Structure of PDB 5mc6 Chain L Binding Site BS01

Receptor Information

>5mc6 Chain L (length=63) Species: 559292 (Saccharomyces cerevisiae S288C)

TPVTLAKVIKVLGRTGSRGGVTQVRVEFLEDTSRTIVRNVKGPVRENDIL
VLMESEREARRLR

Ligand information

>5mc6 Chain 2 (length=1767)

uaucugguugauccugccaguagucauaugcuugucucaaagauuaagcc
augcaugucuaaguauaagcaauuuauacagugaaacugcgaauggcuca
uuaaaucaguuaucguuuauuugauaguuccuuuacuacaugguauaacu
gugguaauucuagagcuaauacaugcuuaaaaucucgacccuuuggaaga
gauguauuuauuagauaaaaaaucaaugucuucggacucuuugaugauuc
auaauaacuuuucgaaucgcauggccuugugcuggcgaugguucauucaa
auuucugcccuaucaacuuucgaugguaggauaguggccuaccaugguuu
caacggguaacggggaauaaggguucgauuccggagagggagccugagaa
acggcuaccacauccaaggaaggcagcaggcgcgcaaauuacccaauccu
aauucagggagguagugacaauaaauaacgauacagggcccauucggguc
uuguaauuggaaugaguacaauguaaauaccuuaacgaggaacaauugga
gggcaagucuggugccagcagccgcgguaauuccagcuccaauagcguau
auuaaaguuguugcaguuaaaaagcucguaguugaacuuugggcccgguu
ggccggucggauuuccaacggggccuuuccuucuggcuaaccuugagucc
uuguggcucuuggcgaaccaggacuuuuacuuugaaaaaauuagaguguu
caaagcaggcguauugcucgaauauauuagcauggaauaauagaauagga
cguuugguucuauuuuguugguuucuaggaccaucguaaugauuaauagg
gacggucgggggcaucaguauucaauugucagaggugaaauucuuggauu
uauugaagacuaacuacugcgaaagcauuugccaaggacguuuucauuaa
ucaagaacgaaaguuaggggaucgaagaugaucagauaccgucguagucu
uaaccauaaacuaugccgacuagggaucgggugguguuuuuuuaaugacc
cacucggcaccuuacgagaaaucaaagucuuuggguucuggggggaguau
ggucgcaaggcugaaacuuaaaggaauugacggaagggcaccaccaggag
uggagccugcggcuuaauuugacucaacacggggaaacucaccaggucca
gacacaauaaggauugacagauugagagcucuuucuugauuuugugggug
guggugcauggccguucuuaguugguggagugauuugucugcuuaauugc
gauaacgaacgagaccuuaaccuacuaaauaguggugcuagcauuugcug
guuauccacuucuuagagggacuaucgguuucaagccgauggaaguuuga
ggcaauaacaggucugugaugcccuuagacguucugggccgcacgcgcgc
uacacugacggagccagcgagucuaaccuuggccgagaggucuugguaau
cuugugaaacuccgucgugcuggggauagagcauuguaauuauugcucuu
caacgaggaauuccuaguaagcgcaagucaucagcuugcguugauuacgu
cccugcccuuuguacacaccgcccgucgcuaguaccgauugaauggcuua
gugaggccucaggaucugcuuagagaucucagagcggagaauuuggacaa
acuuggucauuuagaggaacuaaaagucguaacaagguuuccguagguga
accugcggaaggaucau

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5mc6 The cryo-EM structure of a ribosome-Ski2-Ski3-Ski8 helicase complex.
• Resolution: 3.8 Å
• Binding residue (original residue number in PDB): R18 S21 R22 G23 P47
• Binding residue (residue number reindexed from 1): R14 S17 R18 G19 P43

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome

Biological Process

• GO:0000028 ribosomal small subunit assembly
• GO:0000054 ribosomal subunit export from nucleus
• GO:0002181 cytoplasmic translation
• GO:0006412 translation
• GO:0030490 maturation of SSU-rRNA
• GO:1900153 positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay

Cellular Component

• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0022627 cytosolic small ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:5mc6, PDBe:5mc6, PDBj:5mc6
• PDBsum: 5mc6
• PubMed: 27980209
• UniProt: P0C0X0|RS28B_YEAST Small ribosomal subunit protein eS28B (Gene Name=RPS28B)