Structure of PDB 4u6f Chain sM Binding Site BS02

Receptor Information

>4u6f Chain sM (length=104) Species: 559292 (Saccharomyces cerevisiae S288C)

KEIVKSNTSSKKADVPPPSADPSKARKNRPRPSGNEGAIRDKTAGRRNNR
SKDVTDSATTKKSAEKEAQADAAAEIAEDAAEAELNQQANNQFNKVPEAK
KVEL

Ligand information

>4u6f Chain 5 (length=3150)

uugaccucaaaucagguaggaguacccgcugaacuuaagcauaucaauaa
gcggaggaaaagaaaccaaccgggauugccuuaguaacggcgagugaagc
ggcaaaagcucaaauuugaaaucugguaccuucggugcccgaguuguaau
uuggagagggcaacuuuggggccguuccuugucuauguuccuuggaacag
gacgucauagagggugagaaucccguguggcgaggagugcgguucuuugu
aaagugccuucgaagagucgaguuguuugggaaugcagcucuaagugggu
gguaaauuccaucuaaagcuaaauauuggcgagagaccgauagcgaacaa
guacagugauggaaagaugaaaagaacuuugaaaagagagugaaaaagua
cgugaaauuguugaaagggaagggcauuugaucagacauggcugggccag
caucaguuuugguggcaggauaaauccauaggaauguagcuugccucggu
aaguauuauagccugugggaauacugccagcugggacugaggacugcgac
guaagucaaggaugcuggcauaaugguuauaugccgcccgucuugaaaca
cggaccaaggagucuaacgucuaugcgaguguuuggguguaaaacccaua
cgcguaaugaaagugaacguagguuggggccucgcaagaggugcacaauc
gaccgauccugaugucuucggauggauuugaguaagagcauagcuguugg
gacccgaaagauggugaacuaugccugaauagggugaagccagaggaaac
ucugguggaggcucguagcgguucugacgugcaaaucgaucgucgaauuu
ggguauaggggcgaaagacuaaucgaaccaucuaguagcugguuccugcc
gaaguuucccucaggauagcagaagcucguaucaguuuuaugagguaaag
cgaaugauuagagguuccggggucgaaaugaccuugaccuauucucaaac
uuuaaauauguaagaaguccuuguuacuuaauugaacguggacauuugaa
ugaagagcuuuuagugggccauuuuugguaagcagaacuggcgaugcggg
augaaccgaacguagaguuaaggugccggaauacacgcucaucagacacc
acaaaagguguuaguucaucuagacagccggacgguggccauggaagucg
gaauccgcuaaggaguguguaacaacucaccggccgaaugaacuagcccu
gaaaauggauggcgcucaagcguguuaccuauacucuaccgucaggguug
auaugaugcccugacgaguaggcaggcguggaggucagugacgaagccua
gaccguaaggucgggucgaacggccucuagugcagaucuuggugguagua
gcaaauauucaaaugagaacuuugaagacugaaguggggaaagguuccac
gucaacagcaguuggacguggguuagucgauccuaagagauggggaagcu
ccguuucaaaggccugauuuuaugcaggccaccaucgaaagggaauccgg
uuaagauuccggaaccuggauauggauucuucacgguaacguaacugaau
guggagacgucggcgcgagcccugggaggaguuaucuuuucuucuuaaca
gcuuaucaccccggaauugguuuauccggagauggggucuuauggcugga
agaggccagcaccuuugcuggcuccggugcgcuugugacggcccgugaaa
auccacaggaaggaauaguuuucaugccaggucguacugauaaccgcagc
aggucuccaaggugaacagccucuaguugauagaauaauguagauaaggg
aagucggcaaaauagauccguaacuucgggauaaggauuggcucuaaggg
ucggacgaucaacuuagaacugguacggacaaggggaaucugacugucua
auuaaaacauagcauugcgauggucagaaagugauguugacgcaauguga
uuucugcccagugcucugaaugucaaagugaagaaauucaaccaagcgcg
gguaaacggcgggaguaacuaugacucucuuaagguagccaaaugccucg
ucaucuaauuagugacgcgcaugaauggauuaacgagauucccacugucc
cuaucuacuaucuagcgaaaccacagccaagggaacgggcuuggcagaau
cagcggggaaagaagacccuguugagcuugacucuaguuugacauuguga
agagacguuucuuuacuuauucaaugaagcggagcuggaauucauuuucc
acguucuagcauucaaggucccauucggggcugauccggguugaagacau
ugucagguggggaguuuggcuggggcggcacaucuguuaaacgauaacgc
agauguccuaaggggggcucauggagaacagaaaucuccaguagaacaaa
aggguaaaagcccccuugauuuugauuuucagugugaauacaaaccauga
aaguguggccuaucgauccuuuagucccucggaauuugaggcuagaggug
ccagaaaaguuaccacagggauaacuggcuuguggcagucaagcguucau
agcgacauugcuuuuugauucuucgaugucggcucuuccuaucauaccga
agcagaauucgguaagcguuggauuguucacccacuaauagggaacguga
gcuggguuuagaccgucgugagacagguuaguuuuacccuacugaugaau
guuaccgcaauaguaauugaacuuaguacgagaggaacaguucauucgga
uaauugguuuuugcggcugucugaucaggcauugccgcgaagcuaccauc
cgcuggauuauggcugaacgccucuaagucagaauccaugcuagaacgcg
gugauuucuuugcuccacacaauauagauggauacgaauaaggcguccuu
guggcgucgcugaaccauagcaggcuagcaacggugcacuuggcggaaag
gccuugggugcuugcuggcgaauugcaaugucauuuugcguggggauaaa
ucauuuguauacgacuuagauguacaacgggguauuguaagcaguagagu
agccuuguuguuacgaucugcugagauuaagccuuuguugucugauuugu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4u6f ?
• Resolution: 3.1 Å
• Binding residue (original residue number in PDB): K27 T30 S31 S32 K33 K34 A42 D43 P44 K46 A47 R48 R51
• Binding residue (residue number reindexed from 1): K5 T8 S9 S10 K11 K12 A20 D21 P22 K24 A25 R26 R29

Gene Ontology

Molecular Function

• GO:0003676 nucleic acid binding
• GO:0003677 DNA binding
• GO:0003723 RNA binding
• GO:0005515 protein binding
• GO:0030371 translation repressor activity
• GO:0042162 telomeric DNA binding
• GO:0043022 ribosome binding
• GO:0045142 triplex DNA binding
• GO:0061770 translation elongation factor binding

Biological Process

• GO:0000723 telomere maintenance
• GO:0006414 translational elongation
• GO:0006417 regulation of translation
• GO:0031929 TOR signaling
• GO:0043066 negative regulation of apoptotic process
• GO:0043558 regulation of translational initiation in response to stress
• GO:0141014 ribosome hibernation

Cellular Component

• GO:0005634 nucleus
• GO:0005737 cytoplasm
• GO:0048471 perinuclear region of cytoplasm

External links

• PDB: RCSB:4u6f, PDBe:4u6f, PDBj:4u6f
• PDBsum: 4u6f
• PubMed: 25209664
• UniProt: P39015|STM1_YEAST Suppressor protein STM1 (Gene Name=STM1)