucaucagacacc
acaaaagguguuaguucaucuaagccggacgguggccauggaagucggaa
uccgcuaaggaguguguaacaacucaccggccgaaugaacuagcccugaa
aauggauggcgcucaagcguguuaccuauacucuaccgucaggguugaua
ugaugcccugacgaguaggcaggcguggaggucagugacgaagccuagac
cguaaggucgggucgaacggccucuagugcagaucuuggugguaguagca
aauauucaaaugagaacuuugaagacugaaguggggaaagguuccacguc
aacagcaguuggacguggguuagucgauccuaagagauggggaagcuccg
uuucaaaggccugauuuuaugcaggccaccaucgaaagggaauccgguua
agauuccggaaccuggauauggauucuucacgguaacguaacugaaugug
gagacgucggcgcgagcccugggaggaguuaucuuuucuucuuaacagcu
uaucaccccggaauugguuuauccggagauggggucuuauggcuggaaga
ggccagcaccuuugcuggcuccggugcgcuugugacggcccgugaaaauc
cacaggaaggaauaguuuucaugccaggucguacugauaaccgcagcagg
ucuccaaggugaacagccucuaguugauagaauaauguagauaagggaag
ucggcaaaauagauccguaacuucgggauaaggauuggcucuaagggucg
gacgaucaacuuagaacugguacggacaaggggaaucugacugucuaauu
aaaacauagcauugcgauggucagaaagugauguugacgcaaugugauuu
cugcccagugcucugaaugucaaagugaagaaauucaaccaagcgcgggu
aaacggcgggaguaacuaugacucucuuaagguagccaaaugccucguca
ucuaauuagugacgcgcaugaauggauuaacgagauucccacugucccua
ucuacuaucuagcgaaaccacagccaagggaacgggcuuggcagaaucag
cggggaaagaagacccuguugagcuugacucuaguuugacauugugaaga
gacguuucuuuacuuauucaaugaagcggagcuggaauucauuuuccacg
uucuagcauucaaggucccauucggggcugauccggguugaagacauugu
cagguggggaguuuggcuggggcggcacaucuguuaaacgauaacgcaga
uguccuaaggggggcucauggagaacagaaaucuccaguagaacaaaagg
guaaaagcccccuugauuuugauuuucagugugaauacaaaccaugaaag
uguggccuaucgauccuuuagucccucggaauuugaggcuagaggugcca
gaaaaguuaccacagggauaacuggcuuguggcagucaagcguucauagc
gacauugcuuuuugauucuucgaugucggcucuuccuaucauaccgaagc
agaauucgguaagcguuggauuguucacccacuaauagggaacgugagcu
ggguuuagaccgucgugagacagguuaguuuuacccuacugaugaauguu
accgcaauaguaauugaacuuaguacgagaggaacaguucauucggauaa
uugguuuuugcggcugucugaucaggcauugccgcgaagcuaccauccgc
uggauuauggcugaacgccucuaagucagaauccaugcuagaacgcggug
auuucuuugcuccacacaauauagauggauacgaauaaggcguccuugug
gcgucgcugaaccauagcaggcuagcaacggugcacuuggcggaaaggcc
uugggugcuugcuggcgaauugcaaugucauuuugcguggggauaaauca
uuuguauacgacuuagauguacaacgggguauuguaagcaguagaguagc
cuuguuguuacgaucugcugagauuaagccuuuguugucugauuugu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4v8y Molecular architecture of a eukaryotic translational initiation complex.
• Resolution: 4.3 Å
• Binding residue (original residue number in PDB): K16 V18 N20 S22 G24 S48 R51 Y52 F57 H68 R94 N95 F96 S97 A98 T99 N101 G103 F104 G105 I106 D107 G124 M125 D126 Y128 V130 K142
• Binding residue (residue number reindexed from 1): K11 V13 N15 S17 G19 S43 R46 Y47 F52 H63 R89 N90 F91 S92 A93 T94 N96 G98 F99 G100 I101 D102 G119 M120 D121 Y123 V125 K137

Gene Ontology

Molecular Function

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

Biological Process

• GO:0000027 ribosomal large subunit assembly
• GO:0002181 cytoplasmic translation
• GO:0006412 translation

Cellular Component

• GO:0005634 nucleus
• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0022625 cytosolic large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:4v8y, PDBe:4v8y, PDBj:4v8y
• PDBsum: 4v8y
• PubMed: 24200810
• UniProt: P0C0W9|RL11A_YEAST Large ribosomal subunit protein uL5A (Gene Name=RPL11A)