Structure of PDB 8ccs Chain M Binding Site BS01

Receptor Information
>8ccs Chain M (length=148) Species: 4932 (Saccharomyces cerevisiae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PSRFTKTRKHRGHVSAGKGRIGKHRKHPGGRGMAGGQHHHRINMDKYHPG
YFGKVGMRYFHKQQAHFWKPVLNLDKLWTLIPEDKRDQYLKSASKETAPV
IDTLAAGYGKILGKGRIPNVPVIVKARFVSKLAEEKIRAAGGVVELIA
Ligand information
>8ccs Chain AA (length=3190) [Search RNA sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
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
Global viewLocal viewStructure summary

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PDB8ccs Cryo-EM analysis of eukaryotic ribosome translocation intermediates
Resolution1.97 Å
Binding residue
(original residue number in PDB)
P2 S3 R4 T6 K7 T8 R9 K10 H11 R12 G13 H14 V15 A17 G18 K19 G20 R21 I22 G23 H25 R26 K27 H28 P29 G30 G31 R32 G33 M34 A35 G36 H39 H40 H41 R42 I43 N44 K47 Y52 F53 G54 K55 V56 G57 M58 R59 Y60 F61 H62 K63 Q64 H67 V72 N74 K77 K111 L113 G114 K115 R117 S131 K132 L133
Binding residue
(residue number reindexed from 1)
P1 S2 R3 T5 K6 T7 R8 K9 H10 R11 G12 H13 V14 A16 G17 K18 G19 R20 I21 G22 H24 R25 K26 H27 P28 G29 G30 R31 G32 M33 A34 G35 H38 H39 H40 R41 I42 N43 K46 Y51 F52 G53 K54 V55 G56 M57 R58 Y59 F60 H61 K62 Q63 H66 V71 N73 K76 K110 L112 G113 K114 R116 S130 K131 L132
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0003723 RNA binding
GO:0003735 structural constituent of ribosome
Biological Process
GO:0002181 cytoplasmic translation
GO:0006412 translation
Cellular Component
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0005840 ribosome
GO:0015934 large ribosomal subunit
GO:0022625 cytosolic large ribosomal subunit
GO:0043232 intracellular non-membrane-bounded organelle
GO:1990904 ribonucleoprotein complex

View graph for
Molecular Function

View graph for
Biological Process

View graph for
Cellular Component
External links
PDB RCSB:8ccs, PDBe:8ccs, PDBj:8ccs
PDBsum8ccs
PubMed38030725
UniProtP02406|RL28_YEAST Large ribosomal subunit protein uL15 (Gene Name=RPL28)

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