Structure of PDB 5m1j Chain Q5 Binding Site BS01

Receptor Information

>5m1j Chain Q5 (length=185) Species: 4932 (Saccharomyces cerevisiae)

GIDHTSKQHKRSGHRTAPKSDNVYLKLLVKLYTFLARRTDAPFNKVVLKA
LFLSKINRPPVSVSRIARALKQEGAANKTVVVVGTVTDDARIFEFPKTTV
AALRFTAGARAKIVKAGGECITLDQLAVRAPKGQNTLILRGPRNSREAVR
HFGMGPHKGKAPRILSTGRKFERARGRRRSKGFKV

Ligand information

>5m1j Chain 14 (length=3295)

uugaccucaaaucagguaggaguacccgcugaacuuaagcauaucaauaa
gcggaggaaaagaaaccaaccgggauugccuuaguaacggcgagugaagc
ggcaaaagcucaaauuugaaaucugguaccuucggugcccgaguuguaau
uuggagagggcaacuuuggggccguuccuugucuauguuccuuggaacag
gacgucauagagggugagaaucccguguggcgaggagugcgguucuuugu
aaagugccuucgaagagucgaguuguuugggaaugcagcucuaagugggu
gguaaauuccaucuaaagcuaaauauuggcgagagaccgauagcgaacaa
guacagugauggaaagaugaaaagaacuuugaaaagagagugaaaaagua
cgugaaauuguugaaagggaagggcauuugaucagacaggccagcaucag
uuuugguggcaggauaaauccauaggaauguagcuugccucgguaaguau
uauagccugugggaauacugccagcugggacugaggacugcgacguaagu
caaggaugcuggcauaaugguuauaugccgcccgucuugaaacacggacc
aaggagucuaacgucuaugcgaguguuuggguguaaaacccauacgcgua
augaaagugaacguagguuggggccucgcaagaggugcacaaucgaccga
uccugaugucuucggauggauuugaguaagagcauagcuguugggacccg
aaagauggugaacuaugccugaauagggugaagccagaggaaacucuggu
ggaggcucguagcgguucugacgugcaaaucgaucgucgaauuuggguau
aggggcgaaagacuaaucgaaccaucuaguagcugguuccugccgaaguu
ucccucaggauagcagaagcucguaucaguuuuaugagguaaagcgaaug
auuagagguuccggggucgaaaugaccuugaccuauucucaaacuuuaaa
uauguaagaaguccuuguuacuuaauugaacguggacauuugaaugaaga
gcuuuuagugggccauuuuugguaagcagaacuggcgaugcgggaugaac
cgaacguagaguuaaggugccggaauacacgcucaucagacaccacaaaa
gguguuaguucaucuagacagccggacgguggccauggaagucggaaucc
gcuaaggaguguguaacaacucaccggccgaaugaacuagcccugaaaau
ggauggcgcucaagcguguuaccuauacucuaccgucaggguugauauga
ugcccugacgaguaggcaggcguggaggucagugacgaagccuagaccgu
aaggucgggucgaacggccucuagugcagaucuuggugguaguagcaaau
auucaaaugagaacuuugaagacugaaguggggaaagguuccacgucaac
agcaguuggacguggguuagucgauccuaagagauggggaagcuccguuu
caaaggccugauuuuaugcaggccaccaucgaaagggaauccgguuaaga
uuccggaaccuggauauggauucuucacgguaacguaacugaauguggag
acgucggcgcgagcccugggaggaguuaucuuuucuucuuaacagcuuau
caccccggaauugguuuauccggagauggggucuuauggcuggaagaggc
cagcaccuuugcuggcuccggugcgcuugugacggcccgugaaaauccac
aggaaggaauaguuuucaugccaggucguacugauaaccgcagcaggucu
ccaaggugaacagccucuaguugauagaauaauguagauaagggaagucg
gcaaaauagauccguaacuucgggauaaggauuggcucuaagggucgggu
agugagggccuuggucagacgcagcgggcgugcgugccuuguuguagacg
gccuugguaggucucuuguagaccgucgcuugcuacaauuaacgaucaac
uuagaacugguacggacaaggggaaucugacugucuaauuaaaacauagc
auugcgauggucagaaagugauguugacgcaaugugauuucugcccagug
