Structure of PDB 4v6i Chain BQ Binding Site BS01

Receptor Information

>4v6i Chain BQ (length=297) Species: 4932 (Saccharomyces cerevisiae)

MAFQKDAKSSAYSSRFQTPFRRRREGKTDYYQRKRLVTQHKAKYNTPKYR
LVVRFTNKDIICQIISSTITGDVVLAAAYSHELPRYGITHGLTNWAAAYA
TGLLIARRTLQRLGLDETYKGVEEVEGEYELTEAVEDGPRPFKVFLDIGL
QRTTTGARVFGALKGASDGGLYVPHSENRFPGWDFETEEIDPELLRSYIF
GGHVSQYMEELADDDEERFSELFKGYLADDIDADSLEDIYTSAHEAIRAD
PAFKPTEKKFTKEQYAAESKKYRQTKLSKEERAARVAAKIAALAGQQ

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): K5 S10 A11 Y12 R15 T18 R23 G26 T28 D29 Y31 Q32 R35 L36 Q39 K41 L110 T118 K120 D137 R140 F142 K143 F145 L146 I148 L150 Q151 R152 T153 G170 P174 H175 S176 R179
• Binding residue (residue number reindexed from 1): K5 S10 A11 Y12 R15 T18 R23 G26 T28 D29 Y31 Q32 R35 L36 Q39 K41 L110 T118 K120 D137 R140 F142 K143 F145 L146 I148 L150 Q151 R152 T153 G170 P174 H175 S176 R179

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome
• GO:0005515 protein binding
• GO:0008097 5S rRNA binding
• 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:4v6i, PDBe:4v6i, PDBj:4v6i
• PDBsum: 4v6i
• PubMed: 20980660
• UniProt: P26321|RL5_YEAST Large ribosomal subunit protein uL18 (Gene Name=RPL5)