Structure of PDB 8bsj Chain LB Binding Site BS01

Receptor Information

>8bsj Chain LB (length=374) Species: 5741 (Giardia intestinalis)

SHRKFSCCRKGNLGYLPRKRCTRGRGRCKTFPPDVQGAPIHLTAFLGYKA
GCTHVMRFIDHRLHNRQAIDQATIIDAPPMICTAIIGYAKTPKGLRAVTT
VWAAHIAEPAMRRFYRNYFHAEKTAFSTYMKKAADGTYIKEQLGRLKQHA
DVIRIVAHTQPALTPLKQKKADIMEIQVNGGANVAEKVDYAYALMEKPIS
IKDVFSVGAQIDTISITRGRGFEGVVTRWGVTRLPRKTRRGNRKVACIGA
WHPANVQYTVARAGQMGYFHRTDTNKQVFMIDTAENPRCCTTEFDLTDKS
INPVGGFVNYGRVQGDFIMIKGTCPGPKRRPVVMRNALLPHRNCPPVQLQ
WISTASKFGHGIFETVEERRQFYA

Ligand information

>8bsj Chain Lt (length=2593)

ggcgggccugaggcggcgggggcgacgggcggaacuuaagcauaucagua
cgccccggaggagaaaccaaccgggauuccccgcuagcggcgagcgacgc
gggaggagcccgccccgaaggcgcgcuguggggccgcgagggggcccgag
ggccccgcccgagagggugcaagccccguacggcgaguagcgcugcuuga
gcgugcagcgcgaagggaggcgcggcccuuccaaggcuaaauacgccccg
ggaccgauagcggaccaaguagcgcgagcgaacggugaaaaggacgcccu
gcggccgcucaaaagaccugaacccggccggccgccggcccgccggcccc
gucucgaaacacggaccgaggagccacgcgccgcggcgagcccgagggag
cccccgcggcggagcgagcgcgagacgccccgggcccgccaugccccugc
gggcgugcgcgggccgagccgcggcgcgugggcccgaaaggcggugaucu
augcccggcgagggcgaggccgggcgaaagccugguggaggcccgccgcg
gugcugacgcgcagaucgcucgucggagccgggcaugggggcgaaagacu
caucgaaccgccugguagcugguugccuccgaaaugucucccaggacagc
cgccgccccgcaguugcggcccguagagcgcuggccggcgggagcggggg
gccugccccucgcccgccccccaaacuccgaagggccgcgccgccccgcc
gcuggccugggcggggcgggcgaaugcgggcggcgcgugggccccuccug
guaagcaggacgggcgaggcgggacgauccggacgccgggccagggugcg
ccgccggggcccgcggaacggcgucggccggucccgacagccgaaucggc
cggcccggaaaauggagcgcgccggagccccggacccgcgcccggccgcc
gcgcgcggcggguaggaggccgcagaggccccgggggcgaaggcggcgcg
caggccccgccggaccggccucuggugcagaucucggcagcaguagccgc
uacuccgcgccccggaggacugagggggagacggguuccgcggcgccugc
aucuggccgcgggugacucgggccuaagcggcgggugaagaccgggaagg
ggcgcccgcccgucgaacggggagccggcggagacuccggcaggcgcggc
ccccgcggagacgcccgccccccggcgacgcgcacggggaccgcggcggg
cggcgccccggcccgcgaacgccccgcagcccccggacgccuugcgcgga
gaggggggcccgggggcggaccgcgcguccccggccgccccugaaaagcc
ggggggcgccggccgcgcgccguaccgaccgcagcaggacuccgggguca
gcagccucuagcgcgggagcgaacgcggcucagggaagucggcaagccgg
cuccguaaccucgggaaaaggaguggcucugacggcgccgggucagaacu
ggaacggacgcggggaucccgacuguuuacuagaaacacagcgucgcgag
ggccgcacccggcgcuggcgcgacgugauuucugcccagugccacgaccg
ucaccgugaagcgauccgccgaagcccugguaaacggcgggaguaacuau
gacucucuuaagguagccaaaugccucgucgggcaauuuccgacgugcau
gaauggaccaacgaggaucccacugucccgagccgcgccuccgcgagccu
ccagccucgggaacgggcgagggccggccagcggggcaagaagacccuuu
ugagcuugacuccagcccgggccuguggggcggggcggccggcgcagcgc
acaggggaggccgcgccccugagacacccugacggccgccgccgccccgc
ucacccggucgcgcggggacccgcccgggcggggaguucggcuggggcgg
cgcgccugcuacaccggaccgcaggcgucccacggcgggcucagcgagga
cggagaccucccgcggagcagaagggcacaagcccgcccgacccgcgccc
cccgugccggcgcgggccgcgaaagcggggccuaccgauccuucgccgcc
ccggccgcgggcgcggagguggcagaaaaguuaccacagggauaacuggc
uuguggccgccgagcgcccgcagcgacgcggcuuuuugauccuucgaugu
cggcucuuccuaccguccgcgcgcaccggcgcggaagcgucggauuguuc
acccguucaagggaucgugagcuggguuuagaccgucgugagacagguua
guuuuacccuacuggccccggggccagagcacggcgggccaguacgagag
gaacgcccgccgcgggccgccagccccgcgguugcccggccgggcagcgc
cgcgccgccgcgcccgggggcccugcgcugaccgccucuaagcgcgcacc
ccgccucgcgccccgcccggccgcgcgccccagccccgugccccgucgcc
gagcggcccccgcccggggagaccacccggcgcggcgcuccuguacggcg
cagagcccugcgaucgccugagggacgcgccugcagagcgcgg

