Structure of PDB 8jiv Chain CL Binding Site BS01

Receptor Information

>8jiv Chain CL (length=200) Species: 4565 (Triticum aestivum)

VKHNNVIPNGHFKKHWQNYVKTWFNQPARKQRRRIARQKNAVKIFPRPTS
GPLRPIVQCQTRKYNMKARAGRGFTLEELKSAGIPKKLAPTIGISVDHRR
KNRSLEGMQSNIQRLKTYKAKLVIFPRRARKVKAGDSTPEELANATQVQG
DYMPIARGEKRSVEVVKVTEEMKEFKAYGKLRVERMNQRQLGARQKKAAE

Ligand information

>8jiv Chain Aa (length=2863)

gcgaccccaggucaggcgggacuacccgcugaguuuaagcauauaaauaa
gcggaggagaagaaacuuacaaggauuccccuaguaacggcgagcgaacc
gggagcagcccagcuugagaaucgggcggcugugccguccgaauuguagu
cuggagaggcguccugcgacggaccgggcccaaguccccuggaaaggggc
gccugggagggugagagccccguccggcccggacccugucgcgaggcgcc
ucaacgagucggguuguuugggaaugcagcccaaaucgggcgguagacuc
cguccaaggcuaaauacaggcgagagaccgauagcgaacaaguaccgcga
gggaaagaugaaaaggacuuugaaaagagagucaaaagugcuugaaauug
ccgggagggaagcggaugggggccggcgaugcgccccggccguaugcgga
acggcugguccgccgcucggcucgggguguggacuguugucggccgcgcc
ggcggccaaagcccgggggcccuaggugcccccgguggccgucgucggca
cggccgcgcgccuaaaggcgugucccucggggcacugcgcugcaacggcc
ugcgggcuccccauccgacccgucuugaaacacggaccaaggagucugac
augcgugcgagucgacggguucugaaaccugggaugcgcaaggaagcuga
cgagcgggaggcccugggccgcaccgcuggccgacccugaucuucuguga
aggguucgaguuggagcacgccugucgggacccgaaagauggugaacuau
gccugagcggggcgaagccagaggcucugguggaggcucgaagcgauacu
gacgugcaaaucguucgucugacuuggguauaggggcgaaagacuaaucg
aaccaucuaguagcugguucccuccgaaguuucccucaggauagcuggag
cccaacgaguucuaucagguaaagccaaugauuagaggccuauucucaaa
cuuuaaauagguaggauggcgcggcugcuucggugagccgugccauggaa
ucgggcuccaagugggccauuuuugguaagcagaacuggcgaugcgggau
gaaccggaagccggguuacggugcccaacugcgcgcuaaccuagaaccca
caaaggguguuggucgaacuagccccgaaaauggauggcgcugaagcgcg
cgacccacacccggccaucugggcgagcgccaugccccgaugaguaggag
ggcgcggcggccgcugcaaaacccggggcgcgagcccgggcggagcggcc
gucggugcagaucuuggugguaguagcaaauauucaaaugagaacuuuga
aggccgaagaggagaaagguuccaugugaacggcacuugcacauggguaa
gccgauccuaagggacgggguaaccccggcagauagcgcacgcgccccga
aagggaaucggguuaagauuucccgagccgggauguggcgguugacggcg
acguuaggaaguccggagacgccggcgggggccucgggaagaguuaucuu
uucugcuuaacggccugccaacccuggaaacgguucagccggagguaggg
uccaguggccggaagagcaccggguguccggugcgcccccggcggcccau
gaaaauccggaggaccgccguucacgcccggucguacucauaaccgcauc
aggucuccaaggugaacagccucuggccaauggaacaauguaggcaaggg
aagucggcaaaacggauccguaacuucgggaaaaggauuggcucugagga
ccgacucagaacugguacggacaaggggaauccgacuguuuaauuaaaac
aaagcauugcgaugguccucgcggaugcugacgcaaugugauuucugccc
agugcucugaaugucaaagugaagaaauucaaccaagcgcggguaaacgg
caagguagccaaaugccucgucaucuaauuagugacgcgcaugaauggau
uaacgagauucccacugucccugucuacuauccagcgaaaccacagccaa
gggaacgggcuuggcggaaucagcggggaaagaagacccuguugagcuug
acucuaguccgacuuugugaauacuuauuccgugggucggaaguuuuggc
uccaaggccggccgauccgggcggaagacauugucagguggggaguuugg
cuggggcggcacaucuguuaaaagauaacgcagguguccuaagaugagcu
caacgagaacagaaaucucguguggaacaaaaggguaaaagcucguuuga
uucugauuuccaguacgaauacgaaccgugaaagcguggccuaucgaucc
uuuagcuucggaguuugaagcuagaggugucagaaaaguuaccacaggga
uaacuggcuuguggcagccaagcgauagcgacguugcuuuuugauccuuc
gaugucggcucuuccuaucauugugaagcagaauucaccaaguguuggau
uguucacccaccaauagggaacgugagcuggguuuagaccgucgugagac
agguuaguuuuacccuacugaugacagugucgcgauaguaauucaaccua
guacgagaggaaccguugauucacacaauuggucaucgcgcuugguugaa
aagccaguggcgcgaagcuaccgugugccggauuaugacugaacccucua
agucagaauccaagcuagcaugcgacgccucgacccacguuaggcccaag
ggcccgugggccgaagugcagcucccuucccgaauccuuugcagacgacu
uaagacggggcauuguaaguggcagagugacgauccacugagauccagcc
ccgucgcauucgu

