Structure of PDB 6n8o Chain v Binding Site BS01

Receptor Information

>6n8o Chain v (length=98) Species: 559292 (Saccharomyces cerevisiae S288C)

VKTGIAIGLNKGKKVTSMTPAPKISYKKGAASNRTKFVRSLVREIAGLSP
YERRLIDLIRNSGEKRARKVAKKRLGSFTRAKAKVEEMNNIIAASRRH

Ligand information

>6n8o Chain A (length=3201)

uugaccucaaaucagguaggaguacccgcugaacuuaagcauaucaauaa
gcggaggaaaagaaaccaaccgggauugccuuaguaacggcgagugaagc
ggcaaaagcucaaauuugaaaucugguaccuucggugcccgaguuguaau
uuggagagggcaacuuuggggccguuccuugucuauguuccuuggaacag
gacgucauagagggugagaaucccguguggcgaggagugcgguucuuugu
aaagugccuucgaagagucgaguuguuugggaaugcagcucuaagugggu
gguaaauuccaucuaaagcuaaauauuggcgagagaccgauagcgaacaa
guacagugauggaaagaugaaaagaacuuugaaaagagagugaaaaagua
cgugaaauuguugaaagggaagggcauuugaucagacggccagcaucagu
uuugguggcaggauaaauccauaggaauguagcuugccucgguaaguauu
auagccugugggaauacugccagcugggacugaggacugcgacguaaguc
aaggaugcuggcauaaugguuauaugccgcccgucuugaaacacggacca
aggagucuaacgucuaugcgaguguuuggguguaaaacccauacgcguaa
ugaaagugaacguagguuggggccucgcaagaggugcacaaucgaccgau
ccugaugucuucggauggauuugaguaagagcauagcuguugggacccga
aagauggugaacuaugccugaauagggugaagccagaggaaacucuggug
gaggcucguagcgguucugacgugcaaaucgaucgucgaauuuggguaua
ggggcgaaagacuaaucgaaccaucuaguagcugguuccugccgaaguuu
cccucaggauagcagaagcucguaucaguuuuaugagguaaagcgaauga
uuagagguuccggggucgaaaugaccuugaccuauucucaaacuuuaaau
auguaagaaguccuuguuacuuaauugaacguggacauuugaaugaagag
cuuuuagugggccauuuuugguaagcagaacuggcgaugcgggaugaacc
gaacguagaguuaaggugccggaauacacgcucaucagacaccacaaaag
guguuaguucaucuagacagccggacgguggccauggaagucggaauccg
cuaaggaguguguaacaacucaccggccgaaugaacuagcccugaaaaug
gauggcgcucaagcguguuaccuauacucuaccgucaggguugauaugau
gcccugacgaguaggcaggcguggaggucagugacgaagccuagaccgua
aggucgggucgaacggccucuagugcagaucuuggugguaguagcaaaua
uucaaaugagaacuuugaagacugaaguggggaaagguuccacgucaaca
gcaguuggacguggguuagucgauccuaagagauggggaagcuccguuuc
aaaggccugauuuuaugcaggccaccaucgaaagggaauccgguuaagau
uccggaaccuggauauggauucuucacgguaacguaacugaauguggaga
cgucggcgcgagcccugggaggaguuaucuuuucuucuuaacagcuuauc
accccggaauugguuuauccggagauggggucuuauggcuggaagaggcc
agcaccuuugcuggcuccggugcgcuugugacggcccgugaaaauccaca
ggaaggaauaguuuucaugccaggucguacugauaaccgcagcaggucuc
caaggugaacagccucuaguugauagaauaauguagauaagggaagucgg
caaaauagauccguaacuucgggauaaggauuggcucuaagggucggacg
aucaacuuagaacugguacggacaaggggaaucugacugucuaauuaaaa
cauagcauugcgauggucagaaagugauguugacgcaaugugauuucugc
ccagugcucugaaugucaaagugaagaaauucaaccaagcgcggguaaac
ggcgggaguaacuaugacucucuuaagguagccaaaugccucgucaucua
auuagugacgcgcaugaauggauuaacgagauucccacugucccuaucua
cuaucuagcgaaaccacagccaagggaacgggcuuggcagaaucagcggg
gaaagaagacccuguugagcuugacucuaguuugacauugugaagagaca
uagaggguguagaauaagugggagcuucggcgccagugaaauaccacuac
cuuuauaguuucuuuacuuauucaaugaagcggagcuggaauucauuuuc
cacguucuagcauucaaggucccauucggggcugauccggguugaagaca
uugucagguggggaguuuggcuggggcggcacaucuguuaaacgauaacg
cagauguccuaaggggggcucauggagaacagaaaucuccaguagaacaa
aaggguaaaagcccccuugauuuugauuuucagugugaauacaaaccaug
aaaguguggccuaucgauccuuuagucccucggaauuugaggcuagaggu
gccagaaaaguuaccacagggauaacuggcuuguggcagucaagcguuca
uagcgacauugcuuuuugauucuucgaugucggcucuuccuaucauaccg
aagcagaauucgguaagcguuggauuguucacccacuaauagggaacgug
agcuggguuuagaccgucgugagacagguuaguuuuacccuacugaugaa
uguuaccgcaauaguaauugaacuuaguacgagaggaacaguucauucgg
auaauugguuuuugcggcugucugaucaggcauugccgcgaagcuaccau
ccgcuggauuauggcugaacgccucuaagucagaauccaugcuagaacgc
ggugauuucuuugcuccacacaauauagauggauacgaauaaggcguccu
uguggcgucgcugaaccauagcaggcuagcaacggugcacuuggcggaaa
ggccuugggugcuugcuggcgaauugcaaugucauuuugcguggggauaa
aucauuuguauacgacuuagauguacaacgggguauuguaagcaguagag
uagccuuguuguuacgaucugcugagauuaagccuuuguugucugauuug
u

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6n8o Tightly-orchestrated rearrangements govern catalytic center assembly of the ribosome.
• Resolution: 3.5 Å
• Binding residue (original residue number in PDB): K13 V17 K25 I26 S27 Y28 K29 K30 G31 A33 S34 N35 R36 R41 Y53 R68 R76 G78 R82 K84
• Binding residue (residue number reindexed from 1): K11 V15 K23 I24 S25 Y26 K27 K28 G29 A31 S32 N33 R34 R39 Y51 R66 R74 G76 R80 K82

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

External links

• PDB: RCSB:6n8o, PDBe:6n8o, PDBj:6n8o
• PDBsum: 6n8o
• PubMed: 30814529
• UniProt: P05745|RL36A_YEAST Large ribosomal subunit protein eL36A (Gene Name=RPL36A)