Structure of PDB 4v7r Chain DW Binding Site BS01

Receptor Information

>4v7r Chain DW (length=94) Species: 4932 (Saccharomyces cerevisiae)

YASKAVPHYNRLDSYKVIEQPITSETAMKKVEDGNILVFQVSMKANKYQI
KKAVKELYEVDVLKVNTLVRPNGTKKAYVRLTADYDALDIANRI

Ligand information

>4v7r Chain D1 (length=3206)

uugaccucaaaucagguaggaguacccgcugaacuuaagcauaucaauaa
gcggaggaaaagaaaccaaccgggauugccuuaguaacggcgagugaagc
ggcaaaagcucaaauuugaaaucugguaccuucggugcccgaguuguaau
uuggagagggcaacuuuggggccguuccuugucuauguuccuuggaacag
gacgucauagagggugagaaucccguguggcgaggagugcgguucuuugu
aaagugccuucgaagagucgaguuguuugggaaugcagcucuaagugggu
gguaaauuccaucuaaagcuaaauauuggcgagagaccgauagcgaacaa
guacagugauggaaagaugaaaagaacuuugaaaagagagugaaaaagua
cgugaaauuguugaaagggaagggcauuugaucagacauugggccagcau
caguuuugguggcaggauaaauccauaggaauguagcuugccucgguaag
uauuauagccugugggaauacugccagcugggacugaggacugcgacgua
agucaaggaugcuggcauaaugguuauaugccgcccgucuugaaacacgg
accaaggagucuaacgucuaugcgaguguuuggguguaaaacccauacgc
guaaugaaagugaacguagguuggggccucgcaagaggugcacaaucgac
cgauccugaugucuucggauggauuugaguaagagcauagcuguugggac
ccgaaagauggugaacuaugccugaauagggugaagccagaggaaacucu
gguggaggcucguagcgguucugacgugcaaaucgaucgucgaauuuggg
uauaggggcgaaagacuaaucgaaccaucuaguagcugguuccugccgaa
guuucccucaggauagcagaagcucguaucaguuuuaugagguaaagcga
augauuagagguuccggggucgaaaugaccuugaccuauucucaaacuuu
aaauauguaagaaguccuuguuacuuaauugaacguggacauuugaauga
agagcuuuuagugggccauuuuugguaagcagaacuggcgaugcgggaug
aaccgaacguagaguuaaggugccggaauacacgcucaucagacaccaca
aaagguguuaguucaucuagacagccggacgguggccauggaagucggaa
uccgcuaaggaguguguaacaacucaccggccgaaugaacuagcccugaa
aauggauggcgcucaagcguguuaccuauacucuaccgucaggguugaua
ugaugcccugacgaguaggcaggcguggaggucagugacgaagccuagac
cguaaggucgggucgaacggccucuagugcagaucuuggugguaguagca
aauauucaaaugagaacuuugaagacugaaguggggaaagguuccacguc
aacagcaguuggacguggguuagucgauccuaagagauggggaagcuccg
uuucaaaggccugauuuuaugcaggccaccaucgaaagggaauccgguua
agauuccggaaccuggauauggauucuucacgguaacguaacugaaugug
gagacgucggcgcgagcccugggaggaguuaucuuuucuucuuaacagcu
uaucaccccggaauugguuuauccggagauggggucuuauggcuggaaga
ggccagcaccuuugcuggcuccggugcgcuugugacggcccgugaaaauc
cacaggaaggaauaguuuucaugccaggucguacugauaaccgcagcagg
ucuccaaggugaacagccucuaguugauagaauaauguagauaagggaag
ucggcaaaauagauccguaacuucgggauaaggauuggcucuaagggucg
gaacgaucaacuuagaacugguacggacaaggggaaucugacugucuaau
uaaaacauagcauugcgauggucagaaagugauguugacgcaaugugauu
ucugcccagugcucugaaugucaaagugaagaaauucaaccaagcgcggg
uaaacggcgggaguaacuaugacucucuuaagguagccaaaugccucguc
aucuaauuagugacgcgcaugaauggauuaacgagauucccacugucccu
aucuacuaucuagcgaaaccacagccaagggaacgggcuuggcagaauca
gcggggaaagaagacccuguugagcuugacucuaguuugacauugugaag
agacauagaggguguagaauaagugggagcuucggcgccagugaaauacc
acuaccuuuauaguuucuuuacuuauucaaugaagcggagcuggaauuca
uuuuccacguucuagcauucaaggucccauucggggcugauccggguuga
agacauugucagguggggaguuuggcuggggcggcacaucuguuaaacga
uaacgcagauguccuaaggggggcucauggagaacagaaaucuccaguag
aacaaaaggguaaaagcccccuugauuuugauuuucagugugaauacaaa
ccaugaaaguguggccuaucgauccuuuagucccucggaauuugaggcua
gaggugccagaaaaguuaccacagggauaacuggcuuguggcagucaagc
guucauagcgacauugcuuuuugauucuucgaugucggcucuuccuauca
uaccgaagcagaauucgguaagcguuggauuguucacccacuaauaggga
acgugagcuggguuuagaccgucgugagacagguuaguuuuacccuacug
augaauguuaccgcaauaguaauugaacuuaguacgagaggaacaguuca
uucggauaauugguuuuugcggcugucugaucaggcauugccgcgaagcu
accauccgcuggauuauggcugaacgccucuaagucagaauccaugcuag
aacgcggugauuucuuugcuccacacaauauagauggauacgaauaaggc
guccuuguggcgucgcugaaccauagcaggcuagcaacggugcacuuggc
ggaaaggccuugggugcuugcuggcgaauugcaaugucauuuugcguggg
gauaaaucauuuguauacgacuuagauguacaacgggguauuguaagcag
uagaguagccuuguuguuacgaucugcugagauuaagccuuuguugucug
auuugu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4v7r Crystal structure of the eukaryotic ribosome.
• Resolution: 4.0 Å
• Binding residue (original residue number in PDB): Y46 A47 K49 K92 N111 L113
• Binding residue (residue number reindexed from 1): Y1 A2 K4 K47 N66 L68

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:4v7r, PDBe:4v7r, PDBj:4v7r
• PDBsum: 4v7r
• PubMed: 21109664
• UniProt: P04456|RL25_YEAST Large ribosomal subunit protein uL23 (Gene Name=RPL25)