Structure of PDB 6n8m Chain H Binding Site BS01

Receptor Information

>6n8m Chain H (length=155) Species: 559292 (Saccharomyces cerevisiae S288C)

SAQKAPKWYPSEDVAALKKTRKAARPQKLRASLVPGTVLILLAGRFRGKR
VVYLKHLEDNTLLISGPFKVNGVPLRRVNARYVIATSTKVSVEGVNVEKF
NVEYFAKEIKAERVEDQKVVDKALIAEIKKTPLLKQYLSASFSLKNGDKP
HMLKF

Ligand information

>6n8m 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: 6n8m Tightly-orchestrated rearrangements govern catalytic center assembly of the ribosome.
• Resolution: 3.5 Å
• Binding residue (original residue number in PDB): S2 A3 K5 K8 W9 A17 L18 K19 K20 R22 K23 A24 R26 Q28 A44 G45 R46 R48 T62 F69 K70 G73 P75 R77 R78 N80 R82 Y83 K108 I130 Q157 A161 S162 K166 N167
• Binding residue (residue number reindexed from 1): S1 A2 K4 K7 W8 A16 L17 K18 K19 R21 K22 A23 R25 Q27 A43 G44 R45 R47 T61 F68 K69 G72 P74 R76 R77 N79 R81 Y82 K107 I109 Q136 A140 S141 K145 N146

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome

Biological Process

• GO:0000027 ribosomal large subunit assembly
• 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:6n8m, PDBe:6n8m, PDBj:6n8m
• PDBsum: 6n8m
• PubMed: 30814529
• UniProt: Q02326|RL6A_YEAST Large ribosomal subunit protein eL6A (Gene Name=RPL6A)