Structure of PDB 6eml Chain Y Binding Site BS01

Receptor Information

>6eml Chain Y (length=150) Species: 559292 (Saccharomyces cerevisiae S288C)

GRMHSAGKGISSSAIPYSRNAPAWFKLSSESVIEQIVKYARKGLTPSQIG
VLLRDAHGVTQARVITGNKIMRILKSNGLAPEIPEDLYYLIKKAVSVRKH
LERNRKDKDAKFRLILIESRIHRLARYYRTVAVLPPNWKYESATASALVN

Ligand information

>6eml Chain 2 (length=1675)

uaucugguugauccugccaguagucauaugcuugucucaaagauuaagcc
augcaugucuaaguauaagcaauuuauacagugaaacugcgaauggcuca
uuaaaucaguuaucguuuauuugauaguuccuuuacuacaugguauaacu
gugguaauucuagagcuaauacaugcuuaaaaucucgacccuuuggaaga
gauguauuuauuagauaaaaaaucaaugucuucggacucuuugaugauuc
auaauaacuuuucgaaucgcauggccuugugcuggcgaugguucauucaa
auuucugcccuaucaacuuucgaugguaggauaguggccuaccaugguuu
caacggguaacggggaauaaggguucgauuccggagagggagccugagaa
acggcuaccacauccaaggaaggcagcaggcgcgcaaauuacccaauccu
aauucagggagguagugacaauaaauaacgauacagggcccauucggguc
uuguaauuggaaugaguacaauguaaauaccuuaacgaggaacaauugga
gggcaagucuggugccagcagccgcgguaauuccagcuccaauagcguau
auuaaaguuguugcaguuaaaaagcucguaguugaacuuugggcccgguu
ggccggucggauuuccaacggggccuuuccuucuggcuaaccaggacuuu
uacuuugaaaaaauuagaguguucaaagcaggcguauugcucgaauauau
uagcauggaauaauagaauaggacguuugguucuauuuuguugguuucua
ggaccaucguaaugauuaauagggacggucgggggcaucaguauucaauu
gucagaggugaaauucuuggauuuauugaagacuaacuacugcgaaagca
uuugccaaggacguuuucauuaaucaagaacgaaaguuaggggaucgaag
augaucgucguagucuuaaccauaaacuaugccgacuagggaucgggugg
uguuuuuuuaaugacccacucggcaccuuacgagaaaucaaagucuuugg
guucuggggggaguauggucgcaaggcugaaacuuaaaggaauugacgga
agggcaccaccaggaguggagccugcggcuuaauuuggaaacucaccagg
uccagacacaauaaggauugacagauugagagcucuuucuugauuuugug
ggugguggugcauggccguaguugguggagugauuugucugcuuaauugc
gauaacgaacgagaccuuaaccuacuaaauaguggugcuagcauuugcug
guuauccacuucuuagagggacuauauggaaguuugaggacaggucugug
augcccuuagacguucugggccgcacgcgcgcuacacugacggagccagc
gagucuaaccuuggccgagaggucuugguaaucuugugaaacuccgucgu
gcuggggauagagcauuguaauuauugcucuucaacgaggaauuccuagu
aagcgcaagucaucagcuugcguugauuacgucccugcccuuuguacgcu
aguaccgauugaauggcuuagugaggccucaggaucugcuuagagaucuc
agagcggagaauuuggacaaacuuggucauuuagaggaacuaauuuccgu
aggugaaccugcggaaggaucauua

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6eml Cryo-EM structure of a late pre-40S ribosomal subunit fromSaccharomyces cerevisiae.
• Resolution: 3.6 Å
• Binding residue (original residue number in PDB): G2 R3 M4 K9 G10 I11 S12 S13 S14 A15 I16 P17 R20 P47 S48 G51 V52 T61 R64 K70 I71 M72 R73 K76 E86 Y90 L91 K94 S97 V98 H101 R104 N105 K107 D108 D110 F113 R114 L117 S120 R121 R124 R127 Y128
• Binding residue (residue number reindexed from 1): G1 R2 M3 K8 G9 I10 S11 S12 S13 A14 I15 P16 R19 P46 S47 G50 V51 T60 R63 K69 I70 M71 R72 K75 E85 Y89 L90 K93 S96 V97 H100 R103 N104 K106 D107 D109 F112 R113 L116 S119 R120 R123 R126 Y127

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome
• GO:0070181 small ribosomal subunit rRNA binding

Biological Process

• GO:0000462 maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
• GO:0002181 cytoplasmic translation
• GO:0006412 translation

Cellular Component

• GO:0005730 nucleolus
• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0022627 cytosolic small ribosomal subunit
• GO:0030686 90S preribosome
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:6eml, PDBe:6eml, PDBj:6eml
• PDBsum: 6eml
• PubMed: 29155690
• UniProt: P05756|RS13_YEAST Small ribosomal subunit protein uS15 (Gene Name=RPS13)