Structure of PDB 7bt6 Chain v Binding Site BS01

Receptor Information

>7bt6 Chain v (length=287) Species: 559292 (Saccharomyces cerevisiae S288C)

NARAKRALVKREAKLVENVKQALFIPGQSCNKNLHDIMVDLSALKKPDMK
RFNRKNDIHPFEDMSPLEFFSEKNDCSLMVLMTSSKKRKNNMTFIRTFGY
KIYDMIELMVADNFKLLSDFKKLTFTVGLKPMFTFQGAAFDTHPVYKQIK
SLFLDFFRGESTDLQDVAGLQHVISMTIQGDFQDGEPLPNVLFRVYKLKS
YKSDQGGKRLPRIELVEIGPRLDFKIGRIHTPSPDMVTEAHKKPKQKKNV
ELDIMGDKLGRIHMGKQDLGKLQTRKMKGLKSKFDQG

Ligand information

>7bt6 Chain 1 (length=2962)

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
uuccaucgaaagggaauccgguuaagauuccggaaccuggauauggauuc
uucacgguaacguaacugaauguggagacgucggcgcgagcccugggagg
aguuaucuuuucuucuuaacagcuuaucaccccggaauugguuuauccgg
agauggggucuuauggcuggaagaggccagcaccuuugcuggcuccggug
cgcuugugacggcccgugaaaauccacaggaaggaauaguuuucaugcca
ggucguacugauaaccgcagcaggucuccaaggugaacagccucuaguug
auagaauaauguagauaagggaagucggcaaaauagauccguaacuucgg
gauaaggauuggcucuaagggucggacgaucaacuuagaacugguacgga
caaggggaaucugacugucuaauuaaaacauagcauugcgauggucagaa
agugauguugacgcaaugugauuucugcccagugcucugaaugucaaagu
gaagaaauucaaccaagcgcggguaaacggcgggaguaacuaugacucuc
uuaagguagccaaauggauuaacgagauucccacugucccuaucuacuau
cuagcgaaaccacagccaagggggcuuggcagaaucagcggggaaagaag
acccuguugagcuugacucuaguuugacauugugaagagacauaguuucu
uuacuuauucaagacauugucagguggggaguuugggggcggcacaucug
uuaaacgauaacgcagauguccuaaggggggcucauggagaacagaaauc
uccaguagaacaaaaggguaaaagcccccuugauuuugauuuucagugug
aauacaaaccaugaaaguguggccuaucgauccuuuagucccucggaauu
ugaggcuagaggugccagaaaaguuaccacagggauaacuggcuuguggc
agucaagcguucauagcgacauugcuuuuugauucuucgaugucggcucu
uccuaucauaccgaagcagaauucgguaagcguuggauuguucacccacu
aauagggagugagcuggguuuagaccgucgugagacagguuaguuuuacc
cuacugaugaauguuaccgcaauaguaauugaacuuaguacgagaggaac
aguucauucggauaauugguuuuugcggcugucugaucaggcauugccgc
gaagcuaccauccgcuggauuauggcugaacgccucuaagucagaaucca
ugcuagaacgcggugauuucuuugcuccacacaauauagauggauacgaa
uaaggcguccuuguggcgucgcugaaccauagcaggcuagcaacggugca
cuuggcggaaaggccuugggugcuugcuggcgaauugcaaugucauuuug
cguggggauaaaucauuuguauacgacuuagauguacaacgggguauugu
aagcaguagaguagccuuguuguuacgaucugcugagauuaagccuuugu
ugucugauuugu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7bt6 Structural insights into assembly of the ribosomal nascent polypeptide exit tunnel.
• Resolution: 3.12 Å
• Binding residue (original residue number in PDB): N9 R11 A12 R14 F60 R62 K81 S241 P242 K250 K253 Q254 K261 N262 H276 K279 Q280 L282 Q286 T287 K289 L293 K296
• Binding residue (residue number reindexed from 1): N1 R3 A4 R6 F52 R54 K73 S233 P234 K242 K245 Q246 K248 N249 H263 K266 Q267 L269 Q273 T274 K276 L280 K283

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:7bt6, PDBe:7bt6, PDBj:7bt6
• PDBsum: 7bt6
• PubMed: 33037216
• UniProt: P36160|RPF2_YEAST Ribosome biogenesis protein RPF2 (Gene Name=RPF2)