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8bsj Insights into translocation mechanism and ribosome evolution from cryo-EM structures of translocation intermediates of Giardia intestinalis.
• Resolution: 6.49 Å
• Binding residue (original residue number in PDB): S2 H3 R4 S7 C9 K11 G12 N13 L14 G15 Y16 L17 P18 R19 K20 R21 T23 R24 R26 R28 K30 T31 C53 H62 R63 Q75 Y92 K97 G98 L99 R100 T103 T104 R117 F118 R120 F123 H124 A129 F130 S131 T132 K136 R158 L170 K171 Q172 K173 K174 E179 T221 R222 G223 R224 G225 F226 G228 T231 R232 T236 R237 R240 K241 T242 R243 R244 G245 R247 K248 A250 C251 I252 G253 A254 W255 H256 A258 N259 V260 Q261 Y262 T263 R266 A267 Q269 Y272 H274 R275 T276 D277 T278 N279 K280 G309 V312 N313 Y314 G315 K325 G326 T327 C328 P329 G330 K332 R333 R334 R339 L343 H345 R346 N347 K361 F362 G363 H364 R373 R374 F376 Y377
• Binding residue (residue number reindexed from 1): S1 H2 R3 S6 C8 K10 G11 N12 L13 G14 Y15 L16 P17 R18 K19 R20 T22 R23 R25 R27 K29 T30 C52 H61 R62 Q71 Y88 K93 G94 L95 R96 T99 T100 R113 F114 R116 F119 H120 A125 F126 S127 T128 K132 R154 L166 K167 Q168 K169 K170 E175 T217 R218 G219 R220 G221 F222 G224 T227 R228 T232 R233 R236 K237 T238 R239 R240 G241 R243 K244 A246 C247 I248 G249 A250 W251 H252 A254 N255 V256 Q257 Y258 T259 R262 A263 Q265 Y268 H270 R271 T272 D273 T274 N275 K276 G305 V308 N309 Y310 G311 K321 G322 T323 C324 P325 G326 K328 R329 R330 R335 L339 H341 R342 N343 K357 F358 G359 H360 R369 R370 F372 Y373

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:8bsj, PDBe:8bsj, PDBj:8bsj
• PDBsum: 8bsj
• PubMed: 36912103
• UniProt: A8BRZ3