Structure of PDB 4yzv Chain RY Binding Site BS01

Receptor Information
>4yzv Chain RY (length=102) Species: 300852 (Thermus thermophilus HB8) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
RVKMHVKKGDTVLVASGKYKGRVGKVKEVLPKKYAVIVEGVNIVKKAVRV
SPKYPQGGFIEKEAPLHASKVRPICPACGKPTRVRKKFLENGKKIRVCAK
CG
Ligand information
>4yzv Chain RA (length=2891) [Search RNA sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
agaugguaagggcccacgguggaugccucggcacccgagccgaugaagga
cguggcuaccugcgauaagccagggggagccgguagcgggcguggauccc
uggauguccgaaugggggaacccggccggcgggaacgccggucaccgcgc
gcgcggggggaaccuggggaacugaaacaucucaguacccagaggagagg
aaagagaaaucgacucccugaguagcggcgagcgaaaggggaccagccua
aaccguccggcuuguccgggcggggucguggggcccucggacaccgaauc
cccagccuagccgaagcuguugggaagcagcgccagagagggugaaagcc
ccguaggcgaaagguggggggauaggugaggguacccgaguaccccgugg
uucguggagccaugggggaaucugggcggaccaccgccuaaggcuaagua
cuccgggugaccgauagcgcaccaguaccgugagggaaaggugaaaagaa
ccccgggaggggagugaaauagagccugaaaccgugggcuuacaagcagu
cacggccccgcaagggguuguggcgugccuauugaagcaugagccggcga
cucacggucgugggcgagcuuaagccguugaggcggaggcguagggaaac
cgaguccgaacagggcgcaagcgggccggcccgcaaaguccgcggccgug
gacccgaaaccgggcgagcuagcccuggccagggugaagcuggggugaga
cccaguggaggcccgaaccggugggggaugcaaaccccucggaugagcug
gggcuaggagugaaaagcuaaccgagcccggagauagcugguucuccccg
aaaugacuuuagggucagccucaggcgcugacuggggccuguagagcacu
gauagggcuagggggcccaccagccuaccaaacccugucaaacuccgaag
ggucccagguggagccugggagugagggcgcgagcgauaacguccgcguc
cgagcgcgggaacaaccgagaccgccagcuaaggcccccaagucugggcu
aagugguaaaggauguggcgccgcgaagacagccaggagguuggcuuaga
agcagccauccuuuaaagagugcguaauagcucacuggucgaguggcgcc
gcgccgaaaaugaucggggcuuaagcccagcgccgaagcugcgggucugg
gggaugaccccaggcgguaggggagcguucccgaugccgaugaaggccga
cccgcgagggcggcuggagguaagggaagugcgaaugccggcaugaguaa
cgauaaagagggugagaaucccucucgccguaagcccaaggguuccuacg
caauggucgucagcguaggguuaggcgggaccuaaggugaagccgaaagg
cguagccgaagggcagccgguuaauauuccggcccuucccgcaggugcga
uggggggacgcucuaggcuagggggaccggagccauggacgagcccggcc
agaagcgcagggugggagguaggcaaauccgccucccaacaagcucugcg
ugguggggaagcccguacgggugacaaccccccgaagccagggagccaag
aaaagccucuaagcacaaccugcgggaacccguaccgcaaaccgacacag
gugggcgggugcaagagcacucaggcgcgcgggagaacccucgccaagga
acucugcaaguuggccccguaacuucgggagaaggggugcucccuggggu
gaugagccccggggagccgcagugaacaggcucuggcgacuguuuaccaa
aaacacagcucucugcgaacucguaagaggagguauagggagcgacgcuu
gcccggugccggaaggucaaggggaggggugcaagccccgaaccgaagcc
ccggugaacggcggccguaacuauaacgguccuaagguagcgaaauuccu
ugucggguaaguuccgaccugcacgaaaagcguaacgaccggagcgcugu
cucggcgagggacccggugaaauugaacuggccgugaagaugcggccuac
ccguggcaggacgaaaagaccccguggagcuuuacugcagccugguguug
gcucuuggucgcgccugcguaggauaggugggagccugugaacccccgcc
