Structure of PDB 4v6i Chain BZ Binding Site BS01

Receptor Information

>4v6i Chain BZ (length=73) Species: 4932 (Saccharomyces cerevisiae)

MKVEIDSFSGAKIYPGRGTLFVRGDSKIFRFQNSKSASLFKQRKNPRRIA
WTVLFRKHHKKGITEEVAKKRSR

Ligand information

>4v6i Chain DA (length=3354)

guuugaccucaaaucagguaggaguaccgcugaacuuaagcauaucaaua
agcggaggaaaagaaaccaaccgggauugccuuaguaacggcgagugaag
cggcaaaagcucagaaaucugguaccuucggugcccgaguuguaauuugg
agagggcacuuuggggccguuccuugucuauguuccuuggaacaggacgu
cauagagggugagaaucccguguggcgaggagugcgguucuuuguaaagu
gccuucgaagagucgaguuguuugggaaugcagcucuaagugggugguaa
auuccaucuaaagcuaaauauuggcgagagaccgauagcgaacaaguaca
gugauggaaagaugaaaagaacuuugaaaagagagugaaaaaguacguga
aauuguugaaagggaagggcauuugaucagacaugguguuuugugcccuc
ugcuccuuguggguaggggaaucucgcauuucacugggccagcaucaguu
uugguggcaggauaaauccauaggaauguagcuugccucgguaaguauua
uagccugugggaauacugccagcugggacugaggacugcgacguaaguca
aggaugcuggcauaaugguuauaugccgcccgucuugaaacacggaccaa
ggagucuaacgucuaugcgaguguuuggguguaaaacccauacgcguaau
gaaagugaaagguuggggccucgcaagaggugcacaaucgaccgauccug
augucuucggauggauuugaguaagagcauagcuguugggacccgaaaga
uggugaacuaugccugaauagggugaagccagaggaaacucugguggagg
cucguagcgguucugacgugcaaaucgaucgucgaauuuggguauagggg
cgaaagacuaaucgaaccaucuaguagcugguuccugccgaaguuucccu
caggauagcagaagcucguaucaguuuuaugagguaaagcgaaugauuag
agguuccggggucgaaaugaccuugaccuauucucaaacuuuaaauaugu
aagaaguccuuguuacuuaauugaacguggacauuugaaugaagagcuuu
uagugggccauuuuugguaagcagaacuggcgaugcgggaugaaccgaac
guagaguuaaggugccggaauacacgcucaucagacaccacaaaaggugu
uaguucaucuagacagccggacgguggccauggaagucggaauccgcuaa
ggaguguguaacaacucaccggccgaaugaacuagcccugaaaauggaug
gcgcucaagcguguuaccuauacucuaccgucaggguugauaugaugccc
ugacgaguaggcaggcguggaggucgugacgaagccagacguaaggucgg
gucgaacggccucuagugcagaucuuggugguaguagcaaauauucaaau
gagaacuuugaagacugaaguggggaaagguuccacgucaacagcaguug
gacguggguuagucgauccuaagagauggggaagcuccguuucaaaggcc
ugauuuuaugcaggccaccaucgaaagggaauccgguuaagauuccggaa
ccugguauggauucuucacggaacguaacugaauguggagacgucggcgc
gagcccugggaggaguuaucuuuucuucuuaacagcuuaucaccccggaa
uugguuuauccggagaugggucuuauggcuggaagaggccagcaccuuug
cuggcuccggugcgcuugugacggcccgugaaaauccacaggaaggaaua
guuuuaugccaggucguacugauaaccgcagcaggucuccaaggugaaca
gccucuaguugauagaauaauguagauaagggaagucggcaaaauagauc
cguaacuucgggauaaggauuggcucuaagggucggguagugagggccuu
ggucagacgcagcgggcgugcuuguggacugcuugguggggcuugcucug
cuaggcggacuacuugcgugccuuguuguagacggccuugguaggucucu
uguagaccgucgcuugcuacaauuaacgaucaacuuagaacugguacgga
caaggggaaucugacugucuaauuaaaacauagcauugcgauggucagaa
gugauguugacgcaaugugauuucugcccagugcucugaaugucaaagug
aagaaauucaaccaagcgcggguaaacggcgggaguaacuaugacucucu
uaagguagccaaaugccucgucaucuaauuagugacgcgcaugaauggau
uaacgagauucccacugucccuaucuacuaucuagcgaaaccacagccaa
gggaacgggcuuggcagaaucagcggggaaagaagacccuguugagcuug
acucuaguuugacauugugaagagacauagaggguguagaauaaguggga
gcuucggcgccagugaaauaccacuaccuuuauaguuucuuuacuuauuc
aaugaagcggagcuggaauucauuuuccaaaggucccauucggggcugau
ccggguugaagacauugucagguggggaguuuggcuggggcggcacaucu
guuaaacgauaacgcagauguccuaaggggggcucauggagaacagaaau
cuccaguagaacaaaaggguaaaagcccccuugauuuugauuuucagugu
gaauacaaaccaugaaaguguggccuaucgauccuuuaguccucggaauu
ugaggcuagaggugccagaaaaguuaccacagggauaacuggcuuguggc
agucaagcguucauagcgacauugcuuuuugauucuucgaugucggcucu
uccuaucauaccgaagcagaauucgguaagguuggauuguucacccacua
auagggaacgugagcuggguuuagaccgucgugagacagguuaguuuuac
ccuacugaugauguuaccgcaauaguaauugaacuuaguacgagaggaac
aguucauucggauaauugguuuuugcggcgucugaucaggcauugccgcg
aagcuaccauccgcuggauuauggcugaacgccucuaagucagaauccau
gcuagaacgcggugauuucuuugcuccacacaauauagauggauacgaau
aaggcguccuuguggcgucgcugaaccauagcaggcuagcaacggugcac
uuggcggaaaggccuugggugcuugcuggcgaauugcaaugucauuuugc
gugggauaaucauuuguauacgacuuagauguacaacggggauuguaagc
aguagaguagccuuguuguuacgaucugcugagauuauuuguugucugau
uugu

