Structure of PDB 8cdr Chain X Binding Site BS01

Receptor Information

>8cdr Chain X (length=50) Species: 4932 (Saccharomyces cerevisiae)

AAQKSFRIKQKMAKAKKQNRPLPQWIRLRTNNTIRYNAKRRNWRRTKMNI

Ligand information

>8cdr Chain AA (length=3197)

uugaccucaaaucagguaggaguacccgcugaacuuaagcauaucaauaa
gcggaggaaaagaaaccaaccgggauugccuuaguaacggcgagugaagc
ggcaaaagcucaaauuugaaaucugguaccuucggugcccgaguuguaau
uuggagagggcaacuuuggggccguuccuugucuauguuccuuggaacag
gacgucauagagggugagaaucccguguggcgaggagugcgguucuuugu
aaagugccuucgaagagucgaguuguuugggaaugcagcucuaagugggu
gguaaauuccaucuaaagcuaaauauuggcgagagaccgauagcgaacaa
guacagugauggaaagaugaaaagaacuuugaaaagagagugaaaaagua
cgugaaauuguugaaagggaagggcauuugaucagaggccagcaucaguu
uugguggcaggauaaauccauaggaauguagcuugccucgguaaguauua
uagccugugggaauacugccagcugggacugaggacugcgacguaaguca
aggaugcuggcauaaugguuauaugccgcccgucuugaaacacggaccaa
ggagucuaacgucuaugcgaguguuuggguguaaaacccauacgcguaau
gaaagugaacguagguuggggccucgcaagaggugcacaaucgaccgauc
cugaugucuucggauggauuugaguaagagcauagcuguugggacccgaa
agauggugaacuaugccugaauagggugaagccagaggaaacucuggugg
aggcucguagcgguucugacgugcaaaucgaucgucgaauuuggguauag
gggcgaaagacuaaucgaaccaucuaguagcugguuccugccgaaguuuc
ccucaggauagcagaagcucguaucaguuuuaugagguaaagcgaaugau
uagagguuccggggucgaaaugaccuugaccuauucucaaacuuuaaaua
uguaagaaguccuuguuacuuaauugaacguggacauuugaaugaagagc
uuuuagugggccauuuuugguaagcagaacuggcgaugcgggaugaaccg
aacguagaguuaaggugccggaauacacgcucaucagacaccacaaaagg
uguuaguucaucuagacagccggacgguggccauggaagucggaauccgc
uaaggaguguguaacaacucaccggccgaaugaacuagcccugaaaaugg
auggcgcucaagcguguuaccuauacucuaccgucaggguugauaugaug
cccugacgaguaggcaggcguggaggucagugacgaagccuagaccguaa
ggucgggucgaacggccucuagugcagaucuuggugguaguagcaaauau
ucaaaugagaacuuugaagacugaaguggggaaagguuccacgucaacag
caguuggacguggguuagucgauccuaagagauggggaagcuccguuuca
aaggccugauuuuaugcaggccaccaucgaaagggaauccgguuaagauu
ccggaaccuggauauggauucuucacgguaacguaacugaauguggagac
gucggcgcgagcccugggaggaguuaucuuuucuucuuaacagcuuauca
ccccggaauugguuuauccggagauggggucuuauggcuggaagaggcca
gcaccuuugcuggcuccggugcgcuugugacggcccgugaaaauccacag
gaaggaauaguuuucaugccaggucguacugauaaccgcagcaggucucc
aaggugaacagccucuaguugauagaauaauguagauaagggaagucggc
aaaauagauccguaacuucgggauaaggauuggcucuaagggucgacgau
caacuuagaacugguacggacaaggggaaucugacugucuaauuaaaaca
uagcauugcgauggucagaaagugauguugacgcaaugugauuucugccc
agugcucugaaugucaaagugaagaaauucaaccaagcgcggguaaacgg
cgggaguaacuaugacucucuuaagguagccaaaugccucgucaucuaau
uagugacgcgcaugaauggauuaacgagauucccacugucccuaucuacu
aucuagcgaaaccacagccaagggaacgggcuuggcagaaucagcgggga
aagaagacccuguugagcuugacucuaguuugacauugugaagagacaua
gaggguguagaauaagugggagcuucggcgccagugaaauaccacuaccu
uuauaguuucuuuacuuauucaaugaagcggagcuggaauucauuuucca
cguucuagcauucaaggucccauucggggcugauccggguugaagacauu
gucagguggggaguuuggcuggggcggcacaucuguuaaacgauaacgca
gauguccuaaggggggcucauggagaacagaaaucuccaguagaacaaaa
ggguaaaagcccccuugauuuugauuuucagugugaauacaaaccaugaa
aguguggccuaucgauccuuuagucccucggaauuugaggcuagaggugc
cagaaaaguuaccacagggauaacuggcuuguggcagucaagcguucaua
gcgacauugcuuuuugauucuucgaugucggcucuuccuaucauaccgaa
gcagaauucgguaagcguuggauuguucacccacuaauagggaacgugag
cuggguuuagaccgucgugagacagguuaguuuuacccuacugaugaaug
uuaccgcaauaguaauugaacuuaguacgagaggaacaguucauucggau
aauugguuuuugcggcugucugaucaggcauugccgcgaagcuaccaucc
gcuggauuauggcugaacgccucuaagucagaauccaugcuagaacgcgg
ugauuucuuugcuccacacaauauagauggauacgaauaaggcguccuug
uggcgucgcugaaccauagcaggcuagcaacggugcacuuggcggaaagg
ccuugggugcuugcuggcgaauugcaaugucauuuugcguggggauaaau
cauuuguauacgacuuagauguacaacgggguauuguaagcaguagagua
gccuugguuacgaucugcugagauuaagccuuuguugucugauuugu

