Structure of PDB 7qiw Chain p Binding Site BS02

Receptor Information

>7qiw Chain p (length=99) Species: 4081 (Solanum lycopersicum)

VNVPKTKKTYCKSKECKKHTLHKVTQYKKGKDSLAAQGKRRYDRKQSGYG
GQTKPVFHKKAKTTKKIVLRLQCQGCKHVSQHPIKRCKHFEIGGDKKGK

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): V2 N3 P5 K8 K9 Y11 K13 K19 H20 Y28 K30 G31 D33 S34 A37 Q38 G39 R41 R42 R45 K46 G49 Y50 G52 Q53 K55 P56 V57 F58 K60 A62 K63 T65 K66 K67 V69 R71 H79 V80 Q82 H83 P84 K86 C88 K89 K97 K98
• Binding residue (residue number reindexed from 1): V1 N2 P4 K7 K8 Y10 K12 K18 H19 Y27 K29 G30 D32 S33 A36 Q37 G38 R40 R41 R44 K45 G48 Y49 G51 Q52 K54 P55 V56 F57 K59 A61 K62 T64 K65 K66 V68 R70 H78 V79 Q81 H82 P83 K85 C87 K88 K96 K97

Gene Ontology

Molecular Function

• 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:7qiw, PDBe:7qiw, PDBj:7qiw
• PDBsum: 7qiw
• PubMed: 35643637
• UniProt: A0A3Q7H1I0