..........................<<<<<.....<......>......
>>>.>.>.........<<....>>..<<<<<......<<.....>>....
.>>>>>..<<<......<<.<<<<<<...>>>>>>.>>............
.<<<<.<<<<<<<<<<<<<<<<<<<<<<.....<<<<......>>>>.(.
......<<<......)>>>....>>>>>>>.>.>>>>>>>>....>>>>>
>>>.>>........<<<<<<<........>>>>>>>.....<<<<<..[[
.[[.>>>>>..>>>................................<.<<
....>>...>...........<<<......>>>.................
...................<<<.<<<<<<<....<<<<...<<<..<<<<
<<<.<<....>>>>>>>>>......>>>...>>>>..<<<<<<<.<<<<<
..<.<<<<<<.<<...<<<.<<<<..<<<<<<<<<<....>>>>>>..>>
>>.>>>>.>>>.>>.>>>>>>..>..>>>>>....<<..<<<....>>>.
>>..>>>>>>>.><.>>>>>>.>>>....<<<<........>>>><<<<<
<...<.<<<<<.<<<<<<..<<...<<<<<.....>>>>>...>>...<<
....>>.....<<<<..<<<<<....>>>>>...>>>>....<<<<<<..
..<....>....>>>>.>>.......>>>>>>.>>>>>.>.<<.<...<<
<<<<.....<<<<<<<<<..<<<....<<<<<<<....>>>>>>>.....
>>>...<<<<.<<.<<........>>>>>>>>....>>>>>>>>>...<<
.......>>......>>>>>>......>.>>..<<<<<<....<.<<<..
..>>>.><.<<<<<<<..........<<.<<......<<..........<
..<......<.............>....>..>........>>.......>
>.>>..<..<<<<..<......>...>>>>..>...........>>>>>>
>..>..<<<<.<<<<<.....>>>>>.>>>>....<<<......>>>...
<<<<<<<..<<<<(((.....<<<<<<..................<<..<
<<<<<<<<.......<<<<<.<<....<<.........>>....>>....
.....<<......>>...>>>>>...>>>>>>>>>.>>...........)
))......>>>>>>.>>>>..>>>>>>><<<<<<<<<.........>>>>
>>>>>....>>>>>><..<<<<<<<<<.....<.<<.<.<....>.>.>>
.>...>>>>>>>>>...>.....>>>>>><<.....<<.....<<<<<<.
......>>>>>><<<<.....<<<<<.<<...<<<<<<...<<.....>>
.>>>>>>....((<<<<<<...<<....<<<....>>>........<<<<
<<........>>>>>>....>>....>>>..<<<<<........>>>>>)
)<<<<<<<.<<.................<<...<<<<<<...<<<<.<<<
<.<..<<<<<<<<<<.......>>>>>><...<.<......<...<....
.<<<.....>>>.......>..>......>.>....>.<<<<<<....>>
>>>>..>>>>.....>>>>>.>>>>.........>>>>>>...>......
>.>>.>>>>>>>.>>>..>>.....<<......>>>>>>>..<<<.....
>>>...>>>>..<<<<.....<<<<<<<.<<...............<<<<
<.....<..>......>>>>><<.<<<<<<<<<<<.<<<<<<<<.<<<..
<<<<....<<<<<<<<<<<<<..<<<<.<<<<<<<<<<<<<....>>>>>
>>>>>>>>.>>>>..>>>>>>>.>>>>>>....>>>>..>>>.<<<<<..
