Structure of PDB 6em3 Chain A Binding Site BS01

Receptor Information

>6em3 Chain A (length=145) Species: 559292 (Saccharomyces cerevisiae S288C)

MNKQRTLLISSRGVNYRHRHLIQDLSGLLPHSRKEPKLDTLQQLNEIAEL
YNCNNVLFFEARKHQDLYLWLSKPPNGPTIKFYIQGSRPVLSFDQRFESS
PHYQLIKELLVHNFGVPPNARKSKPFIDHVMSFSIVDDKIWVRTY

Ligand information

>6em3 Chain 1 (length=1250)

guuugaccucaaaucagguaggaguacccgcugaacuuaagcauaucaau
aagcggaggaaaagaaaccaaccgggauugccuuaguaacggcgagugaa
gcggcaaaagcucaaauuugaaaucugguaccuucggugcccgaguugua
auuuggagagggcaacuuuggggccguuccuugucuauguuccuuggaac
aggacgucauagagggugagaaucccguguggcgaggagugcgguucuuu
guaaagugccuucgaagagucgaguuguuugggaaugcagcucuaagugg
gugguuccaucuaaagcuaaauauuggcgagagaccgauagcgaacaagu
acagugauggaaagaugaaaagaacuuugaaaagagagugaaaaaguacg
ugaaauuguugaaagggaagggcauuugaucagacaugguguuuugugcc
cucugcuccuuguggguaggggaaucucgcauuucacugggccagcauca
guuuugguggcaggauaaauccauaggaauguagcuugccucgguaagua
uuauagccugugggaauacugccagcugggacugaggacugcgacguaag
ucaaggaugcuggcauaaugguuauaugccgcccgucuugaaacacggac
caaggagucuaacgucuaugcgaguguuuggguguaaaacccauacgcgu
aaugaaagugaacguagguuggggccucgcaagaggugcacaaucgaccg
auccugaggauggauuugaguaagagcauagcuguugggacccgaaagau
ggugaaaaccaucuaguagcugguuccugccgaaguuucccucaggauag
cagaagcucguaucaguuuuaugaauguaagaaugaagagcuuuuagugg
gccauuuuugguaagcagaacuggcgaugcgggaugaaccgaacguagag
uuaaggugccggaauacacgcucaucagauggcgcucaagcguguuaccu
auacucuaccgucaggguugauaugaugcccugacgaguaggcaggcgug
gaggucagugacgaagccuagaccguaaggucgggucgaacggccucuag
ugcagaucuuggugguaguagcaagcgaaaccacagccaagggaacgggc
uuggcagagcuccacacagauggauacgaauaaggcguccuuguggcguc
gcugaaccauagcaggcuagcugcuggcgaauugcaaugcguggggauaa

..........................<<<<<<..................
.>>>>>.>...<.....<<....>>..<<<<<......<<.....>>...
..>>>>>..<<<...........<<.<<<<<<...>>>>>>.>>......
.......<<<<<<<.<<<<<<<<<<<<<<<<<<<<<....<<<<......
>>>>.(.......<<<......)>>>..>.>>>>>>>>..>>>>>>>>..
..>>>>>>>>>>>........<<<<<<<........>>>>>>>.....<<
<<<<..>>>>>>..>>>....>............................
.<<....>>...............<<<......>>>..............
....................<<<<<.<<<<<<.....<<<<...<<<..<
<<<<<<<<.....>>>>>>>>>......>>>...>>>>..<<<<<<<.<<
<<<<<<<<<<<<<.....<<<<<<<<<....<.<<<<<......>>>>>>
......>>>>>>>>..>.>>>>>.>>>>>>>>>>........<<<....>
>>.....>>>>>>>....>>>>>>.>>>>>..<<<<........>>>><<
<<<<....<<<<<<.<<<<<<..<<<...<<<<.....>>>>...>>>..
.<<....>>.......<<<<<..<<<<<....>>>>>...>>>>>.<<<<
<<<<.......>>>.>>>.>>....>>>>>>.>>>>>>..<<.<...<<<
<<<....>>>>>>......>.>>..<<<<<<......<<......>>..<
<<<<<<<<....<<<.<<<<<<<..>>>>>.>>>>>..>>>>>>>.>>..
<<<<.<<<<<.....>>>>>.>>>>....<<<......>>>...<<<<<<
<..<<<<(((.....<<<<<<......<..))).>....>>>>>>.>>>>
..>>>>>>><<<<<<<<<.........>>>>>>>>>....>>>>>><.<<
<<<<<<.<<......<<<<.<<<<....>>>>>>>>...>>>>>>>>>>.
.>.....>>>>>><<.....<<..>>....>>....<<<<<........>
>>>>.....<<<<<<......<<..........<<<<<<.....>>>>>>
......>>.......<<<<<<.>>>>>>............>>>>>>....

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6em3 Visualizing the Assembly Pathway of Nucleolar Pre-60S Ribosomes.
• Resolution: 3.2 Å
• Binding residue (original residue number in PDB): G40 V41 N42 H45 P63
• Binding residue (residue number reindexed from 1): G13 V14 N15 H18 P36

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0005515 protein binding
• GO:0008097 5S rRNA binding
• GO:0019843 rRNA binding
• GO:0042134 rRNA primary transcript binding

Biological Process

• GO:0000027 ribosomal large subunit assembly
• GO:0000464 endonucleolytic cleavage in ITS1 upstream of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
• GO:0000465 exonucleolytic trimming to generate mature 5'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
• GO:0006364 rRNA processing
• GO:0042254 ribosome biogenesis

Cellular Component

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

External links

• PDB: RCSB:6em3, PDBe:6em3, PDBj:6em3
• PDBsum: 6em3
• PubMed: 29245012
• UniProt: Q08235|BRX1_YEAST Ribosome biogenesis protein BRX1 (Gene Name=BRX1)