Structure of PDB 6em1 Chain r Binding Site BS01

Receptor Information
>6em1 Chain r (length=73) Species: 559292 (Saccharomyces cerevisiae S288C) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PQNDYIERHIKQHGKRLDHEERKRKREARESHKISERAQKLTGWKGKQFA
KKRYAEKVSMRKKIKAHEQSKVK
Ligand information
>6em1 Chain 1 (length=1785) [Search RNA sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
guuugaccucaaaucagguaggaguacccgcugaacuuaagcauaucaau
aagcggaggaaaagaaaccaaccgggauugccuuaguaacggcgagugaa
gcggcaaaagcucaaauuugaaaucugguaccuucggugcccgaguugua
auuuggagagggcaacuuuggggccguuccuugucuauguuccuuggaac
aggacgucauagagggugagaaucccguguggcgaggagugcgguucuuu
guaaagugccuucgaagagucgaguuguuugggaaugcagcucuaagugg
gugguuccaucuaaagcuaaauauuggcgagagaccgauagcgaacaagu
acagugauggaaagaugaaaagaacuuugaaaagagagugaaaaaguacg
ugaaauuguugaaagggaagggcauuugaucagacaugguguuuugugcc
cucugcuccuuguggguaggggaaucucgcauuucacugggccagcauca
guuuugguggcaggauaaauccauaggaauguagcuugccucgguaagua
uuauagccugugggaauacugccagcugggacugaggacugcgacguaag
ucaaggaugcuggcauaaugguuauaugccgcccgucuugaaacacggac
caaggagucuaacgucuaugcgaguguuuggguguaaaacccauacgcgu
aaugaaagugaacguagguuggggccucgcaagaggugcacaaucgaccg
auccugaggauggauuugaguaagagcauagcuguugggacccgaaagau
ggugaaaaccaucuaguagcugguuccugccgaaguuucccucaggauag
cagaagcucguaucaguuuuaugaauguaagaaugaagagcuuuuagugg
gccauuuuugguaagcagaacuggcgaugcgggaugaaccgaacguagag
uuaaggugccggaauacacgcucaucagacaccacaaaagguguuaguuc
aucuagacagccggacgguggccauggaagucggaauccgcuaaggagug
uguaacaacucaccggccgaaugaacuagcccugaaaauggauggcgcuc
aagcguguuaccuauacucuaccgucaggguugauaugaugcccugacga
guaggcaggcguggaggucagugacgaagccuagaccguaaggucggguc
gaacggccucuagugcagaucuuggugguaguagcaagcgaaaccacagc
caagggaacgggcuuggcagaaucagcgggggcuuguggcagucaagcgu
ucauagcgacauugcucggcucuuccuaucauaccgaagcagaauucggu
aagcguuggauuguucacccacuaauagggaacgugagcucccuacugau
gaauguuaccgcaauaguaauugaacuuaguacgagaggaacaguucauu
cggauaauugguuuuugcggcugucugaucaggcauugccgcgaagcuac
cauccgcuggauuauggcugaacgccucuaagucagaauccaugcuagaa
cgcggugaugcuccacacagauggauacgaauaaggcguccuuguggcgu
cgcugaaccauagcaggcuagcaacggugcacuuggcggaaaggccuugg
gugcuugcuggcgaauugcaaugcguggggauaaaucauuuguauacgac
uuagauguacaacgggguauuguaagcaguagaguagccuuguuguuacg
aucugcugagauuaagccuuuguugucugauuugu
...........................<<<<<..................
.>>>>>...........<<....>>..<<<<<......<<.....>>...
..>>>>>..<<<...........<<.<<<<<<...>>>>>>.>>......
.......<<<<<<<.<<<<<<<<<<<<<<<<<<<<<....<<<<......
>>>>.(.......<<<......)>>>..>.>>>>>>>>..>>>>>>>>..
..>>>>>>>>>>>........<<<<<<<........>>>>>>>.....<<
<<<<..>>>>>>..>>>.................................
.<<....>>...............<<<......>>>..............
....................<<<<<.<<<<<<.....<<<<...<<<..<
<<<<<<<<.....>>>>>>>>>......>>>...>>>>..<<<<<<<<<<
<<<<<<<<<<<<<.....<<<<<<<<<....<.<<<<<......>>>>>>
......>>>>>>>.>.>.>>>>>.>>>>>>>>>>........<<<....>
>>....>>>>>>>>....>>>>>>.>>>>>..<<<<.<....>.>>>><<
<<<<....<<<<<<.<<<<<<..<<<...<<<<.....>>>>...>>>..
.<<....>>.......<<<<<..<<<<<....>>>>>...>>>>>.<<<<
<<<<.......>>>.>>>.>>....>>>>>>.>>>>>>..<<.<...<<<
<<<....>>>>>>......>.>>..<<<<<<......<........>..<
<<<<<<<<....<<<.<<<<<<<..>>>>>.>>>>>..>>>>>>>.>>..
<<<<.<<<<<.....>>>>>.>>>>....<<<......>>>...<<<<<<
<..<<<<(((.....<<<<<<......<..........<<<.<<<<<<<<
<<.......<<<<<.<<<...<<.........>>...>>>.........<
<......>>...>>>>>...>>>>>>>>>>>>>..........))).>..
..>>>>>>.>>>>..>>>>>>><<<<<<<<<.........>>>>>>>>>.
...>>>>>><.<<<<<<<<.<<......<<<<.<<<<....>>>>>>>>.
..>>>>>>>>>>..>.....>>>>>><<.....<<..>>....>>....<
<<<<........>>>>>....<<<<<..<<.......<<<<<....<<..
.....>>....>>>>>..<<..<<<<<..<.<<<<<<<......>>>>>>
>...>.<<<.........>>>.....>>>>>......>>...>>.>>>>>
....<<<<<<<<..<<<<.<.<<<<<<...............>>>>>>.>
<<<<<...<<<<....<<<<<<<<........>>>..>>>>>...>>>>.
.>>>>>.<<<<...<<<<<...........>>>>>...>>>>.>>>>...
.>>>>>>>>.<<<<<<......<<..........<<<<<<.....>>>>>
>......>>.......<<<<<<...<<<<<.<..<<<......>>>..>.
>>>>>.>>>>>>............>>>>>>.<<<<<<.............
........<<<<<<<<<.<<<....<<<<....<<<<........>>>>.
..>>>>...>>>....>>>>.>>>>>..>>>>>>.
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB6em1 Visualizing the Assembly Pathway of Nucleolar Pre-60S Ribosomes.
Resolution3.6 Å
Binding residue
(original residue number in PDB)		P2 Q3 N4 D5 Y6 I7 K12 R23 R25 K26 A29 R30 S32 H33 K34 S36 A39 Q40 T43 G44 W45 K46 K48 Q49 R54 Y55 K58 V59
Binding residue
(residue number reindexed from 1)		P1 Q2 N3 D4 Y5 I6 K11 R22 R24 K25 A28 R29 S31 H32 K33 S35 A38 Q39 T42 G43 W44 K45 K47 Q48 R53 Y54 K57 V58
Enzymatic activity
Enzyme Commision number ?
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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:6em1, PDBe:6em1, PDBj:6em1
PDBsum6em1
PubMed29245012
UniProtP40078|NSA2_YEAST Ribosome biogenesis protein NSA2 (Gene Name=NSA2)

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