Structure of PDB 6bz6 Chain RX Binding Site BS01

Receptor Information

>6bz6 Chain RX (length=92) Species: 300852 (Thermus thermophilus HB8)

TAYDVILAPVLSEKAYAGFAEGKYTFWVHPKATKTEIKNAVETAFKVKVV
KVNTLHVRGKKKRLGRYLGKRPDRKKAIVQVAPGQKIEALEG

Ligand information

>6bz6 Chain RA (length=2882)

agaugguaagggcccacgguggaugccucggcacccgagccgaugaagga
cguggcuaccugcgauaagccagggggagccgguagcgggcguggauccc
uggauguccgaaugggggaacccggccggcgggaacgccggucaccgcgc
ugcgcggggggaaccuggggaacugaaacaucucaguacccagaggagag
gaaagagaaaucgacucccugaguagcggcgagcgaaaggggaccagccu
aaaccguccggcuuguccgggcggggucguggggcccucggacaccgaau
ccccagccuagccgaagcuguugggaagcagcgccagagagggugaaagc
cccguaggcgaaagguggggggauaggugaggguacccgaguaccccgug
guucguggagccaugggggaaucugggcggaccaccgccuaaggcuaagu
acuccgggugaccgauagcgcaccaguaccgugagggaaaggugaaaaga
accccgggaggggagugaaauagagccugaaaccgugggcuuacaagcag
ucacggccccgcaagggguuguggcgugccuauugaagcaugagccggcg
acucacggucgugggcgagcuuaagccguugaggcggaggcguagggaaa
ccgaguccgaacagggcgcaagcgcaaaguccgcggccguggacccgaaa
ccgggcgagcuagcccuggccagggugaagcuggggugagacccagugga
ggcccgaaccggugggggaugcaaaccccucggaugagcuggggcuagga
gugaaaagcuaaccgagcccggagauagcugguucuccccgaaaugacuu
uagggucagccucaggcgcugacuggggccuguagagcacugauagggcu
agggggcccaccagccuaccaaacccugucaaacuccgaagggucccagg
uggagccugggagugagggcgcgagcgauaacguccgcguccgagcgcgg
gaacaaccgagaccgccagcuaaggcccccaagucugggcuaagugguaa
aggauguggcgccgcgaagacagccaggagguuggcuuagaagcagccau
ccuuuaaagagugcguaauagcucacuggucgaguggcgccgcgccgaaa
augaucggggcuuaagcccagcgccgaagcugcgggucugggggaugacc
ccaggcgguaggggagcguucccgaugccgaugaaggccgacccgcgagg
gcggcuggagguaagggaagugcgaaugccggcaugaguaacgauaaaga
gggugagaaucccucucgccguaagcccaaggguuccuacgcaauggucg
ucagcguaggguuaggcgggaccuaaggugaagccgaaaggcguagccga
agggcagccgguuaauauuccggcccuucccgcaggugcgauggggggac
gcucuaggcuagggggaccggagccauggacgagcccggccagaagcgca
gggugggagguaggcaaauccgccucccaacaagcucugcguggugggga
agcccguacgggugacaaccccccgaagccagggagccaagaaaagccuc
uaagcacaaccugcgggaacccguaccgcaaaccgacacaggugggcggg
ugcaagagcacucaggcgcgcgggagaacccucgccaaggaacucugcaa
guuggccccguaacuucgggagaaggggugcucccuggggugaugagccc
cggggagccgcagugaacaggcucuggcgacuguuuaccaaaaacacagc
ucucugcgaacucguaagaggagguauagggagcgacgcuugcccggugc
cggaaggucaaggggaggggugcaagccccgaaccgaagccccggugaac
ggcggccguaacuauaacgguccuaagguagcgaaauuccuugucgggua
aguuccgaccugcacgaaaagcguaacgaccggagcgcugucucggcgag
ggacccggugaaauugaacuggccgugaagaugcggccuacccguggcag
gacgaaaagaccccguggagcuuuacugcagccugguguuggcucuuggu
cgcgccugcguaggauaggugggagccugugaacccccgccuccgggugg
gggggaggcgccggugaaauaccacccuggcgcggcugggggccuaaccc
ucggauggggggacagcgcuuggcgggcaguuugacuggggcggucgccu
ccuaaaagguaacggaggcgcccaaagguccccucaggcgggacggaaau
ccgccggagagcgcaaggguagaagggggccugacugcgaggccugcaag
ccgagcaggggcgaaagccgggccuagugaaccgguggucccguguggaa
gggccaucgaucaacggauaaaaguuaccccggggauaacaggcugaucu
cccccgagcguccacagcggcggggagguuuggcaccucgaugucggcuc
gucgcauccuggggcugaagaaggucccaaggguugggcuguucgcccau
uaaagcggcacgcgagcuggguucagaacgucgugagacaguucggucuc
uauccgccacgggcgcaggaggcuugaggggggcucuuccuaguacgaga
ggaccggaagggacgcaccucugguuucccagcugucccuccaggggcau
aagcuggguagccaugugcggaagggauaaccgcugaaagcaucuaagcg
ggaagcccgccccaagaugaggccucccacggcgucaagccgguaaggac
ccgggaagaccacccgguggaugggccggggguguaagcgccgcgaggcg
uugagccgaccggucccaaucguccgaggucu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6bz6 Ribosomal ambiguity (ram) mutations promote the open (off) to closed (on) transition and thereby increase miscoding.
• Resolution: 3.18 Å
• Binding residue (original residue number in PDB): S14 K16 K25 T35 K36 T37 K40 N41 E44 N55 T56 H58 R60 K62 K64 Y69 G71 K72 P74 D75 K78
• Binding residue (residue number reindexed from 1): S12 K14 K23 T33 K34 T35 K38 N39 E42 N53 T54 H56 R58 K60 K62 Y67 G69 K70 P72 D73 K76

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome
• GO:0019843 rRNA binding

Biological Process

• GO:0000027 ribosomal large subunit assembly
• GO:0006412 translation

Cellular Component

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

External links

• PDB: RCSB:6bz6, PDBe:6bz6, PDBj:6bz6
• PDBsum: 6bz6
• PubMed: 30476222
• UniProt: Q5SHP0|RL23_THET8 Large ribosomal subunit protein uL23 (Gene Name=rplW)