Structure of PDB 8y0w Chain LO Binding Site BS01

Receptor Information

>8y0w Chain LO (length=201) Species: 9606 (Homo sapiens)

EVQVLVLDGRGHLLGRLAAIVAKQVLLGRKVVVVRCEGINISGNFYRNKL
KYLAFLRKRMNTNPSRGPYHFRAPSRIFWRTVRGMLPHKTKRGQAALDRL
KVFDGIPPPYDKKKRMVVPAALKVVRLKPTRKFAYLGRLAHEVGWKYQAV
TATLEEKRKEKAKIHYRKKKQLMRLRKQAEKNVEKKIDKYTEVLKTHGLL
V

Ligand information

>8y0w Chain L5 (length=3666)

cgcgaccucagaucagacguggcgacccgcugaauuuaagcauauuaguc
agcggaggagaagaaacuaaccaggauucccucaguaacggcgagugaac
agggaagagcccagcgccgaauccccgccccgcggcggggcgcgggacau
guggcguacggaagacccgcuccccggcgccgcucguggggggcccaagu
ccuucugaucgaggcccagcccguggacggugugaggccgguagcggccc
ccggcgcgccgggcccgggucuucccggagucggguugcuugggaaugca
gcccaaagcgggugguaaacuccaucuaaggcuaaauaccggcacgagac
cgauagucaacaaguaccguaagggaaaguugaaaagaacuuugaagaga
gaguucaagagggcgugaaaccguuaagagguaaacgggugggguccgcg
caguccgcccggaggauucaacccggcggcggguccggccgugucggcgg
cccggcggaucuuucccgcgcgggggaccgucccccgaccggcgaccggc
cgccgccgggcgcauuuccaccgcggcggugcgccgcgaccggcuccggg
acggcugggaaggcccggcggggaagguggcucgggggcccccgaguguu
acagcccccccggcagcagcacucgccgaaucccggggccgagggagcga
gacccgucgccgcgcucuccccccucccggcgcgccggggggggccgggc
caccccucccacggcgcgaccgcucggggcggacuguccccagugcgccc
cgggcgggucgcgccgucgggcccgggggaggccacgcgcgcgucccccg
aagagggggacggcggagcgagcgcacggggucggcggcgacgucggcua
cccacccgacccgucuugaaacacggaccaaggagucuaacacgugcgcg
agucgggggcucgcacgaaagccgccguggcgcaaugaaggugaaggccg
gcgcgcucgccggccgaggugggaucccgaggccucuccaguccgccgag
ggcgcaccaccggcccgucucgcccgccgcgccggggagguggagcacga
gcgcacguguuaggacccgaaagauggugaacuaugccugggcagggcga
agccagaggaaacucugguggagguccguagcgguccugacgugcaaauc
ggucguccgaccuggguauaggggcgaaagacuaaucgaaccaucuagua
gcugguucccuccgaaguuucccucaggauagcuggcgcucucgcagacc
cgacgcccgccacgcaguuuuauccgguaaagcgaaugauuagaggucuu
ggggccgaaacgaucucaaccuauucucaaacuuuaaauggguaagaagc
ccggcucgcuggcguggagccgggcguggaaugcgagugccuagugggcc
acuuuugguaagcagaacuggcgcugcgggaugaaccgaacgccggguua
aggcgcccgaugccgacgcucaucagaccccagaaaagguguugguugau
auagacagcaggacgguggccauggaagucggaauccgcuaaggagugug
uaacaacucaccugccgaaucaacuagcccugaaaauggauggcgcugga
gcgucgggcccauacccggccgucgccggcagucgagaguggacgggagc
ggcggccggagccccgcggacgcuacgccgcgacgaguaggagggccgcu
gcggugagccuugaagccuagggcgcgggcccggguggagccgccgcagg
ugcagaucuuggugguaguagcaaauauucaaacgagaacuuugaaggcc
gaaguggagaaggguuccaugugaacagcaguugaacaugggucagucgg
uccugagagaugggcgagcgccguuccgaagggacgggcgauggccuccg
uugcccucggccgaucgaaagggagucggguucagauccccgaauccgga
guggcggagaugggcgccgcgaggcguccagugcgguaacgcgaccgauc
ccggagaagccggcgggagccccggggagaguucucuuuucuuugugaag
ggcagggcgcccuggaauggguucgccccgagagaggggcccgugccuug
gaaagcgucgcgguuccggcggcguccggugagcucucgcuggcccuuga
aaauccgggggagaggguguaaaucucgcgccgggccguacccauauccg
cagcaggucuccaaggugaacagccucuggcauguuggaacaauguaggu
aagggaagucggcaagccggauccguaacuucgggauaaggauuggcucu
aagggcugggucggucgcggccggcgccuagcagccgacuuagaacuggu
gcggaccaggggaauccgacuguuuaauuaaaacaaagcaucgcgaaggc
ccgcggcggguguugacgcgaugugauuucugcccagugcucugaauguc
aaagugaagaaauucaaugaagcgcggguaaacggcgggaguaacuauga
cucucuuaagguagccaaaugccucgucaucuaauuagugacgcgcauga