........................<<<<<<.....<......>......>
>>>>.>.........<<....>>..<<<<<......<<.....>>.....
>>>>>..<<<...<.......<<.<<<<<<...>>>>>>.>>.......>
.....<<<<<<.<<<<<..<<<<<<<<<<<<<<<....<<<<......>>
>>.(.......<<<......)>>>..>.>>>>>>>>>..>>>>>......
>>>>>>>>>>>........<<<<<<<........>>>>>>>.....<<<<
<..((((((>>>>>..>>>...............................
...<<....>>...............<<<<....>>>>............
......................<<<<<.<<<<<....<<<<<<<.<<<<<
<<<<<<<<<<.....<<<<<<<<<......<<<<<<<..>>>>>>>....
...>>>>>>>.>.>.>>>>>.>>>>>>>>>>........<<<....>>>.
....>>>>>>>.....>>>>>.>>>>>..<<<<........>>>><<<<<
<...<<<<<<<.<<<<<<..<<<...<<<<.....>>>>...>>>...<<
....>>.......<<<<<..<<<<<....>>>>>...>>>>>.<<<<<<<
<...<<....>>...>>>.>>>.>>....>>>>>>.>>>>>>>.<<.<..
<<<<<<<.....<<<<<<<<<..<<<....<<<<<<<....>>>>>>>..
...>>>...<<<..<<.<<........>>>>.>>>....>>>>>>>>>..
.<<.......>>......>>>>>>...>..>.>>..<<<<<<....<.<<
<....>>>.><<<<<<<<<<...<<<.<<<<<<<.....<<<....<<<.
.<.<<<<....<<<<<.....>>>>>..>>>>.>..>>>..>.>>.....
>>>>>...<<<<.<<<<.<......>>>>>.>>>>.....>>>>>.>>>>
>>>>.>>..<<<<.<<<<<.....>>>>>.>>>>....<<<......>>>
...<<<<<<<..<<<<(((.....<<<<<<......<..........<<<
.<<<<<<<<<<.......<<<<<.<<<...<<.........>>...>>>.
........<<......>>...>>>>>...>>>>>>>>>>>>>........
..))).>....>>>>>>.>>>>..>>>>>>><<<<<<<<<.........>
>>>>>>>>....>>>>>>..<<<<<<<<.<<......<<<<.<<<<....
>>>>>>>>...>>>>>>>>>>........>>>>>><<.....<<.....<
<<<<<.......>>>>>><<<<.....<<<<<.<<...<<<<<<...<<.
....>>.>>>>>>....((<<<<<<...<<....<<<....>>>......
...<..<...........>..>....>>....>>...<<<<<........
>>>>>))<<<<.<<<<<<<.....<<<....>>>...<...<<<<<<...
<<<<.<<<<<<<.<<<<<<<<<<..[[[..>>>>>><...<<<<<....<
<<<<<....<<<.....>>>....>>>>>>.....>>>>>....><<<<<
<<<....>>>>>>>>>>>>...>>>>>>>.>>>>.........>>>>>>.
..>......>>>..>>>>>>>>>>>>..>>.....<<......>>>>>>>
.<<<<.....>>>>..>>>>..<<<<.....<<<<<<<.<<.........
......<<<<<....<....>.....>>>>><<.<<<<<<<<<<<.>>>>
>..>>>>>>.>>............<<<<<<<<<..<<<.........>>>
