Structure of PDB 6m62 Chain r Binding Site BS01

Receptor Information

>6m62 Chain r (length=230) Species: 559292 (Saccharomyces cerevisiae S288C)

PQNDYIERHIKQHGKRLDHEERKRKREARESHKISERAQKLTGWKGKQFA
KKRYAEKVSMRKKIKAHEQSKVKDALPTYLLDREQKFSVPLPKVRGISEE
EMFKVIKTGKSRSKSWKRMITKHTFVGEGFTRRPVKMERIIRPSALRQKK
ANVTHPELGVTVFLPILAVKKNPQSPMYTQLGVLTKGTIIEVNVSELGMV
TAGGKVVWGKYAQVTNEPDRDGCVNAVLLV

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): P2 Q3 D5 Y6 I7 E8 R25 K26 R27 R30 S32 H33 S36 A39 Q40 L42 T43 G44 W45 K48 R54 Y55 K58 K135 I137 T139 K141 S142 R143 K145 W147 E159 R163 R164 V166 K167 E169 R170 I171 I172 R173 P174 S175 A176 N183 F194 K236 T246 N247 R251 D252 C254 N256
• Binding residue (residue number reindexed from 1): P1 Q2 D4 Y5 I6 E7 R24 K25 R26 R29 S31 H32 S35 A38 Q39 L41 T42 G43 W44 K47 R53 Y54 K57 K104 I106 T108 K110 S111 R112 K114 W116 E128 R132 R133 V135 K136 E138 R139 I140 I141 R142 P143 S144 A145 N152 F163 K205 T215 N216 R220 D221 C223 N225

Gene Ontology

Molecular Function

• GO:0003674 molecular_function
• GO:0005515 protein binding

Biological Process

• GO:0000460 maturation of 5.8S rRNA
• 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:0042254 ribosome biogenesis
• GO:0042273 ribosomal large subunit biogenesis

Cellular Component

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

External links

• PDB: RCSB:6m62, PDBe:6m62, PDBj:6m62
• PDBsum: 6m62
• PubMed: 32719344
• UniProt: P40078|NSA2_YEAST Ribosome biogenesis protein NSA2 (Gene Name=NSA2)