Structure of PDB 8ipb Chain PA Binding Site BS01

Receptor Information

>8ipb Chain PA (length=130) Species: 4565 (Triticum aestivum)

MKRNPRVTSSRRKCRKAHFTAPSSVRRVLMSAALSSELRHKYNVRSIPIR
KDDEVQVVRGTYKGREGKVVQVYRRRWVIHVERITREKVNGSTVNVGIHP
SKVIVTKLKLDKDRKALLDRKARGRAADKA

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): M1 K2 R3 N4 T8 S9 R11 K13 C14 R15 H18 A33 R39 R45 S46 R59 G60 T61 K63 R76 R86 K88 V89 N90 H99 S101 K102 K121 G124 R125
• Binding residue (residue number reindexed from 1): M1 K2 R3 N4 T8 S9 R11 K13 C14 R15 H18 A33 R39 R45 S46 R59 G60 T61 K63 R76 R86 K88 V89 N90 H99 S101 K102 K121 G124 R125

Gene Ontology

Molecular Function

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

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006412 translation
• GO:0042273 ribosomal large subunit biogenesis

Cellular Component

• GO:0005840 ribosome
• GO:0015934 large ribosomal subunit
• GO:0022625 cytosolic large ribosomal subunit

External links

• PDB: RCSB:8ipb, PDBe:8ipb, PDBj:8ipb
• PDBsum: 8ipb
• PubMed: 38267667
• UniProt: A0A3B6GQI2