...>>>>>....>>>>>>>>......>>>>>..>>>>>>.>>........
....<<<<<<<<<..<<<.........>>>..<<<<<<<.....<<<...
.>>>.......>>>>>>>...<<..<<<..<<<<<<....<<<.....<<
<<....>>>>.....>>>.>>>>..>>>>><<<<<<.......>>>>>>.
.......<...........<<<<<.......>>>>>.....>.....>>.
...>>.>>>>>>>.....>>.>>>>>>>..>>>>>>....>>....<<<<
<........>>>>>....<<<<<..<<<.<<......<<<<.<<<<<<..
<<<<<.<<<<<<<<..<<<<<<<<<<<<<<<<<..........<<<<<..
<<....>>............>>>>>.>>>>>>>.>>>>>>>>>>...<<<
<<.....<<<<..<<<<<......>>>>>..<<<<<<....>>>>>>..>
>>>..>>>>>.....>>>>>>>>..>>>>>...<<<.....>>>..<<<<
<<...........>>>>>>..<<...<<<<<<<...<<<<<<.......>
>>>>>.....<<...(((>>....>>>>>>>...<<<..<<<<.......
>>>>..>>>.<<<....>>>.>>))).....<.<<<<<<.<<<<.]].]]
.>>>>>>>>>>>.........>>>>..>>>>>>.......<<.<...<<<
<<<...<<.......>>...>>>>>>....>..>>.......<<<<<..<
<<<<..<.<<<<<<<......>>>>>>>..>.<<<.........>>>...
..>>>>>......>>>.>>....<<<<<<<....>>>.>>>>....>>..
>>>.>>>>>....<<<<<<...<<<<.<.<<<<<<...............
>>>>>>.><<<<<....<<<...<<<<<.<<<<....>>>>....>>>>>
..>>>...>>>>>.<<<<...<<<<<...........>>>>>...>>>>.
>>>>.....>>>>>>.........<<<<<.<<<<......<.........
...<<.<......>>>..........<.......>.......<<<<<<.<
<.<<<......>>>..>>>>>>>.>......(....>..>>)....>>>.
>>>>>..<<<<.<.............>.....<<<<<<<...<<....<<
<<....<<<<<......>>>>>...>>>>...>>...>>.>>>>>..>>>
>...

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4v6i Cryo-EM structure and rRNA model of a translating eukaryotic 80S ribosome at 5.5-A resolution.
• Resolution: 8.8 Å
• Binding residue (original residue number in PDB): R17 S34 Q42 R48 I49 W51 T52 R56 E65 S72
• Binding residue (residue number reindexed from 1): R17 S34 Q42 R48 I49 W51 T52 R56 E65 S72

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003729 mRNA binding
• GO:0003735 structural constituent of ribosome

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006413 translational initiation
• GO:0006414 translational elongation

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:4v6i, PDBe:4v6i, PDBj:4v6i
• PDBsum: 4v6i
• PubMed: 20980660
• UniProt: P04449|RL24A_YEAST Large ribosomal subunit protein eL24A (Gene Name=RPL24A)