Structure of PDB 8brm Chain LA Binding Site BS01

Receptor Information

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

GRRIRVQRKGAGSVFRAHVARRLGAAKLRANDFAERTGSVRGVVKAILHD
RGRGAPLARVQFPNMRGEGRVNELFIAPEGMYTGQEVFSGNKATLHIGNI
LPVGNIPEGTYVCNVEEKPMDRGCLARASGTYCLVVAHNMETNKTRIRLP
SGQKKLISSKARAMIGLVAGGGRTDKPLLKAGNAYHKYKAKRNCWPVVRG
VAMNPVDHPHGGGNHQHIGVSSCVPRNAVPGQKVGLIAARRTGCSGGKRR

Ligand information

>8brm Chain Lt (length=2594)

ggcgggccugaggcggcgggggcgacgggcggaacuuaagcauaucagua
cgccccggaggagaaaccaaccgggauuccccgcuagcggcgagcgacgc
gggaggagcccgccccgaaggcgcgcuguggggccgcgagggggcccgag
ggccccgcccgagagggugcaagccccguacggcgaguagcgcugcuuga
gcgugcagcgcgaagggaggcgcggcccuuccaaggcuaaauacgccccg
ggaccgauagcggaccaaguagcgcgagcgaacggugaaaaggacgcccu
gcggccgcucaaaagaccugaacccggccggccgccggcccgccggcccc
gucucgaaacacggaccgaggagccacgcgccgcggcgagcccgagggag
cccccgcggcggagcgagcgcgagacgccccgggcccgccaugccccugc
gggcgugcgcgggccgagccgcggcgcgugggcccgaaaggcggugaucu
augcccggcgagggcgaggccgggcgaaagccugguggaggcccgccgcg
gugcugacgcgcagaucgcucgucggagccgggcaugggggcgaaagacu
caucgaaccgccugguagcugguugccuccgaaaugucucccaggacagc
cgccgccccgcaguugcggcccguagagcgcuggccggcgggagcggggg
gccugccccucgcccgccccccaaacuccgaagggccgcgccgccccgcc
gcuggccugggcggggcgggcgaaugcgggcggcgcgugggccccuccug
guaagcaggacgggcgaggcgggacgauccggacgccgggccagggugcg
ccgccggggcccgcggaacggcgucggccggucccgacagccgaaucggc
cggcccggaaaauggagcgcgccggagccccggacccgcgcccggccgcc
gcgcgcggcggguaggaggccgcagaggccccgggggcgaaggcggcgcg
caggccccgccggaccggccucuggugcagaucucggcagcaguagccgc
uacuccgcgccccggaggacugagggggagacggguuccgcggcgccugc
aucuggccgcgggugacucgggccuaagcggcgggugaagaccgggaagg
ggcgugcccgcccgucgaacggggagccggcggagacuccggcaggcgcg
gcccccgcggagacgcccgccccccggcgacgcgcacggggaccgcggcg
ggcggcgccccggcccgcgaacgccccgcagcccccggacgccuugcgcg
gagaggggggcccgggggcggaccgcgcguccccggccgccccugaaaag
ccggggggcgccggccgcgcgccguaccgaccgcagcaggacuccggggu
cagcagccucuagcgcgggagcgaacgcggcucagggaagucggcaagcc
ggcuccguaaccucgggaaaaggaguggcucugacggcccgggucagaac
uggaacggacgcggggaucccgacuguuuacuagaaacacagcgucgcga
gggccgcacccggcgcuggcgcgacgugauuucugcccagugccacgacc
gucaccgugaagcgauccgccgaagcccugguaaacggcgggaguaacua
ugacucucuuaagguagccaaaugccucgucgggcaauuuccgacgugca
ugaauggaccaacgaggaucccacugucccgagccgcgccuccgcgagcc
uccagccucgggaacgggcgagggccggccagcggggcaagaagacccuu
uugagcuugacuccagcccgggccuguggggcggggcggccggcgcagcg
cacaggggaggccgcgccccugagacacccugacggccgccgccgccccg
cucacccggucgcgcggggacccgcccgggcggggaguucggcuggggcg
gcgcgccugcuacaccggaccgcaggcgucccacggcgggcucagcgagg
acggagaccucccgcggagcagaagggcacaagcccgcccgacccgcgcc
ccccgugccggcgcgggccgcgaaagcggggccuaccgauccuucgccgc
cccggccgcgggcgcggagguggcagaaaaguuaccacagggauaacugg
cuuguggccgccgagcgcccgcagcgacgcggcuuuuugauccuucgaug
ucggcucuuccuaccguccgcgcgcaccggcgcggaagcgucggauuguu
cacccguucaagggaucgugagcuggguuuagaccgucgugagacagguu
aguuuuacccuacuggccccggggccagagcacggcgggccaguacgaga
ggaacgcccgccgcgggccgccagccccgcgguugcccggccgggcagcg
ccgcgccgccgcgcccgggggcccugcgcugaccgccucuaagcgcgcac
cccgccucgcgccccgcccggccgcgcgccccagccccgugccccgucgc
cgagcggcccccgcccggggagaccacccggcgcggcgcuccuguacggc
gcagagcccugcgaucgccugagggacgcgccugcagagcgcgg

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8brm Insights into translocation mechanism and ribosome evolution from cryo-EM structures of translocation intermediates of Giardia intestinalis.
• Resolution: 3.33 Å
• Binding residue (original residue number in PDB): G2 R3 R4 V7 Q8 R9 K10 G11 A12 S14 V15 F16 R17 A18 H19 V20 R22 R23 G25 F34 R37 H50 R52 R54 R67 G70 R71 E118 K119 M121 R123 C125 L126 A127 R128 A129 S130 G131 T132 L150 P151 S152 K156 G172 G173 R174 T175 K177 L179 L180 K181 A182 G183 Y186 H187 K188 R193 W196 P197 V198 V199 R200 G201 V202 A203 M204 N205 V207 D208 H209 H211 G213 G214 N215 H216 Q217 H218 G220 V221 S222 S223 C224 P226 R227 N228 V230 P231 G232 Q233 K234 V235 G236 L237 I238 A239 A240 R241 R242 T243 G244 C245 K249
• Binding residue (residue number reindexed from 1): G1 R2 R3 V6 Q7 R8 K9 G10 A11 S13 V14 F15 R16 A17 H18 V19 R21 R22 G24 F33 R36 H49 R51 R53 R66 G69 R70 E117 K118 M120 R122 C124 L125 A126 R127 A128 S129 G130 T131 L149 P150 S151 K155 G171 G172 R173 T174 K176 L178 L179 K180 A181 G182 Y185 H186 K187 R192 W195 P196 V197 V198 R199 G200 V201 A202 M203 N204 V206 D207 H208 H210 G212 G213 N214 H215 Q216 H217 G219 V220 S221 S222 C223 P225 R226 N227 V229 P230 G231 Q232 K233 V234 G235 L236 I237 A238 A239 R240 R241 T242 G243 C244 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:8brm, PDBe:8brm, PDBj:8brm
• PDBsum: 8brm
• PubMed: 36912103
• UniProt: E2RTN4