Structure of PDB 8br8 Chain Lb Binding Site BS01

Receptor Information

>8br8 Chain Lb (length=148) Species: 184922 (Giardia lamblia ATCC 50803)

PTRIRKSRKRRGHRQMGYGRVGGHRKHPSGRGKAGGLQHKRTSFDKYHPG
YFGKLGMRNYHVRRNIEYNPTINIDKIWSLIPEEQRDGFLQRKSTTEAPV
VDVTRFGFFKVLGRGSLPQCPIIIKARYFSSDAEKKLREVGGVPLLVP

Ligand information

>8br8 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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..>>>............................<<<<<<..>>>>>>.<<
<<........>>>>.<<<<<....<<<<<<<<<<<<<..<<<...<<<..
..>>>..>>>...<<....>>............<<<<<<<<<<<<<....
>>>>>>>.>>>>>>...>>>>>>>>>>>>>..<<.<..<<<<<<<.....
<<<<<<<<<..<<<....<<<<<<<....>>>>>>>.....>>>...<<<
<.<<.<<........>>>>>>>>....>>>>>>>>>...<<.......>>
......>>>>>>...>..>.>>..<<<<<<....<<<<<....>>>>><<
<<<<<<<<.<<<.<<<<<<<<<...<<<...<<<..<<<<<<..<<<<<<
......>>>>>>>>>>>>..>>>..>>.>...>>>>>>>.<<<<<<<<<<
.........>>>>>>>>>>...>>>>>>>>>>>>>.>>..<<<<.<<<<<
.....>>>>>.>>>>....<<<......>>>...<<<<<<<..<<<<(((
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<....>>>>>....>>>>>>..<<<<<<<<...<<......<<<<<.<<.
...>>.>>>>>...>>>>>>>>>>........>>>>>.<<.....<<...
..<<<<<.....>>>>>..<<.....<<<<..<<...<<<<<<...<...
....>.>>>>>>....((<<<.<<...<<<...<<<....>>>......<
<....>>...>>.>....>>...<<<<<........>>>>>))<<<<<<<
<...<<<....>>>..<<<<<<<<<<...<<<..<<<<<<<<<<<<<<<<
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...>>>>>>...>>>>>>..>>>>>.>>>>>>>..>>>.........>>>
>>>>>>>...>>>>>>>>.>>>..>>..<<......>>.>>>>.<<<<..
...>>>>..>>....<<<<....<<<<<<<<.<<.........<.....<
<<<<....<<..>>.....>>>>><<.<<<<<<<....>>..>>>>>.>>
............<<<<<<<<<..<<<.........>>>..<<<<<<<...
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.>>>>>>........<...........<<<<<<.....>>>>>>.....>
.....>>....>>.>>>>>>>..>..>>.>>>>>>>>.>>>>>>....>>
.(..<<<<<......).>>>>>...((((((..{{{.........{{{..
{{[[[[..<<<<<.<<<<<<<<..<<<<<<<<<<<<<<<<<.........
.<<<<<....................>>>>>.>>>>>>>>.>>>>>>>>>
...<<<<......>>>>.....>>>>>>>>..>>>>>...<<<.....>>
>..<<<<<<...........>>>>>>..<<...<<<<<<<...<.<<<<.
......>>>>.>.....<<...(((>>....>>>>>>>...<<<<<<<<.
........>>>>>>>>.<<<....>>>.>>)))......((((((.((((
(.>>>>>>))))))))))).........]]]]..}}.}}}.......<<.
<...<<<<<<...<<.......>>...>>>>>>....>.>.>.......<
<<<<.<<<<<<..<<<<<<<<<......>>>>>>..>>>.<<<.<.....
>.>>>....>>>>>..>...>>>.>>....<<<<<<<....>>>.>>>>.
.......}}}.))))))..<<<<<..<<<..<<<<<<<<...........
....>>>>>>>><<<<<...<.<<...<<<<<<<<<<}}}.>>>>>..>>
>>>...>>.>.>>>>>.<<<...<<<<<<...........>>>>>>...>
>>..>>>..>>>>><...<<<<<<..........................
..>>>>>>..><<.<<<<.......>>>>..<<<<<<<<<<<....<<<<
....<<...>>...>>>>...>>>>.>>>>>.>>.....>>..

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8br8 Insights into translocation mechanism and ribosome evolution from cryo-EM structures of translocation intermediates of Giardia intestinalis.
• Resolution: 3.35 Å
• Binding residue (original residue number in PDB): P2 T3 R4 I5 R6 K7 S8 R9 K10 R11 R12 G13 R15 Q16 M17 G18 Y19 G20 R21 V22 G23 H25 R26 K27 H28 P29 S30 G31 R32 G33 K34 A35 Q39 H40 R42 T43 S44 K47 Y48 Y52 F53 G54 K55 L56 G57 M58 R59 N60 Y61 H62 V63 R64 R65 N66 I67 T72 N74 K77 K111 L113 G114 R115 R128 Y129 S131 S132 D133
• Binding residue (residue number reindexed from 1): P1 T2 R3 I4 R5 K6 S7 R8 K9 R10 R11 G12 R14 Q15 M16 G17 Y18 G19 R20 V21 G22 H24 R25 K26 H27 P28 S29 G30 R31 G32 K33 A34 Q38 H39 R41 T42 S43 K46 Y47 Y51 F52 G53 K54 L55 G56 M57 R58 N59 Y60 H61 V62 R63 R64 N65 I66 T71 N73 K76 K110 L112 G113 R114 R127 Y128 S130 S131 D132

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome

Biological Process

• GO:0006412 translation

Cellular Component

• GO:0005737 cytoplasm
• GO:0005840 ribosome
• GO:0015934 large ribosomal subunit
• GO:0022625 cytosolic large ribosomal subunit
• GO:0043232 intracellular non-membrane-bounded organelle
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8br8, PDBe:8br8, PDBj:8br8
• PDBsum: 8br8
• PubMed: 36912103
• UniProt: A8BZ78