Structure of PDB 6ft6 Chain v Binding Site BS01

Receptor Information

>6ft6 Chain v (length=287) Species: 559292 (Saccharomyces cerevisiae S288C)

NARAKRALVKREAKLVENVKQALFIPGQSCNKNLHDIMVDLSALKKPDMK
RFNRKNDIHPFEDMSPLEFFSEKNDCSLMVLMTSSKKRKNNMTFIRTFGY
KIYDMIELMVADNFKLLSDFKKLTFTVGLKPMFTFQGAAFDTHPVYKQIK
SLFLDFFRGESTDLQDVAGLQHVISMTIQGDFQDGEPLPNVLFRVYKLKS
YKSDQGGKRLPRIELVEIGPRLDFKIGRIHTPSPDMVTEAHKKPKQKKNV
ELDIMGDKLGRIHMGKQDLGKLQTRKMKGLKSKFDQG

Ligand information

>6ft6 Chain 1 (length=3058)

guuugaccucaaaucagguaggaguacccgcugaacuuaagcauaucaau
aagcggaggaaaagaaaccaaccgggauugccuuaguaacggcgagugaa
gcggcaaaagcucaaauuugaaaucugguaccuucggugcccgaguugua
auuuggagagggcaacuuuggggccguuccuugucuauguuccuuggaac
aggacgucauagagggugagaaucccguguggcgaggagugcgguucuuu
guaaagugccuucgaagagucgaguuguuugggaaugcagcucuaagugg
gugguaaauuccaucuaaagcuaaauauuggcgagagaccgauagcgaac
aaguacagugauggaaagaugaaaagaacuuugaaaagagagugaaaaag
uacgugaaauuguugaaagggaagggcauuugaucagacaggccagcauc
aguuuugguggcaggauaaauccauaggaauguagcuugccucgguaagu
auuauagccugugggaauacugccagcugggacugaggacugcgacguaa
gucaaggaugcuggcauaaugguuauaugccgcccgucuugaaacacgga
ccaaggagucuaacgucuaugcgaguguuuggguguaaaacccauacgcg
uaaugaaagugaacguagguuggggccucgcaagaggugcacaaucgacc
gauccugaugucuucggauggauuugaguaagagcauagcuguugggacc
cgaaagauggugaacuaugccugaauagggugaagccagaggaaacucug
guggaggcucguagcgguucugacgugcaaaucgaucgucgaauuugggu
auaggggcgaaagacuaaucgaaccaucuaguagcugguuccugccgaag
uuucccucaggauagcagaagcucguaucaguuuuaugagguaaagcgaa
aacuuuaaauauguaagaaguccuuguuugaacguggacauuugaaugaa
gagcuuuuagugggccauuuuugguaagcagaacuggcgaugcgggauga
accgaacguagaguuaaggugccggaauacacgcucaucagacaccacaa
aagguguuaguucaucuagacagccggacgguggccauggaagucggaau
ccgcuaaggaguguguaacaacucaccggccgaaugaacuagcccugaaa
auggauggcgcucaagcguguuaccuauacucuaccgucaggguugauau
gaugcccugacgaguaggcaggcguggaggucagugacgaagccuagacc
guaaggucgggucgaacggccucuagugcagaucuuggugguaguagcaa
auauucaaaugagaacuuugaagacugaaguggggaaagguuccacguca
acagcaguuggacguggguuagucgauccuaagagauggggaagcuccgu
uucaaaggccugauuuuaugcaggccaccaucgaaagggaauccgguuaa
gauuccggaaccuggauauggauucuucacgguaacguaacugaaugugg
agacgucggcgcgagcccugggaggaguuaucuuuucuucuuaacagcuu
aucaccccggaauugguuuauccggagauggggucuuauggcuggaagag
gccagcaccuuugcuggcuccggugcgcuugugacggcccgugaaaaucc
acaggaaggaauaguuuucaugccaggucguacugauaaccgcagcaggu
cuccaaggugaacagccucuaguugauagaauaauguagauaagggaagu
cggcaaaauagauccguaacuucgggauaaggauuggcucuaagggucgg
acgaucaacuuagaacugguacggacaaggggaaucugacugucuaauua
aaacauagcauugcgauggucagaaagugauguugacgcaaugugauuuc
ugcccagugcucugaaugucaaagugaagaaauucaaccaagcgcgggua
aacggcgggaguaacuaugacucucuuaagguagccaaauggauuaacga
gauucccacugucccuaucuacuaucuagcgaaaccacagccaagggggc
uuggcagaaucagcggggaaagaagacccuguugagcuugacucuaguuu
gacauugugaagagacauaguuucuuuacuuauucaaugaagcggagcug
gaauucauuuuccacguucuagcauucaaggucccauucggggcugaucc
ggguugaagacauugucagguggggaguuugggggcggcacaucuguuaa
acgauaacgcagauguccuaaggggggcucauggagaacagaaaucucca
guagaacaaaaggguaaaagcccccuugauuuugauuuucagugugaaua
caaaccaugaaaguguggccuaucgauccuuuagucccucggaauuugag
gcuagaggugccagaaaaguuaccacagggauaacuggcuuguggcaguc
aagcguucauagcgacauugcuuuuugauucuucgaugucggcucuuccu
aucauaccgaagcagaauucgguaagcguuggauuguucacccacuaaua
gggagugagcuggguuuagaccgucgugagacagguuaguuuuacccuac
ugaugaauguuaccgcaauaguaauugaacuuaguacgagaggaacaguu
cauucggauaauugguuuuugcggcugucugaucaggcauugccgcgaag
cuaccauccgcuggauuauggcugaacgccucuaagucagaauccaugcu
agaacgcggugauuucuuugcuccacacaauauagauggauacgaauaag
gcguccuuguggcgucgcugaaccauagcaggcuagcaacggugcacuug
gcggaaaggccuugggugcuugcuggcgaauugcaaugucauuuugcgug
gggauaaaucauuuguauacgacuuagauguacaacgggguauuguaagc
aguagaguagccuuguuguuacgaucugcugagauuaagccuuuguuguc
ugauuugu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6ft6 Structure of the nuclear exosome captured on a maturing preribosome.
• Resolution: 3.9 Å
• Binding residue (original residue number in PDB): N9 R11 A12 R14 L16 R62 F77 K81 N82 Q254 K261 H276 M277 Q280 D281 L282 Q286 T287 R288 K289 L293
• Binding residue (residue number reindexed from 1): N1 R3 A4 R6 L8 R54 F69 K73 N74 Q246 K248 H263 M264 Q267 D268 L269 Q273 T274 R275 K276 L280

Gene Ontology

Molecular Function

• GO:0005515 protein binding
• GO:0008097 5S rRNA binding
• GO:0008312 7S RNA binding
• GO:0019843 rRNA binding

Biological Process

• GO:0000027 ribosomal large subunit assembly
• GO:0000463 maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
• GO:0000466 maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
• GO:0000470 maturation of LSU-rRNA
• GO:0006364 rRNA processing
• GO:1902626 assembly of large subunit precursor of preribosome

Cellular Component

• GO:0005634 nucleus
• GO:0005730 nucleolus
• GO:0030687 preribosome, large subunit precursor

External links

• PDB: RCSB:6ft6, PDBe:6ft6, PDBj:6ft6
• PDBsum: 6ft6
• PubMed: 29519915
• UniProt: P36160|RPF2_YEAST Ribosome biogenesis protein RPF2 (Gene Name=RPF2)