Structure of PDB 6n8n Chain q Binding Site BS01

Receptor Information

>6n8n Chain q (length=107) Species: 559292 (Saccharomyces cerevisiae S288C)

LKDVVTREYTINLHKRLHGVSFKKRAPRAVKEIKKFAKLHMGTDDVRLAP
ELNQAIWKRGVKGVEYRLRLRISRKRNEEEDAKNPLFSYVEPVLVASAKG
LQTVVVE

Ligand information

>6n8n Chain A (length=3203)

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
caaaauagauccguaacuucgggauaaggauuggcucuaagggucgggua
cgaucaacuuagaacugguacggacaaggggaaucugacugucuaauuaa
aacauagcauugcgauggucagaaagugauguugacgcaaugugauuucu
gcccagugcucugaaugucaaagugaagaaauucaaccaagcgcggguaa
acggcgggaguaacuaugacucucuuaagguagccaaaugccucgucauc
uaauuagugacgcgcaugaauggauuaacgagauucccacugucccuauc
uacuaucuagcgaaaccacagccaagggaacgggcuuggcagaaucagcg
gggaaagaagacccuguugagcuugacucuaguuugacauugugaagaga
cauagaggguguagaauaagugggagcuucggcgccagugaaauaccacu
accuuuauaguuucuuuacuuauucaaugaagcggagcuggaauucauuu
uccacguucuagcauucaaggucccauucggggcugauccggguugaaga
cauugucagguggggaguuuggcuggggcggcacaucuguuaaacgauaa
cgcagauguccuaaggggggcucauggagaacagaaaucuccaguagaac
aaaaggguaaaagcccccuugauuuugauuuucagugugaauacaaacca
ugaaaguguggccuaucgauccuuuagucccucggaauuugaggcuagag
gugccagaaaaguuaccacagggauaacuggcuuguggcagucaagcguu
cauagcgacauugcuuuuugauucuucgaugucggcucuuccuaucauac
cgaagcagaauucgguaagcguuggauuguucacccacuaauagggaacg
ugagcuggguuuagaccgucgugagacagguuaguuuuacccuacugaug
aauguuaccgcaauaguaauugaacuuaguacgagaggaacaguucauuc
ggauaauugguuuuugcggcugucugaucaggcauugccgcgaagcuacc
auccgcuggauuauggcugaacgccucuaagucagaauccaugcuagaac
gcggugauuucuuugcuccacacaauauagauggauacgaauaaggcguc
cuuguggcgucgcugaaccauagcaggcuagcaacggugcacuuggcgga
aaggccuugggugcuugcuggcgaauugcaaugucauuuugcguggggau
aaaucauuuguauacgacuuagauguacaacgggguauuguaagcaguag
aguagccuuguuguuacgaucugcugagauuaagccuuuguugucugauu
ugu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6n8n Tightly-orchestrated rearrangements govern catalytic center assembly of the ribosome.
• Resolution: 3.8 Å
• Binding residue (original residue number in PDB): R10 T13 N15 H17 K18 R19 H21 G22 S24 F25 K26 V33 K34 H43 L51 N56 Q57 W60 R62 V64 K65 Y69 R70 K102 Q105 T106
• Binding residue (residue number reindexed from 1): R7 T10 N12 H14 K15 R16 H18 G19 S21 F22 K23 V30 K31 H40 L48 N53 Q54 W57 R59 V61 K62 Y66 R67 K99 Q102 T103

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006412 translation
• GO:0006450 regulation of translational fidelity

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:6n8n, PDBe:6n8n, PDBj:6n8n
• PDBsum: 6n8n
• PubMed: 30814529
• UniProt: P0C2H8|RL31A_YEAST Large ribosomal subunit protein eL31A (Gene Name=RPL31A)