Structure of PDB 8ccs Chain F Binding Site BS01

Receptor Information

>8ccs Chain F (length=159) Species: 4932 (Saccharomyces cerevisiae)

GKSHGYRSRTRYMFQRDFRKHGAVHLSTYLKVYKVGDIVDIKANGSIQKG
MPHKFYQGKTGVVYNVTKSSVGVIINKMVGNRYLEKRLNLRVEHIKHSKC
RQEFLERVKANAAKRAEAKAQGVAVQLKRQPAQPRESRIVSTEGNVPQTL
APVPYETFI

Ligand information

>8ccs Chain AA (length=3190)

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
aaaauagauccguaacuucgggauaaggauuggcucuaagggucgcgauc
aacuuagaacugguacggacaaggggaaucugacugucuaauuaaaacau
agcauugcgauggucagaaagugauguugacgcaaugugauuucugccca
gugcucugaaugucaaagugaagaaauucaaccaagcgcggguaaacggc
gggaguaacuaugacucucuuaagguagccaaaugccucgucaucuaauu
agugacgcgcaugaauggauuaacgagauucccacugucccuaucuacua
ucuagcgaaaccacagccaagggaacgggcuuggcagaaucagcggggaa
agaagacccuguugagcuugacucuaguuugacauugugaagagacauag
aggguguagaauaagugggagcuucggcgccagugaaauaccacuaccuu
uauaguuucuuuacuuauucaaugaagcggagcuggaauuccacguucua
gcauucaaggucccauucggggcugauccggguugaagacauugucaggu
ggggaguuuggcuggggcggcacaucuguuaaacgauaacgcagaugucc
uaaggggggcucauggagaacagaaaucuccaguagaacaaaaggguaaa
agcccccuugauuuugauuuucagugugaauacaaaccaugaaagugugg
ccuaucgauccuuuagucccucggaauuugaggcuagaggugccagaaaa
guuaccacagggauaacuggcuuguggcagucaagcguucauagcgacau
ugcuuuuugauucuucgaugucggcucuuccuaucauaccgaagcagaau
ucgguaagcguuggauuguucacccacuaauagggaacgugagcuggguu
uagaccgucgugagacagguuaguuuuacccuacugaugaauguuaccgc
aauaguaauugaacuuaguacgagaggaacaguucauucggauaauuggu
uuuugcggcugucugaucaggcauugccgcgaagcuaccauccgcuggau
uauggcugaacgccucuaagucagaauccaugcuagaacgcggugauuuc
uuugcuccacacaauauagauggauacgaauaaggcguccuuguggcguc
gcugaaccauagcaggcuagcaacggugcacuuggcggaaaggccuuggg
ugcuugcuggcgaauugcaaugucauuuugcguggggauaaaucauuugu
auacgacuuagauguacaacgggguauuguaagcaguagaguagccuugg
uuacgaucugcugagauuaagccuuuguugucugauuugu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8ccs Cryo-EM analysis of eukaryotic ribosome translocation intermediates
• Resolution: 1.97 Å
• Binding residue (original residue number in PDB): G2 K3 S4 H5 G6 Y7 R8 S9 R10 R12 Y13 M14 Q16 R17 F19 H22 G23 K35 D41 K43 G46 S47 Q49 K50 G51 H54 K55 Y57 G59 K60 T61 T68 K69 S70 S71 K78 V80 N82 R83 L85 K87 R88 L89 N90 R92 K100 C101 F105 R108 V109 R116 Q127 L128 K129 R130
• Binding residue (residue number reindexed from 1): G1 K2 S3 H4 G5 Y6 R7 S8 R9 R11 Y12 M13 Q15 R16 F18 H21 G22 K34 D40 K42 G45 S46 Q48 K49 G50 H53 K54 Y56 G58 K59 T60 T67 K68 S69 S70 K77 V79 N81 R82 L84 K86 R87 L88 N89 R91 K99 C100 F104 R107 V108 R115 Q126 L127 K128 R129

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome

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:8ccs, PDBe:8ccs, PDBj:8ccs
• PDBsum: 8ccs
• PubMed: 38030725
• UniProt: Q02753|RL21A_YEAST Large ribosomal subunit protein eL21A (Gene Name=RPL21A)