Structure of PDB 8p8n Chain RQ Binding Site BS01

Receptor Information

>8p8n Chain RQ (length=102) Species: 4932 (Saccharomyces cerevisiae)

VNVPKTRKTYCKGKTCRKHTQHKVTQYKAGKASLFAQGKRRYDRKQSGFG
GQTKPVFHKKAKTTKKVVLRLECVKCKTRAQLTLKRCKHFELGGEKKQKG
QA

Ligand information

>8p8n Chain A (length=3043)

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
cuucgggauaaggauuggcucuaagggucgaucaacuuagaacugguacg
gacaaggggaaucugacugucuaauuaaaacauagcauugcgauggucag
aaagugauguugacgcaaugugauuucugcccagugcucugaaugucaaa
gugaagaaauucaaccaagcgcggguaaacggcggaagguagccaaaugc
cucgucaucuaauuagugacgcgcaugaauggauuaacgagauucccacu
gucccuaucuacuaucuagcgaaaccacagccaagggaacgggcuuggca
gaaucagcggggaaagaagacccuguugagcuugacucuaguuugacauu
gugaaguacuuauucaaugaagcggagcuggaauucauuuuccacguucu
agcauucaaggucccauucggggcugauccggguugaagacauugucagg
uggggaguuuggcuggggcggcacaucuguuaaacgauaacgcagauguc
cuaaggggggcucauggagaacagaaaucuccaguagaacaaaaggguaa
aagcccccuugauuuugauuuucagugugaauacaaaccaugaaagugug
gccuaucgauccuuuagucccucggaauuugaggcuagaggugccagaaa
aguuaccacagggauaacuggcuuguggcagucaagcguucauagcgaca
uugcuuuuugauucuucgaugucggcucuuccuaucauaccgaagcagaa
uucgguaagcguuggauuguucacccacuaauagggaacgugagcugggu
uuagaccgucgugagacagguuaguuuuacccuacugaugaauguuaccg
caauaguaauugaacuuaguacgagaggaacaguucauucggauaauugg
uuuuugcggcugucugaucaggcauugccgcgaagcuaccauccgcugga
uuauggcugaacgccucuaagucagaauccaugcuagaacgcggugauuu
cuuugcuccacacaauauagauggauacgaauaaggcguccuuguggcgu
cgcugaaccauagcaggcuagcaacggugcacuuggcggaaaggccuugg
gugcuugcuggcgaauugcaaugucauuuugcguggggauaaaucauuug
uauacgacuuagauguacaacgggguauuguaagcaguagaguagccuug
uuguuacgaucugcugagauuaagccuuuguugucugauuugu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8p8n Real-space refinement in PHENIX for cryo-EM and crystallography.
• Resolution: 2.15 Å
• Binding residue (original residue number in PDB): V2 N3 P5 R8 T10 Y11 K13 K19 H20 Y28 A30 A33 S34 L35 F36 A37 Q38 G39 R41 R45 K46 G49 F50 G52 Q53 P56 V57 F58 K60 K61 A62 K63 T65 K66 K67 R80 Q82 T84 K86 C88 K89 K97 K98 K100
• Binding residue (residue number reindexed from 1): V1 N2 P4 R7 T9 Y10 K12 K18 H19 Y27 A29 A32 S33 L34 F35 A36 Q37 G38 R40 R44 K45 G48 F49 G51 Q52 P55 V56 F57 K59 K60 A61 K62 T64 K65 K66 R79 Q81 T83 K85 C87 K88 K96 K97 K99

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome
• GO:0008270 zinc ion binding

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0046677 response to antibiotic
• GO:0046898 response to cycloheximide

Cellular Component

• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0022625 cytosolic large ribosomal subunit
• GO:0044391 ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8p8n, PDBe:8p8n, PDBj:8p8n
• PDBsum: 8p8n
• UniProt: P0CX27|RL44A_YEAST Large ribosomal subunit protein eL42A (Gene Name=RPL42A)