Structure of PDB 7jil Chain B Binding Site BS01

Receptor Information

>7jil Chain B (length=271) Species: 986 (Flavobacterium johnsoniae)

VRKLKPITPGQRFRVVNGYDAITTDKPERSLISPIKNSGGRNSQGKMTMR
YTGGGHKQRYRIIDFKRTKDGIPATVKSIEYDPNRTAFIALLAYADGEKT
YIIAQNGLKVGQKLVSGPESQPEIGNTLPLSRIPLGTVISCIELRPGQGA
VIARSAGTFAQLMARDGKYATIKMPSGETRLILLTCSATIGEVSNSDHQL
VVSGKAGRTRWLGRRPRTRPVAMNPVDHPMGGGEGRSSGGHPRSRNGLPA
KGYRTRSKKNPSNKYIVERRK

Ligand information

>7jil Chain 1 (length=2742)

aaauaagggcguauggggaaugccuaggcucucagaggcgaugaaggacg
ugauaagcugcgaaaagcugcggggacuggcacacacagauugauccgca
gauauccgaauggggcaacccgcuauauugaagauauagcacaccgauag
gugggcaaacccgcugaacugaaacaucuaaguaggcggaggagaagaaa
acaaaagugauuccguaaguaguggcgagcgaacgcggauuagcccaaac
cagugcuacggcagugcugggguuguaacaugcagaaccggaaguuacug
gaaagugacgccaaagagggugauagccccguauggguaauaaauguggu
auccugaguagggcgggacacgugaaacccugucugaauucggcgggacc
auccgcuaaggcuaaauacuccugagagaccgauagugaaccaguaccgu
gagggaaaggugaaaagaaccgugaauaacggagugaaauagauccugaa
accauacgcuuacaagcggucggagcccuuucguggggugacggcgugcc
uuuugcauaaugagccuacgaguuaacgcugcuggcaaggauaaguacuu
caguacggauccgcagcgaaagcgagucugaauagggcgcuuuagucagu
aguguuagacgcgaaaccgugugaucuacccaugggcagguugaagcugu
gguaacacacaguggaggaccgaaccgguugacguugaaaagucuucgga
ugaccuguggguaggggugaaaggccaaucaaacucggaaauagcucgua
cuccccgaaaugcauuuaggugcagcguuaguuauaaaguuauacagagg
uagagcuacugauuggaugcgggggcuucaccgcccaccaauuccugaca
aacuccgaaugcuguauaauguucacuaacagugagggcuugggugcuaa
gguccaaguccgagagggaaagaacccagaccaucagcuaagguccccaa
auauaugcuaaguugaaagaacgagguuugucugcccagacagcuaggau
guuggcuuggaagcagcccauuuaaagagcguaacagcucacuagucgag
cggacgagcauggauaauaaucgggcauaagcauauuaccgaagcuaugg
auuugcaaguuugcaagugguaggggagcauucuaacaggguugaagguu
uuucguaaggagggcuggacugguuagaaaagaaaauguaggcauaagua
acgauaaugcgggcgagaaacccgcacaccgaaaaacuaagguuuccaca
gcuaugcuaaucagcuguggguuagucugguccuaaggcgaacccgaaag
ggacagucgauggcuaacggguuaauauucccguacuacuaauuacugug
auggggugacggagugaugaaagcgccgcgaacugacggaauaguucguu
gaaguaccuagcuauagguccuguaguaaaaugcgcaggaacuggugaaa
uacgauaguacucggagucgacaaagagauagugcgccuaagggcuucca
agaaaaaccucuaaacuucagguaauuaguaccaguaccguaaaccgaca
cagguaguugaggagagaauccuaaggugcucgagauauucauggcuaag
gaauuaggcaaaauagaccuguaacuucgggagaaaggucgcccugagca
aucagggccgcagugaagagguccaggcgacuguuuaucaaaaacacagg
gcucugcaaaaucguaagaugaaguauagggccugacaccugcccggugc
uggaagguuaagaggagauguuaucuucggagaagcauugaauugaagcc
ccaguaaacggcggccguaacuauaacgguccuaagguagcgaaauuccu
ugucggguaaguuccgaccugcacgaaugguguaacgaucuggacacugu
cucagccaugagcucggugaaauuguaguaacggugaagaugccguuuac
ccgcagugggacgaaaagacccugugcaccuuuacuauagcuuaguacug
accuuggauaaauguuuaucugaggccuaaccucgcugcgggggacagug
cuugguggguaguuugacugggguggucgccuccaaaagaguaacggagg
cuucuaaagguucccucaguacgcuugguaaccgugcguagagugcaaug
gcauaagggagcuugacugagagacauacaggucgaucagguacgaaagu
agagcauagugauccggugguuccgcauggaagggccaucgcucaaagga
uaaaagguacgccggggauaacaggcugaucucccccaagaguucauauc
gacggggggguuuggcaccucgaugucggcucgucacauccuggggcugg
agaaggucccaaggguugggcuguucgcccauuaaagugguacgcgagcu
ggguucagaacgucgugagacaguucggucucuaucuacugcgggcguua
gaaauuugaguggaucugauucuaguacgagaggaccgaauuggacuaac
cucuaguguaucuguugucccgccaggggcaccgcagaguagcuacguug
ggaagggauaagcgcugaaagcauauaagcgcgaaacccaccacaagaug
agauuucuuuuaaggaucguggaagaugaccacguugauaggcuauagau
guaaaggcaguaaugucauagucgaguaguacuaauaauccg

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7jil Structural basis of sequestration of the anti-Shine-Dalgarno sequence in the Bacteroidetes ribosome.
• Resolution: 2.8 Å
• Binding residue (original residue number in PDB): K7 P8 I9 P11 G12 R14 F15 R31 P36 N39 G42 R43 N44 S45 Q46 G47 K48 M49 T50 M51 G55 H58 K59 Q60 R61 Y62 R63 Y83 P85 R87 D98 G99 K101 R147 V153 A155 R156 S157 A158 G159 T160 K170 Y171 M176 P177 S178 E180 R182 H200 Q201 G206 K207 A208 G209 T211 R212 W213 R216 R217 P218 R219 T220 R221 P222 V223 A224 M225 N226 V228 D229 G234 G235 E236 R238 S239 S240 H243 S246 A252 K253 G254 Y255 R256 T257 R258 K261 S264 R271 K273
• Binding residue (residue number reindexed from 1): K5 P6 I7 P9 G10 R12 F13 R29 P34 N37 G40 R41 N42 S43 Q44 G45 K46 M47 T48 M49 G53 H56 K57 Q58 R59 Y60 R61 Y81 P83 R85 D96 G97 K99 R145 V151 A153 R154 S155 A156 G157 T158 K168 Y169 M174 P175 S176 E178 R180 H198 Q199 G204 K205 A206 G207 T209 R210 W211 R214 R215 P216 R217 T218 R219 P220 V221 A222 M223 N224 V226 D227 G232 G233 E234 R236 S237 S238 H241 S244 A250 K251 G252 Y253 R254 T255 R256 K259 S262 R269 K271

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0016740 transferase activity
• GO:0019843 rRNA binding

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006412 translation

Cellular Component

• GO:0005840 ribosome
• GO:0015934 large ribosomal subunit
• GO:0022625 cytosolic large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:7jil, PDBe:7jil, PDBj:7jil
• PDBsum: 7jil
• PubMed: 33330920
• UniProt: A0A1B2U0Q0