Structure of PDB 4v6i Chain BG Binding Site BS01

Receptor Information

>4v6i Chain BG (length=176) Species: 4932 (Saccharomyces cerevisiae)

MSAQKAPKWYPSEDVAALKKTRKAARPQKLRASLVPGTVLILLAGRFRGK
RVVYLKHLEDNTLLISGPFKVNGVPLRRVNARYVIATSTKVSVEGVNVEK
FNVEYFAKEKLTKKEKKEANLFPEQQNKEIKAERVEDQKVVDKALIAEIK
KTPLLKQYLSASFSLKNGDKPHMLKF

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): D14 A17 L18 K19 T21 R22 A25 K29 L42 R46 F47 G49 K50 V52 K56 H57 L58 P75 L76 R77 R82 Y83 E94 V96 N97 V98 E99 L111 G168 D169
• Binding residue (residue number reindexed from 1): D14 A17 L18 K19 T21 R22 A25 K29 L42 R46 F47 G49 K50 V52 K56 H57 L58 P75 L76 R77 R82 Y83 E94 V96 N97 V98 E99 L111 G168 D169

Gene Ontology

Molecular Function

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

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:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:4v6i, PDBe:4v6i, PDBj:4v6i
• PDBsum: 4v6i
• PubMed: 20980660
• UniProt: Q02326|RL6A_YEAST Large ribosomal subunit protein eL6A (Gene Name=RPL6A)