Structure of PDB 6m62 Chain w Binding Site BS01

Receptor Information

>6m62 Chain w (length=182) Species: 559292 (Saccharomyces cerevisiae S288C)

LPVTVEKPIPVVYDLGNLAAFDSNVLDKNDLDSSNARREEKIKSLTRDNV
QLLINQLLSLPMKTTTESVGGTGGQSSVMTLLQLPDPTTDLPREKPLPKA
KAMTKWEKFAAKKGIKPKERAGKMIYDEASGEWVPKWGYKGANKKLDDQW
LVEVIDPRTLNRAERKRLVKKNEKQQRRNMKN

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): T80 T112 K113 W114 F117 I123 K124 K126 E127 R128 A129 G130 K131 W145 G146 Y147 K148 N151 K152 N191 Q194 Q195 R197 N198
• Binding residue (residue number reindexed from 1): T72 T104 K105 W106 F109 I115 K116 K118 E119 R120 A121 G122 K123 W137 G138 Y139 K140 N143 K144 N172 Q175 Q176 R178 N179

Gene Ontology

Molecular Function

• GO:0003674 molecular_function
• GO:0005515 protein binding

Biological Process

• GO:0000055 ribosomal large subunit export from nucleus
• GO:0000447 endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
• GO:0042254 ribosome biogenesis
• GO:0042273 ribosomal large subunit biogenesis

Cellular Component

• GO:0005634 nucleus
• GO:0005654 nucleoplasm
• GO:0005730 nucleolus
• GO:0030687 preribosome, large subunit precursor
• GO:0034399 nuclear periphery

External links

• PDB: RCSB:6m62, PDBe:6m62, PDBj:6m62
• PDBsum: 6m62
• PubMed: 32719344
• UniProt: Q08746|RRS1_YEAST Regulator of ribosome biosynthesis (Gene Name=RRS1)