Structure of PDB 6hd7 Chain M Binding Site BS01

Receptor Information

>6hd7 Chain M (length=169) Species: 4932 (Saccharomyces cerevisiae)

QNPMRDLKIEKLVLNISVGESGDRLTRASKVLEQLSGQTPVQSKARYTVR
TFGIRRNEKIAVHVTVRGPKAEEILERGLKVKEYQLRDRNFSATGNFGFG
IDEHIDLGIKYDPSIGIFGMDFYVVMNRPGARVTRRKRCKGTVGNSHKTT
KEDTVSWFKQKYDADVLDK

Ligand information

>6hd7 Chain 1 (length=3335)

uugaccucaaaucagguaggaguacccgcugaacuuaagcauaucaauaa
gcggaggaaaagaaaccaaccgggauugccuuaguaacggcgagugaagc
ggcaaaagcucaaauuugaaaucugguaccuucggugcccgaguuguaau
uuggagagggcaacuuuggggccguuccuugucuauguuccuuggaacag
gacgucauagagggugagaaucccguguggcgaggagugcgguucuuugu
aaagugccuucgaagagucgaguuguuugggaaugcagcucuaagugggu
gguaaauuccaucuaaagcuaaauauuggcgagagaccgauagcgaacaa
guacagugauggaaagaugaaaagaacuuugaaaagagagugaaaaagua
cgugaaauuguugaaagggaagggcauuugaucagacaugguguuuugug
cccucugcuccuuguggguaggggaaucucgcauuucacugggccagcau
caguuuugguggcaggauaaauccauaggaauguagcuugccucgguaag
uauuauagccugugggaauacugccagcugggacugaggacugcgacgua
agucaaggaugcuggcauaaugguuauaugccgcccgucuugaaacacgg
accaaggagucuaacgucuaugcgaguguuuggguguaaaacccauacgc
guaaugaaagugaacguagguuggggccucgcaagaggugcacaaucgac
cgauccugaugucuucggauggauuugaguaagagcauagcuguugggac
ccgaaagauggugaacuaugccugaauagggugaagccagaggaaacucu
gguggaggcucguagcgguucugacgugcaaaucgaucgucgaauuuggg
uauaggggcgaaagacuaaucgaaccaucuaguagcugguuccugccgaa
guuucccucaggauagcagaagcucguaucaguuuuaugagguaaagcga
augauuagagguuccggggucgaaaugaccuugaccuauucucaaacuuu
aaauauguaagaaguccuuguuacuuaauugaacguggacauuugaauga
agagcuuuuagugggccauuuuugguaagcagaacuggcgaugcgggaug
aaccgaacguagaguuaaggugccggaauacacgcucaucagacaccaca
aaagguguuaguucaucuagacagccggacgguggccauggaagucggaa
uccgcuaaggaguguguaacaacucaccggccgaaugaacuagcccugaa
aauggauggcgcucaagcguguuaccuauacucuaccgucaggguugaua
ugaugcccugacgaguaggcaggcguggaggucagugacgaagccuagac
cguaaggucgggucgaacggccucuagugcagaucuuggugguaguagca
aauauucaaaugagaacuuugaagacugaaguggggaaagguuccacguc
aacagcaguuggacguggguuagucgauccuaagagauggggaagcuccg
uuucaaaggccugauuuuaugcaggccaccaucgaaagggaauccgguua
agauuccggaaccuggauauggauucuucacgguaacguaacugaaugug
gagacgucggcgcgagcccugggaggaguuaucuuuucuucuuaacagcu
uaucaccccggaauugguuuauccggagauggggucuuauggcuggaaga
ggccagcaccuuugcuggcuccggugcgcuugugacggcccgugaaaauc
cacaggaaggaauaguuuucaugccaggucguacugauaaccgcagcagg
ucuccaaggugaacagccucuaguugauagaauaauguagauaagggaag
ucggcaaaauagauccguaacuucgggauaaggauuggcucuaagggucg
gguagugagggccuuggucagacgcagcgggcgugcuuguggacugcuug
guggggcuugcucugcuaggcggacuacuugcgugccuuguuguagacgg
ccuuggucuugcuacaauuaacgaucaacuuagaacugguacggacaagg
ggaaucugacugucuaauuaaaacauagcauugcgauggucagaaaguga
uguugacgcaaugugauuucugcccagugcucugaaugucaaagugaaga
aauucaaccaagcgcggguaaacggcgggaguaacuaugacucucuuaag
guagccaaaugccucgucaucuaauuagugacgcgcaugaauggauuaac
gagauucccacugucccuaucuacuaucuagcgaaaccacagccaaggga
acgggcuuggcagaaucagcggggaaagaagacccuguugagcuugacuc
uaguuugacauugugaagagacauagagggcuaccuuuauaguuucuuua
cuuauucaaugaagcggagcuggaauucauuuuccacguucuagcauuca
aggucccauucggggcugauccggguugaagacauugucagguggggagu
uuggcuggggcggcacaucuguuaaacgauaacgcagauguccuaagggg
ggcucauggagaacagaaaucuccaguagaacaaaaggguaaaagccccc
uugauuuugauuuucagugugaauacaaaccaugaaaguguggccuaucg
auccuuuagucccucggaauuugaggcuagaggugccagaaaaguuacca
cagggauaacuggcuuguggcagucaagcguucauagcgacauugcuuuu
ugauucuucgaugucggcucuuccuaucauaccgaagcagaauucgguaa
gcguuggauuguucacccacuaauagggaacgugagcuggguuuagaccg
ucgugagacagguuaguuuuacccuacugaugaauguuaccgcaauagua
auugaacuuaguacgagaggaacaguucauucggauaauugguuuuugcg
gcugucugaucaggcauugccgcgaagcuaccauccgcuggauuauggcu
gaacgccucuaagucagaauccaugcuagaacgcggugauuucuuugcuc
cacacaauauagauggauacgaauaaggcguccuuguggcgucgcugaac
cauagcaggcuagcaacggugcacuuggcggaaaggccuugggugcuugc
uggcgaauugcaaugucauuuugcguggggauaaaucauuuguauacgac
uuagauguacaacgggguauuguaagcaguagaguagccuuguuguuacg
aucugcugagauuaagccuuuguugucugauuugu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6hd7 Ribosome-NatA architecture reveals that rRNA expansion segments coordinate N-terminal acetylation.
• Resolution: 3.4 Å
• Binding residue (original residue number in PDB): N20 S22 A50 R51 Y52 V54 T56 F57 I65 A66 R94 N95 F96 S97 T99 G103 F104 G105 I106 D107 G124 M125 D126 Y128 K142
• Binding residue (residue number reindexed from 1): N15 S17 A45 R46 Y47 V49 T51 F52 I60 A61 R89 N90 F91 S92 T94 G98 F99 G100 I101 D102 G119 M120 D121 Y123 K137

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0019843 rRNA binding

Biological Process

• GO:0000027 ribosomal large subunit assembly
• GO:0002181 cytoplasmic translation
• GO:0006412 translation

Cellular Component

• GO:0005634 nucleus
• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0022625 cytosolic large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:6hd7, PDBe:6hd7, PDBj:6hd7
• PDBsum: 6hd7
• PubMed: 30559462
• UniProt: P0C0W9|RL11A_YEAST Large ribosomal subunit protein uL5A (Gene Name=RPL11A)