..<<<<<<<....<<<<.....>>>>......>>>>>>>...<<..<<<.
.<<<<<<....<<<.....<<<<....>>>>.....>>>.>>>>..>>>>
><<<<<<.......>>>>>>........<...........<<<<<.....
..>>>>>.....>.....>>....>>.>>>>>>>.....>>.>>>>>>>.
.>>>>>>....>>....<<<<<........>>>>>....<<<<<..<<<.
<<......<<<<.<<<<<<..<<<<<.<<<<<<<<..<<<<<<<<<<<<.
<<<<<..........................................>>>
>>>>.>>>>>>>>>>...<<<<<.....<<<<..<<<<<......>>>>>
...............<<<<<<....>>>>>>..>>>>..>>>>>.....>
>>>>>>>..>>>>>...<<<.....>>>..<<<<<<...........>>>
>>>..<<...<<<<<<<...<<<<<<.......>>>>>>.....<<...(
((>>....>>>>>>>...<<<.<<<<<.......>>>>.>>>>.<<<...
.>>>.>>)))......<<<<<<<..<<<<.))))))>>>>>>>>>>>...
......>>>>..>>>>>>.......<<.<...<<<<<<...<<.......
>>...>>>>>>....>.>.>.......<<<<<.<<<<<<..<.<<<<<<<
......>>>>>>>...>.<<<.........>>>.....>>>>>..>...>
>>.>>....<<<<<<<....>>>.>>>>....>>..>>>.>>>>>....<
<<<<<<<..<<<<.<.<<<<<<...............>>>>>>.><<<<<
...<<<<....<<<<<<<<<<]]].>>>>>..>>>>>...>>>>..>>>>
>.<<<<...<<<<<...........>>>>>...>>>>.>>>>....>>>>
>>>>.......<<<<<<.<<<.<<....<<..........<<<<<<....
.>>>>>>......>>.......<<<<<<...<<<<<.<..<<<......>
>>..>.>>>>>.>>>>>>.............>>.>>>.>>>>>>..<<<<
<.<.............>.....<<<<<<<<<.<<<....<<<<.<..<<<
<<....>>>>>..>>>>>...>>>....>>>>.>>>>>..>>>>>..

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8cdr mRNA reading frame maintenance during eukaryotic ribosome translocation
• Resolution: 2.04 Å
• Binding residue (original residue number in PDB): A2 A3 Q4 K5 F7 K10 M13 K17 P22 I35 Y37 N38 A39 R41 R42 W44 R45 T47 K48 M49
• Binding residue (residue number reindexed from 1): A1 A2 Q3 K4 F6 K9 M12 K16 P21 I34 Y36 N37 A38 R40 R41 W43 R44 T46 K47 M48

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome
• GO:0005515 protein binding

Biological Process

• 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:8cdr, PDBe:8cdr, PDBj:8cdr
• PDBsum: 8cdr
• PubMed: 38030725
• UniProt: P04650|RL39_YEAST Large ribosomal subunit protein eL39 (Gene Name=RPL39)