........................<<<<<<.....<<....>>......>
>>>>.>.........<<....>>..<<<<<.......<.....>......
>>>>>..<<<....<......<<<<<<<<<...>>>>>>>>>......>.
.....<<<<<<<<.<<<<<<<<.<<<<<<<.....<<<<......>>>>.
((......<<<.....))>>>....>>>>>>>...>>>>>>>>.>>>>>>
>>........<<<<<<<........>>>>>>>.....<<<<<..((((((
>>>>>..>>>..................................<<....
>>...............<<<<....>>>>.....................
............<<<<<<<<<<<<......<.<<<<<<.<.......<<.
..<.>...>>........>..>.>>>>>.>.<.<<<<<<......<<...
.<..<......<..<<..<.......>.>>...>.....>..>....>>.
.......<<.<.<....>.>....<......>......>>..>>>>>>.>
....>>>.>>>>>>>>>..<<<<........>>>><<<<<<....<<<<<
<.<<<<<<..<<...<<<<<<....>>>>>>....>>...<<....>>..
..<<<<<..<<<<<.>>>>>...>>>>><<<<<<<<.....<....>...
..>>.>>>.>>>...>>>>>>.>>>>>>..<<.<..<<<<<<<.....<<
<<<<<<<..<<<....<<<<<<<.>>>>>>>.....>>>...<<<<.<<.
<<........>>>>>>>>....>>>>>>>>>...<<.......>>.....
.>>>>>>...>..>.>>..<<<<<<....<.<<<....>>>.><<<<<<<
.<<..<<<.<<<<<<<.....<<<....<<<..<.<<..>>.>..>>>..
>>.>.....>>>>>...<<<<<<<<<.<......>>>>>>>>>>....>>
>>>>>>>>>>.>>..<<<<.<<<<<.....>>>>>.>>>>....<<<...
...>>>...<<<<<<<...<<<(((.....<<<<<<.......<......
....<<<.<<<<<<...>>>>>>>>>..........))).>....>>>>>
>.>>>...>>>>>>><<<<.<<<<.........>>>>.>>>>....>>>>
>><.<<<<<<<<<<.......<<<.<<<<....>>>>>>>....>>>>>>
>>>>..>.....>>>>>><<.....<<.....<<<<<<.......>>>>>
><<<<<....<<<<<.<<...<<<<<....<<.....>>..>>>>>....
((<<<<<<...<<<...<<<....>>>........<<<..>>>..>>>..
..>>...<<<<<.........>>>>>))<<<<.<<<<<<<<...<<<...
.>>>...<...<<<<<<...<<<<.<<<<<<<.<<<<<.<<<<...[[..
>>>>.><...<<<<<.....<<<<<<....<<<<...>>>>....>>>>>
>.....>>>>>....><<<<<.>>>>>>>>>...>>>>>>>.>>>>....
.....>>>>>>...>..>>>>.>>>>>>>>>>>>..>>.....<<.....
.>>>>>>>.<<<<.....>>>>.>>>>>..<<<<.....<<<<<<<.<<.
........<.....<<<<<....<<..>>.....>>>>><<.<<<<<<..
....>>>>>>.>>............<<<<<<<<<..<<<.........>>
>..<<<<<<<....<<<<....>>>>......>>>>>>>...<<..<<<.
.<<<<<<....<<<.....<<<<....>>>>.....>>>.>>>>..>>>>
>......<...........<<<<<.......>>>>>.....>.....>>.
...>>.>>>>>>>..>..>>.>>>>>>>..>>>>>>....>>....<<<<
<........>>>>>....<<<<<..<<<.<<......<<<<.<<<<<<..
<<<<<.<<<.<<<...<<<..>>>...<<<<<.....<<<<.........
.....<<<..>>>..>>>>..>>>>>......>>>.>>>..>>>>>...<
<<.....>>>..<<<<<<...........>>>>>>..<<...<<<<<<<.
..<<<<<<.......>>>>>>.....<<...(((>>....>>>>>>>...
<<<..<<<<.......>>>>..>>>.<<<....>>>.>>))).......<
<<<<<<<<<.))))))>>>>>>>>>>..........>>>>..>>>>>>..
.....<<.<.<.<<<<<<...<<....>>...>>>>>>...>>.>.>...
....<<<<<..<<<<<..<<<.<<<<<......>>>>>...>>>.<<<..
.......>>>.....>>>>>......>>>.>>....<<<<<<<....>>>
.>>>>....>>..>>>.>>>>>....<<<<<<<..<<<<...<<<<<...
..............>>>>>..<<<<<...<<<<....<<<<<<<<<.]].
..>>>>..>>>>>...>>>>..>>>>>..<<<...<<<<<..........
>>>>>...>>>..>>>>....>>>>>>>.....<<.......<..>....
>>.............................<<<<..<............
.>.<<<<<<<.<<<....<<<<.<..<<.>>..>>>>>...>>>....>>
>>>>>..>>>>..

