Structure of PDB 8cg8 Chain Y Binding Site BS01

Receptor Information

>8cg8 Chain Y (length=52) Species: 4932 (Saccharomyces cerevisiae)

IIEPSLKALASKYNCDKSVCRKCYARLPPRATNCRKRKCGHTNQLRPKKK
LK

Ligand information

>8cg8 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: 8cg8 Cryo-EM analysis of eukaryotic ribosome translocation intermediates
• Resolution: 2.57 Å
• Binding residue (original residue number in PDB): R97 Y100 R102 P104 R106 N109 R111 K112 R113 K114 G116 H117 N119 R122 K124 K125 K128
• Binding residue (residue number reindexed from 1): R21 Y24 R26 P28 R30 N33 R35 K36 R37 K38 G40 H41 N43 R46 K48 K49 K52

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome
• GO:0008270 zinc ion binding
• GO:0031386 protein tag activity
• GO:0031625 ubiquitin protein ligase binding

Biological Process

• GO:0000027 ribosomal large subunit assembly
• GO:0000055 ribosomal large subunit export from nucleus
• GO:0002181 cytoplasmic translation
• GO:0006412 translation
• GO:0016567 protein ubiquitination
• GO:0019941 modification-dependent protein catabolic process
• GO:0042254 ribosome biogenesis

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:8cg8, PDBe:8cg8, PDBj:8cg8
• PDBsum: 8cg8
• PubMed: 38030725
• UniProt: P0CH08|RL40A_YEAST Ubiquitin-ribosomal protein eL40A fusion protein (Gene Name=RPL40A)