Structure of PDB 4v6i Chain BX Binding Site BS01

Receptor Information

>4v6i Chain BX (length=122) Species: 4932 (Saccharomyces cerevisiae)

KKALKVRTSATFRLPKTLKLARAPKYASKAVPHYNRLDSYKVIEQPITSE
TAMKKVEDGNILVFQVSMKANKYQIKKAVKELYEVDVLKVNTLVRPNGTK
KAYVRLTADYDALDIANRIGYI

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): K22 L24 K25 P35 K36 L38 K39 L40 K45 A47 S48 A50 S69 T71 N91 K92 Y93 N111 T112 L113 V114 K121 R125
• Binding residue (residue number reindexed from 1): K2 L4 K5 P15 K16 L18 K19 L20 K25 A27 S28 A30 S49 T51 N71 K72 Y73 N91 T92 L93 V94 K101 R105

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:4v6i, PDBe:4v6i, PDBj:4v6i
• PDBsum: 4v6i
• PubMed: 20980660
• UniProt: P04456|RL25_YEAST Large ribosomal subunit protein uL23 (Gene Name=RPL25)