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8jiv Cryo-EM structure of wheat ribosome reveals unique features of the plant ribosomes.
• Resolution: 2.84 Å
• Binding residue (original residue number in PDB): V2 K3 H4 N6 V7 P9 N10 H12 F13 K14 K15 H16 W17 K22 W24 Q27 P28 R30 K31 Q32 R34 R35 R38 R55 V58 Q59 C60 Q61 T62 Y65 N66 M67 K68 R70 G72 R73 L77 K88 D98 H99 R100 R101 K102 R104 S105 R128 V133 R158 E160 K161 R162 Y179 R183 R186 M187 R190 Q191 G193 R195
• Binding residue (residue number reindexed from 1): V1 K2 H3 N5 V6 P8 N9 H11 F12 K13 K14 H15 W16 K21 W23 Q26 P27 R29 K30 Q31 R33 R34 R37 R54 V57 Q58 C59 Q60 T61 Y64 N65 M66 K67 R69 G71 R72 L76 K87 D97 H98 R99 R100 K101 R103 S104 R127 V132 R157 E159 K160 R161 Y178 R182 R185 M186 R189 Q190 G192 R194

Gene Ontology

Molecular Function

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

Biological Process

• GO:0006412 translation

Cellular Component

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

External links

• PDB: RCSB:8jiv, PDBe:8jiv, PDBj:8jiv
• PDBsum: 8jiv
• PubMed: 38458197
• UniProt: A0A3B6QBU0