auggaugaacgagauucccacugucccuaccuacuauccagcgaaaccac
agccaagggaacgggcuuggcggaaucagcggggaaagaagacccuguug
agcuugacucuagucuggcacggugaagagacaugagugaucguuuuuuc
acugacccggugaggcgggggggcgagccccgaggggcucucgcuucugg
cgccaagcgcccggccgcgcgccggccgggcgcgacccgcuccggggaca
gugccagguggggaguuugacuggggcgguacaccugucaaacgguaacg
cagguguccuaaggcgagcucagggaggacagaaaccucccguggagcag
aagggcaaaagcucgcuugaucuugauuuucaguacgaauacagaccgug
aaagcggggccucacgauccuucugaccuuuuggguuuuaagcaggaggu
gucagaaaaguuaccacagggauaacuggcuuguggcggccaagcguuca
uagcgacgucgcuuuuugauccuucgaugucggcucuuccuaucauugug
aagcagaauucaccaagcguuggauuguucacccacuaauagggaacgug
agcuggguuuagaccgucgugagacagguuaguuuuacccuacugaugau
guguuguugccaugguaauccugcucaguacgagaggaaccgcagguuca
gacauuugguguaugugcuuggcugaggagccaauggggcgaagcuacca
ucugugggauuaugacugaacgccucuaagucagaaucccgcccaggcgg
aacgauacggcagcgccgcggagccucgguuggccucggauagccggucc
cccgccgggguccggugcggagugcccuucguccugggaaacggggcgcg
gccggagaggcggccgcccccucgcccgucacgcaccgcacguucguggg
gaaccuggcgcuaaaccauucguagacgaccugcuucugggucgggguuu
cguacguagcagagcagcucccucgcugcgaucuauugaaagucagcccu
cgacacaaggguuugu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8y0w dormant ribosome with eIF5A, eEF2 and SERBP1
• Resolution: 3.4 Å
• Binding residue (original residue number in PDB): R12 G17 R18 K25 L28 R37 S44 Y48 R49 R59 K60 R61 M62 N63 N65 P66 S67 R68 P70 Y71 H72 F73 R74 R82 T83 R85 G86 M87 P89 H90 K91 K93 R94 Q96 F105 D106 G107 I108 P110 K114 K115 K116 R117 V126 R128 L129 K130 R133 E144 V145 K148 Y149 L156 E157 K159 R160 K161 K163 K165 H167 Y168 R169 K171 K172 M175 R176 K179 K188 L202 V203
• Binding residue (residue number reindexed from 1): R10 G15 R16 K23 L26 R35 S42 Y46 R47 R57 K58 R59 M60 N61 N63 P64 S65 R66 P68 Y69 H70 F71 R72 R80 T81 R83 G84 M85 P87 H88 K89 K91 R92 Q94 F103 D104 G105 I106 P108 K112 K113 K114 R115 V124 R126 L127 K128 R131 E142 V143 K146 Y147 L154 E155 K157 R158 K159 K161 K163 H165 Y166 R167 K169 K170 M173 R174 K177 K186 L200 V201

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003729 mRNA binding
• GO:0003735 structural constituent of ribosome

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006412 translation
• GO:0006417 regulation of translation
• GO:0017148 negative regulation of translation
• GO:0032496 response to lipopolysaccharide
• GO:0042592 homeostatic process
• GO:0048246 macrophage chemotaxis
• GO:0060425 lung morphogenesis
• GO:0071346 cellular response to type II interferon
• GO:1901194 negative regulation of formation of translation preinitiation complex

Cellular Component

• GO:0005634 nucleus
• GO:0005730 nucleolus
• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0005925 focal adhesion
• GO:0015934 large ribosomal subunit
• GO:0016020 membrane
• GO:0022625 cytosolic large ribosomal subunit
• GO:0022626 cytosolic ribosome
• GO:0045202 synapse
• GO:0097452 GAIT complex
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8y0w, PDBe:8y0w, PDBj:8y0w
• PDBsum: 8y0w
• PubMed: 38698775
• UniProt: P40429|RL13A_HUMAN Large ribosomal subunit protein uL13 (Gene Name=RPL13A)