Structure of PDB 6m62 Chain v Binding Site BS01

Receptor Information

>6m62 Chain v (length=245) Species: 559292 (Saccharomyces cerevisiae S288C)

NARAKRALVKREAKLVENVKQALFIPGQSCNKNLHDIMVDLSALKKPDMK
RFNRKNDIHPFEDMSPLEFFSEKNDCSLMVLMTSSKKRKNNMTFIRTFGY
KIYDMIELMVADNFKLLSDFKKLTFTVGLKPMFTFQGAAFDTHPVYKQIK
SLFLDFFRGESTDLQDVAGLQHVISMTIQGDFQDGEPLPNVLFRVYKLKS
YKSDQGGKRLPRIELVEIGPRLDFKIGRIHTPSPDMVTEAHKKPK

Ligand information

>6m62 Chain 1 (length=2972)

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
ugcuggauuaacgagauucccacugucccuaucuacuaucuagcgaaacc
acagccaagggggcuuggcagaaucagcggggaaagaagacccuguugag
cuugacucuaguuugacauugugaagagacauaguuucuuuacuuauuca
augaagcggagcuggaauucauuuuccacguucuagcauucaagguccca
uucggggcugauccggguugaagacauugucagguggggaguuugggggc
ggcacaucuguuaaacgauaacgcagauguccuaaggggggcucauggag
aacagaaaucuccaguagaacaaaaggguaaaagcccccuugauuuugau
uuucagugugaauacaaaccaugaaaguguggccuaucgauccuuuaguc
ccucggaauuugaggcuagaggugccagaaaaguuaccacagggauaacu
ggcuuguggcagucaagcguucauagcgacauugcuuuuugauucuucga
ugucggcucuuccuaucauaccgaagcagaauucgguaagcguuggauug
uucacccacuaauagggagugagcuggguuuagaccgucgugagacaggu
uaguuuuacccuacugaugaauguuaccgcaauaguaauugaacuuagua
cgagaggaacaguucauucggauaauugguuuuugcggcugucugaucag
gcauugccgcgaagcuaccauccgcuggauuauggcugaacgccucuaag
ucagaauccaugcuagaacgcggugauuucuuugcuccacacaauauaga
uggauacgaauaaggcguccuuguggcgucgcugaaccauagcaggcuag
caacggugcacuuggcggaaaggccuugggugcuugcuggcgaauugcaa
ugucauuuugcguggggauaaaucauuuguauacgacuuagauguacaac
gggguauuguaagcaguagaguagccuuguuguuacgaucugcugagauu
aagccuuuguugucugauuugu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6m62 Coupling of 5S RNP rotation with maturation of functional centers during large ribosomal subunit assembly.
• Resolution: 3.2 Å
• Binding residue (original residue number in PDB): N9 A10 R11 K13 R14 F77 F78 K81 N82
• Binding residue (residue number reindexed from 1): N1 A2 R3 K5 R6 F69 F70 K73 N74

Gene Ontology

Molecular Function

• GO:0019843 rRNA binding

Biological Process

• GO:0000027 ribosomal large subunit assembly
• GO:0000470 maturation of LSU-rRNA
• GO:0006364 rRNA processing

External links

• PDB: RCSB:6m62, PDBe:6m62, PDBj:6m62
• PDBsum: 6m62
• PubMed: 32719344
• UniProt: P36160|RPF2_YEAST Ribosome biogenesis protein RPF2 (Gene Name=RPF2)