Structure of PDB 8ipb Chain AA Binding Site BS01

Receptor Information

>8ipb Chain AA (length=229) Species: 4565 (Triticum aestivum)

NPLFEKRPKQFGIGGALPPKKDLHRFVKWPKVVRIQRQRRILKQRLKVPP
ALHQFTRTLDKNLATNLFKMLLKYRPEDKAAKKERLLKRAQAEAEGKTVE
AKKPIVVKYGLNHVTYLIEQSKAQLVVIAHDVDPIELVVWLPALCRKMEV
PYCIVKGKSRLGSIVHKKTASVLCLTTVKNEDKLEFSKILEAIKANFNDK
FDEVRKKWGGGVMGSKSQAKTKARERLIA

Ligand information

>8ipb Chain RB (length=3147)

gcgcgaccccaggucaggcgggacuaccgcugaguuuaagcauauaaaua
agcggaggagaagaaacuuacaaggauuccccuaguaacggcgagcgaac
cgggagcagcccagcuugagaaucgggcggcugugccguccgaauuguag
ucuggagaggcguccucagcgacggaccgggcccaaguccccuggaaagg
ggcgccugggagggugagagccccguccggcccggacccugucgccccac
gaggcgccgucaacgagucggguuguuugggaaugcagcccaaaucgggc
gguagacuccguccaaggcuaaauacaggcgagagaccgauagcgaacaa
guaccgcgagggaaagaugaaaaggacuuugaaaagagagucaaagagug
cuugaaauugccgggagggaagcggaugggggccggcgaugcgccccggc
gcucggggcguggacuguugucggccgcgccggcggccaaagcccggggg
cuccgcgcccccggcagccgucgucggcacggccgguacccgcgcgccga
aaggcgugccccucggggcacugcgcugcaacgcccugcgggcucuccau
ccgacccgucuugaaacacggaccaaggagucugacaugcgugcgagucg
acggguucugaaaccugggaugcgcaaggaagcugacgagcgggaggccc
ucacgggccgcaccgcuggccgacccugaucuucugugaaggguucgagu
uggagcacgccugucgggacccgaaagauggugaacuaugccugagcggg
gcgaagccagaggaaacucugguggaggcucgaagcgauacugacgugca
aaucguucgucugacuuggguauaggggcgaaagacuaaucgaaccaucu
aguagcugguucccuccgaaguuucccucaggauagcuggagcccauuac
gaguucuaucagguaaagccaaugauuagaggcauuggggacgcaacguc
cucgaccuauucucaaacuuuaaauagguaggauggcgcggcugcuucgg
ugagccgugccauggaaucgggugcuccaagugggccauuuuugguaagc
agaacuggcgaugcgggaugaaccggaagccggguuacggugcccaacug
cgcgcuaaccuagaacccacaaaggguguuggucgauuaagacagcagga
cgguggucauggaagucgaaauccgcuaaggaguguguaacaacucaccu
gccgaaucaacuagccccgaaaauggauggcgcugaagcgcgcgacccac
acccggccaucugggcgagugccaugccccgaugaguaggagggcgcggc
ggccgaugcaaaacccggggcgcgagcccgggcggagcggccgucggugc
agaucuuggugguaguagcaaauauucaaaugagaacuuugaaggccgaa
gaggagaaagguuccaugugaacggcacuugcacauggguaagccgaucc
uaagggaagggguaaccccggcagauagcgcgaucacgcgcauccccgaa
agggaaucggguuaagauuucccgagccgggauguggcgguugacggcga
cguuaggaaguccggagacgccggcgggggccucgggaagaguuaucuuu
ucugcuuaacggccugccaacccuggaaacgguucagccggagguagggu
ccaguggccggaagagcacacgucgcgcgguguccggugcgcccccggcg
gcccaugaaaauccggaggaccgaguaccguucacgcccggucguacuca
uaaccgcaucaggucuccaaggugaacagccucuggccaauggaacaaug
uaggcaagggaagucggcaaaacggauccguaacuucgggaaaaggauug
gcucugaggacugacagucgacucagaacugguacggacaaggggaaucc
gacuguuuaauuaaaacaaagcauugcgaugguccucgcggaugcugacg
caaugugauuucugcccagugcucugaaugucaaagugaagaaauucaac
caagcgcggguaaacggcgggaguaacuaugacucucuuaagguagccaa
augccucgucaucuaauuagugacgcgcaugaaugaauuaacgagauucc
cacugucccugucuacuauccagcgaaaccacagccaagggaacgggcuu
ggcggaaucagcggggaaagaagacccuguugagcuugacucuaguccga
cuuugugaaaugaauuuuacuuauuccgugggucggaagcggggcaugcc
ccuccuuuuggcuccaaggcccggucuuaccgggccgauccgggcggaag
acauugucagguggggaguuuggcuggggcggccaaucuguuaaaagaua
acgcagguguccuaagaugagcucaacgagaacagaaaucucguguggaa
caaaaggguaaaagcucguuugauucugauuuccaguacgaauacgaacc
gugaaagcguggccuaucgauccuuuagaucuucggaguuugaagcuaga
ggugucagaaaaguuaccacagggauuacuggcuuguggcagccaagcgu
ucauagcgacguugcuuuuugauccuucgaugucggcucuuccuaucauu
gcgaagcagaauucaccaaguguuggauuguucacccaccaauagggaac
gugagcuggguuuagaccgucgugagacagguuaguuuuacccuacugau
gacagugucgcgauaguaauucaaccuaguacgagaggaaccguugauuc
acacaauuggucaucgcgcuugguugaaaagccaguggcgcgaagcuacc
gugugccggauuaugacugaacgccucuaagucagaauccaagcuagcau
gcgacgccugcgcccgccgcccgccccgacccacguuaggggcgcuugcg
cccccaagggcccgugccauuggcuaagccgguccggccgaagugccgcg
gucggccgccucgaagcucccuucccaacgggcggugggcugaauccuuu
gcagacgacuuaaauacgcgacggggcauuguaaguggcagaguggccuu
gcugccacgauccacugagauccaguccccgggucgcacggauucgu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8ipb Boric acid intercepts 80S ribosome migration from AUG-stop by stabilizing eRF1.
• Resolution: 3.4 Å
• Binding residue (original residue number in PDB): E26 K27 R28 K30 F32 I34 G35 P40 K42 R46 F47 K49 P51 K52 V53 R55 R61 R66 K68 E98 K103 K104 R106 K123 K124 P125 K129 Y130 G131 L132 N133 H134 Y137 D154 P155 L158 S180 K188 K189 A191 S192 M234 G235 S236 K237 S238
• Binding residue (residue number reindexed from 1): E5 K6 R7 K9 F11 I13 G14 P19 K21 R25 F26 K28 P30 K31 V32 R34 R40 R45 K47 E77 K82 K83 R85 K102 K103 P104 K108 Y109 G110 L111 N112 H113 Y116 D133 P134 L137 S159 K167 K168 A170 S171 M213 G214 S215 K216 S217

Gene Ontology

Molecular Function

• GO:0003723 RNA binding

Biological Process

• GO:0000470 maturation of LSU-rRNA
• GO:0042254 ribosome biogenesis

Cellular Component

• GO:0005840 ribosome
• GO:0022625 cytosolic large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8ipb, PDBe:8ipb, PDBj:8ipb
• PDBsum: 8ipb
• PubMed: 38267667
• UniProt: A0A3B6RED0