Structure of PDB 8p8u Chain QW Binding Site BS01

Receptor Information

>8p8u Chain QW (length=61) Species: 4932 (Saccharomyces cerevisiae)

MKVEIDSFSGAKIYPGRGTLFVRGDSKIFRFQNSKSASLFKQRKNPRRIA
WTVLFRKHHKK

Ligand information

>8p8u Chain A (length=3045)

uugaccucaaaucagguaggaguacccgcugaacuuaagcauaucaauaa
gcggaggaaaagaaaccaaccgggauugccuuaguaacggcgagugaagc
ggcaaaagcucaaauuugaaaucugguaccuucggugcccgaguuguaau
uuggagagggcaacuuuggggccguuccuugucuauguuccuuggaacag
gacgucauagagggugagaaucccguguggcgaggagugcgguucuuugu
aaagugccuucgaagagucgaguuguuugggaaugcagcucuaagugggu
gguaaauuccaucuaaagcuaaauauuggcgagagaccgauagcgaacaa
guacagugauggaaagaugaaaagaacuuugaaaagagagugaaaaagua
cgugaaauuguugaaagggaagggcauuugaucagacaggccagcaucag
uuuugguggcaggauaaauccauaggaauguagcuugccucgguaaguau
uauagccugugggaauacugccagcugggacugaggacugcgacguaagu
caaggaugcuggcauaaugguuauaugccgcccgucuugaaacacggacc
aaggagucuaacgucuaugcgaguguuuggguguaaaacccauacgcgua
augaaagugaacguagguuggggccucgcaagaggugcacaaucgaccga
uccugaugucuucggauggauuugaguaagagcauagcuguugggacccg
aaagauggugaacuaugccugaauagggugaagccagaggaaacucuggu
ggaggcucguagcgguucugacgugcaaaucgaucgucgaauuuggguau
aggggcgaaagacuaaucgaaccaucuaguagcugguuccugccgaaguu
ucccucaggauagcagaagcucguaucaguuuuaugagguaaagcgaaug
auuagagguuccggggucuugaccuauucucaaacuuuaaauauguaaga
aguccuuguuacuuaauugaacguggacauuugaaugaagagcuuuuagu
gggccauuuuugguaagcagaacuggcgaugcgggaugaaccgaacguag
aguuaaggugccggaauacacgcucaucagacaccacaaaagguguuagu
ucaucuagacaggaaugaacuagcccugaaaauggauggcgcucaagcgu
guuaccuauacucuaccgucaggguugauaugaugcccugacgaguaggc
aggcguggaggucagugacgaagccuagaccguaaggucgggucgaacgg
ccucuagugcagaucuuggugguaguagcaaauauucaaaugagaacuuu
gaagacugaaguggggaaagguuccacgucaacagcaguuggacgugggu
uagucgauccuaagagauggggaagcuccguuucaaaggccugauuuuau
gcaggccaccaucgaaagggaauccgguuaagauuccggaaccuggauau
ggauucuucacgguaacguaacugaauguggagacgucggcgcgagcccu
gggaggaguuaucuuuucuucuuaacagcuuaucaccccggaauugguuu
auccggagauggggucuuauggcuggaagaggccagcaccuuugcuggcu
ccggugcgcuugugacggcccgugaaaauccacaggaaggaauaguuuuc
augccaggucguacugauaaccgcagcaggucuccaaggugaacagccuc
uaguugauagaauaauguagauaagggaagucggcaaaauagauccguaa
cuucgggauaaggauuggcucuaagggucgcgaucaacuuagaacuggua
cggacaaggggaaucugacugucuaauuaaaacauagcauugcgaugguc
agaaagugauguugacgcaaugugauuucugcccagugcucugaauguca
aagugaagaaauucaaccaagcgcggguaaacggcggaagguagccaaau
gccucgucaucuaauuagugacgcgcaugaauggauuaacgagauuccca
cugucccuaucuacuaucuagcgaaaccacagccaagggaacgggcuugg
cagaaucagcggggaaagaagacccuguugagcuugacucuaguuugaca
uugugaaguacuuauucaaugaagcggagcuggaauucauuuuccacguu
cuagcauucaaggucccauucggggcugauccggguugaagacauuguca
gguggggaguuuggcuggggcggcacaucuguuaaacgauaacgcagaug
uccuaaggggggcucauggagaacagaaaucuccaguagaacaaaagggu
aaaagcccccuugauuuugauuuucagugugaauacaaaccaugaaagug
uggccuaucgauccuuuagucccucggaauuugaggcuagaggugccaga
aaaguuaccacagggauaacuggcuuguggcagucaagcguucauagcga
cauugcuuuuugauucuucgaugucggcucuuccuaucauaccgaagcag
aauucgguaagcguuggauuguucacccacuaauagggaacgugagcugg
guuuagaccgucgugagacagguuaguuuuacccuacugaugaauguuac
cgcaauaguaauugaacuuaguacgagaggaacaguucauucggauaauu
gguuuuugcggcugucugaucaggcauugccgcgaagcuaccauccgcug
gauuauggcugaacgccucuaagucagaauccaugcuagaacgcggugau
uucuuugcuccacacaauauagauggauacgaauaaggcguccuuguggc
gucgcugaaccauagcaggcuagcaacggugcacuuggcggaaaggccuu
gggugcuugcuggcgaauugcaaugucauuuugcguggggauaaaucauu
uguauacgacuuagauguacaacgggguauuguaagcaguagaguagccu
uguuguuacgaucugcugagauuaagccuuuguugucugauuugu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8p8u Real-space refinement in PHENIX for cryo-EM and crystallography.
• Resolution: 2.23 Å
• Binding residue (original residue number in PDB): G16 G18 S34 K35 S38 Q42 K44 R48 I49 A50 W51 R56 K61
• Binding residue (residue number reindexed from 1): G16 G18 S34 K35 S38 Q42 K44 R48 I49 A50 W51 R56 K61

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:8p8u, PDBe:8p8u, PDBj:8p8u
• PDBsum: 8p8u
• UniProt: P04449|RL24A_YEAST Large ribosomal subunit protein eL24A (Gene Name=RPL24A)