Structure of PDB 8btd Chain LA Binding Site BS01

Receptor Information

>8btd Chain LA (length=250) Species: 184922 (Giardia lamblia ATCC 50803)

GRRIRVQRKGAGSVFRAHVARRLGAAKLRANDFAERTGSVRGVVKAILHD
RGRGAPLARVQFPNMRGEGRVNELFIAPEGMYTGQEVFSGNKATLHIGNI
LPVGNIPEGTYVCNVEEKPMDRGCLARASGTYCLVVAHNMETNKTRIRLP
SGQKKLISSKARAMIGLVAGGGRTDKPLLKAGNAYHKYKAKRNCWPVVRG
VAMNPVDHPHGGGNHQHIGVSSCVPRNAVPGQKVGLIAARRTGCSGGKRR

Ligand information

>8btd 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

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8btd Insights into translocation mechanism and ribosome evolution from cryo-EM structures of translocation intermediates of Giardia intestinalis.
• Resolution: 4.9 Å
• Binding residue (original residue number in PDB): G2 R3 R4 V7 Q8 R9 G11 S14 V15 F16 A18 H19 V20 R22 R23 G25 F34 R37 H50 R52 R54 M66 R67 E69 G70 E118 K119 P120 M121 R123 C125 L126 A127 R128 A129 S130 G131 T132 L150 P151 S152 Q154 K156 G173 R174 T175 K177 L179 L180 K181 A182 G183 H187 K188 K190 R193 N194 W196 P197 V198 V199 R200 G201 V202 M204 N205 P206 V207 D208 H209 H211 G213 G214 N215 H216 Q217 H218 V221 S222 S223 C224 P226 R227 N228 V230 P231 G232 Q233 K234 V235 G236 L237 I238 A239 A240 R241 R242 T243 G244 K249
• Binding residue (residue number reindexed from 1): G1 R2 R3 V6 Q7 R8 G10 S13 V14 F15 A17 H18 V19 R21 R22 G24 F33 R36 H49 R51 R53 M65 R66 E68 G69 E117 K118 P119 M120 R122 C124 L125 A126 R127 A128 S129 G130 T131 L149 P150 S151 Q153 K155 G172 R173 T174 K176 L178 L179 K180 A181 G182 H186 K187 K189 R192 N193 W195 P196 V197 V198 R199 G200 V201 M203 N204 P205 V206 D207 H208 H210 G212 G213 N214 H215 Q216 H217 V220 S221 S222 C223 P225 R226 N227 V229 P230 G231 Q232 K233 V234 G235 L236 I237 A238 A239 R240 R241 T242 G243 K248

Gene Ontology

Molecular Function

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

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006412 translation

Cellular Component

• GO:0005840 ribosome
• GO:0022625 cytosolic large ribosomal subunit
• GO:0022626 cytosolic ribosome
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8btd, PDBe:8btd, PDBj:8btd
• PDBsum: 8btd
• PubMed: 36912103
• UniProt: E2RTN4