cucugaaugucaaagugaagaaauucaaccaagcgcggguaaacggcggg
aguaacuaugacucucuuaagguagccaaaugccucgucaucuaauuagu
gacgcgcaugaauggauuaacgagauucccacugucccuaucuacuaucu
agcgaaaccacagccaagggaacgggcuuggcagaaucagcggggaaaga
agacccuguugagcuugacucuaguuugacauugugaagagacauagagg
guguagaauaagugggagcuucggcgccagugaaauaccacuaccuuuau
aguuucuuuacuuauucaaugaagcggagcuggaauucauuuuccacguu
cuagcauucaaggucccauucggggcugauccggguugaagacauuguca
gguggggaguuuggcuggggcggcacaucuguuaaacgauaacgcagaug
uccuaaggggggcucauggagaacagaaaucuccaguagaacaaaagggu
aaaagcccccuugauuuugauuuucagugugaauacaaaccaugaaagug
uggccuaucgauccuuuagucccucggaauuugaggcuagaggugccaga
aaaguuaccacagggauaacuggcuuguggcagucaagcguucauagcga
cauugcuuuuugauucuucgaugucggcucuuccuaucauaccgaagcag
aauucgguaagcguuggauuguucacccacuaauagggaacgugagcugg
guuuagaccgucgugagacagguuaguuuuacccuacugaugaauguuac
cgcaauaguaauugaacuuaguacgagaggaacaguucauucggauaauu
gguuuuugcggcugucugaucaggcauugccgcgaagcuaccauccgcug
gauuauggcugaacgccucuaagucagaauccaugcuagaacgcggugau
uucuuugcuccacacaauauagauggauacgaauaaggcguccuuguggc
gucgcugaaccauagcaggcuagcaacggugcacuuggcggaaaggccuu
gggugcuugcuggcgaauugcaaugucauuuugcguggggauaaaucauu
uguauacgacuuagauguacaacgggguauuguaagcaguagaguagccu
uguuguuacgaucugcugagauuaagccuuuguugucugauuugu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5m1j Structural insights into ribosomal rescue by Dom34 and Hbs1 at near-atomic resolution.
• Resolution: 3.3 Å
• Binding residue (original residue number in PDB): G2 I3 H5 S7 K8 Q9 H10 K11 R12 G14 H15 R16 K20 S21 K31 F35 R38 R39 P43 F44 L54 S55 K56 P61 S63 S65 R66 R69 Q73 T86 T88 D89 D90 R92 I93 R105 T107 A108 N136 T137 I139 R141 G142 P143 R144 N145 S146 R147 E148 R151 F153 P157 G160 A162 R164 S167 R170 K171 F172 E173 R176 R179 R180 S181 K182 F184 K185
• Binding residue (residue number reindexed from 1): G1 I2 H4 S6 K7 Q8 H9 K10 R11 G13 H14 R15 K19 S20 K30 F34 R37 R38 P42 F43 L53 S54 K55 P60 S62 S64 R65 R68 Q72 T85 T87 D88 D89 R91 I92 R104 T106 A107 N135 T136 I138 R140 G141 P142 R143 N144 S145 R146 E147 R150 F152 P156 G159 A161 R163 S166 R169 K170 F171 E172 R175 R178 R179 S180 K181 F183 K184

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006412 translation

Cellular Component

• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0022625 cytosolic large ribosomal subunit
• GO:0043232 intracellular non-membrane-bounded organelle
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:5m1j, PDBe:5m1j, PDBj:5m1j
• PDBsum: 5m1j
• PubMed: 27995908
• UniProt: P0CX49|RL18A_YEAST Large ribosomal subunit protein eL18A (Gene Name=RPL18A)