Structure of PDB 7qiw Chain L Binding Site BS01

Receptor Information

>7qiw Chain L (length=207) Species: 4081 (Solanum lycopersicum)

GRRPARCYRQIKNKPYPKSRFCRGVPDPKIRIYDVGMKKKGVDEFPFCVH
LVSWEKENVSSEALEAARIACNKYMTKSAGKDAFHLRVRVHPFHVLRINK
GMRGAFGKPQGVCARVAIGQVLLSVRCKDGNANHAQEALRRAKFKFPGRQ
KIIVSRKWGFTKFSRTDYLKYKSENRIVPDGVNAKLLGCHGRLAARQPGR
AFLEAAN

Ligand information

>7qiw Chain 2 (length=3098)

gcgaccccaggucaggcgggauuacccgcugaguuuaagcauaucaauaa
gcggaggaaaagaaacuuacaaggauuccccuaguaacggcgagcgaacc
gggaacagcccagccuuagaaucgggcggcuccgucguccgaauuguagu
cuggagaagcguccucagcggcggaccgggcccaaguccccuggaagggg
gcgccggagagggugagagccccgucgugcccggacccugucgcaccacg
aggcgcugucuacgagucggguuguuugggaaugcagcccaaaucgggcg
gugaauuccguccaaggcuaaauacuggcgagagaccgauagcgaacaag
uaccgcgagggaaagaugaaaaggacuuugaaaagagagucaaagagugc
uugaaauugucgggagggaagcggaugggggccggcgaugcgccccgguc
gguguggaacggcgagccgguccgccgaucgacucggggcguggaccagc
guggauugggggggcggccaaagcccgggcucucgauacgcccguggaac
gccgucuccccgauuguggaaggcagcgcgcgccuccggcgugcuucggc
aucugcgcgcuccggacgcuggccugugggcuccccauucgacccgucuu
gaaacacggaccaaggagucugacaugugugcgagucaacgggcgaguaa
acccguaaggcguaaggaagcugauuggugggaucccccugaggggugca
ccgccgaccgaccuugaucuucugagaaggguucgagugugagcauaccu
gucgggacccgaaagauggugaacuaugccugagcggggcgaagccagag
gaaacucugguggaggcccgcagcgauacugacgugcaaaucguucgucu
gacuuggguauaggggcgaaagacuaaucgaaccgucuaguagcugguuc
ccuccgaaguuucccucaggauagcuggagcucgcgugcgaguucuaucg
gguaaagccaaugauuagaggccucggggccucgaccuauucucaaacuu
uaaauagguaggacggcgcggcugcuuuguugagccgcgccacggaauca
agagcuccaagugggccauuuuugguaagcagaacuggcgaugcgggaug
aaccggaagccggguuacggugccaaacugcgcgcuaaccuagaucccac
aaaggguguuggucgauuaagacagcagcugccgaaucaacuagccccga
aaauggauggcgcuuaagcgcgcgaccuacacccggccgucggggcaagu
gccaggccccgaugaguaggagggcgcggcggucgcugcaaaaccuuggg
cgcgagccugggcggagcggccgucggugcagaucuuggugguaguagca
aauauucaaaugagaacuuugaaggccgaagaggggaaagguuccaugug
aacggcacuugcacauggguuagucgauccuaagggucgggggaaccccg
acagauagcgcgucgcgcguacuccgaaagggaaucggguuaaaauuccu
gaaccgggacguggcgguugacggcaacguuaggaaguccggagacgucg
gcgggagccucgggaagaguuaucuuuucuguuuaacagccugcccaccc
uggaaucggcucagccggagguaggguccagcggcuggaagagcaccgca
cgugguguccggugcgcucccggcggcccuugaaaauccggaggaccgaa
ugccguccacgcccggucguacucauaaccgcaucaggucuccaagguga
acagccucuggucgauggaacaauguaggcaagggaagucggcaaaaugg
auccguaacuucgggaaaaggauuggcucugagggcuggacagccaacuc
agaacugguacggacaaggggaauccgacuguuuaauuaaaacaaagcau
ugcgauggucccaacggauguuuacgcaaugugauuucugcccagugcuc
ugaugucaaagugaagaaauucaaccaagcgcggguaaacggcgggagua
acuaugacucucuuaagguagccaaaugccucgucaucuaauuagugacg
cgcaugaauggauuaacgagauucccacugucccugucuacuauccagcg
aaaccacagccaagggaacgggcuuggcagaaucagcggggaaagaagac
ccuguugagcuugacucuaguccgacuuugugaaaugacguuauuuuacu
uauuccgugaaucggaagcggguuuuuggacccaaggcucgcuucgcggg
ccgauccgggcggaagacauugucagguggggaguuuggcuggggcggca
caucuguuaaaagauaacgcagguguccuaagaugagcucaacgagaaca
gaaaucucguguggaacagaaggguaaaagcucguuugauucugauuucc
aguacgaauacgaaccgugaaagcguggccuaacgauccuuuagaccuuc
ggaauucgaagcuagaggugucagaaaaguuaccacagggauaacuggcu
uguggcagccaagcguucauagcgacguugcuuuuugauccuucgauguc
ggcucuuccuaucauugugaagcagaauucaccaaguguuggauuguuca
cccaccaauagggaacgugagcuggguuuagaccgucgugagacagguua
guuuuacccuacugaugacagugucgcaauaguaauucaaccuaguacga
gaggaaccguugauucacacaauuggccaucgcgcuugguugaaaagcca
guggcgcgaagcuaccgugugcuggauuaugacugaacgccucuaaguca
gaauccgggcuagaagcgacgcaugcgcccgccguccggccgacccgcag
uaggggccggcccccaagggcacgugucguuggcuaagucgccgcgacgg
aagcgucgcggugaccgccuugaaguacaauuuccaucgagcggcgggua
gaauccuuugcagacgacuuaaacgcgacgggguauuguaaguggcagag
uggccgccacgauccacugagauucagcccuuugucgcuccgauucgu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7qiw Cryo-EM structure and rRNA modification sites of a plant ribosome.
• Resolution: 2.35 Å
• Binding residue (original residue number in PDB): R3 R4 A6 R7 Y9 K13 N14 K15 P16 F22 D35 K39 S61 E63 A64 R90 H92 F94 R98 N100 G114 M115 R116 A118 F119 G120 R154 F157 K158 P160 K175 D193 G194 N196 K198
• Binding residue (residue number reindexed from 1): R2 R3 A5 R6 Y8 K12 N13 K14 P15 F21 D34 K38 S60 E62 A63 R89 H91 F93 R97 N99 G101 M102 R103 A105 F106 G107 R141 F144 K145 P147 K162 D180 G181 N183 K185

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome

Biological Process

• GO:0000027 ribosomal large subunit assembly
• GO:0006412 translation

Cellular Component

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

External links

• PDB: RCSB:7qiw, PDBe:7qiw, PDBj:7qiw
• PDBsum: 7qiw
• PubMed: 35643637
• UniProt: Q3SC85