uccgggugggggggaggcgccggugaaauaccacccuggcgcggcugggg
gccuaacccucggauggggggacagcgcuuggcgggcaguuugacugggg
cggucgccuccuaaaagguaacggaggcgcccaaagguccccucaggcgg
gacggaaauccgccggagagcgcaaggguagaagggggccugacugcgag
gccugcaagccgagcaggggcgaaagccgggccuagugaaccgguggucc
cguguggaagggccaucgaucaacggauaaaaguuaccccggggauaaca
ggcugaucucccccgagcguccacagcggcggggagguuuggcaccucga
ugucggcucgucgcauccuggggcugaagaaggucccaaggguugggcug
uucgcccauuaaagcggcacgcgagcuggguucagaacgucgugagacag
uucggucucuauccgccacgggcgcaggaggcuugaggggggcucuuccu
aguacgagaggaccggaagggacgcaccucugguuucccagcugucccuc
caggggcauaagcuggguagccaugugcggaagggauaaccgcugaaagc
aucuaagcgggaagcccgccccaagaugaggccucccacggcgucaagcc
gguaaggacccgggaagaccacccgguggaugggccggggguguaagcgc
cgcgaggcguugagccgaccggucccaaucguccgaggucu
<<<......<<<<<<<<<<<.....<<..<<<<<<<<<<<<......<<<
<<<.((..((.>>>.....<<<<<<<..<<<))..)).>>>.....>>>>
>>>...>>>....<<<....>>><<<<<<<<....>>>>>>>>.<<<<<.
.>>>>>.>>....<<<<<.....<......>......>>>>>........
...<<....>>...<<<<<.....<<.....>>....>>>>>...<<<..
..<<<<<<<<.....>>>>>>>>......<<<<<<<<<....<<<...<<
<<<.<<<<.<<<...<<<<<......>>>>>((......<<<.....))>
>>...>>>...>>>>..>>>>>..>>>>>>>>>.>>>.....<<<<<<<<
<.......>>>>>>>>>......<<<<<..((((>>>>>..>>>......
>>.>>>>>>.>>...............<<....>>....>>.........
<<<<....>>>>..................>>>>>>>>>>>.......<<
<<<<<<<<<....>>>>>>>>>>>...<............>.<<<<<<..
..<<<<<<<<<<<<<..<<<...<<<.....>>>...>>>...<<....>
>..<<<<.....>>>>....<<<<<<..>>>>>>...>>>>>>>>>>>>>
..<<.<...<<<<<<.....<<<<<<<<<..<<<....<<<<<<......
>>>>>>.....>>>...<<<..<<<<........>>>>.>>>....>>>>
>>>>>...<<<.....>>>......>>>>>>......>.>>..<<<<<<.
...<<<<<....>>>>><<<<<<<<<.....<<<<<<<<<...<<<...<
<<<<<<<.<.<<<<<<......>>>>.>>>..>>>>>>>>..>>.>...>
>>>>>>>>.....>>>>>>>.>>..<<<<<<<.<<......>>.>>>>>>
>.....<<<......>>>...<<<<.<<<...<<<(((.....<<<<<<.
..........<<..<<<<<<<<<........<<<<<.<<<..<<<<....
...>>>>..>>>.........<<......>>...>>>>>....>>>>>>>
>>.>>..........)))......>>>>>>.>>>...>>>>>>><<<<<<
<<.....>>>>>>>>....>>>>>>..<<<<<...<<<......<<<<<.
<<<....>>>>>>>>...>>>..>>>>>........>>>>>><......<
<.....<<<<<<.......>>>>>><<<<....<<<<<.<<...<<<<<<
...<<.....>>.>>>>>>....((<<<<.<<...<<<...<<<....>>
>...>>>...>>...<<<<<........>>>>>))<<<<<<<<<<<<<..
.<<<<....<<<<<.<<<..<<<<<.<<<<.<<..[[[[...>>>>>><<
<...<<<<<<<<<<<<<<<<.<<.....>>>>>>>>>.....>>>>>>>>
>..>>><...<<<<....>>>>.....>>>>>>...>>>..>>>>>....
.....>>>>...>>...>>>>>>>>>>>>>>>..>>.....<<......>
>>>>>>.<<<<<....>>>>>..>>>>..<<<<....<<<<<<<<.<<..
.......<.....<<<<<.....<..>......>>>>><<<<<<<<<<<<
.....>>>>>>>>>>>>............<<<<<<<<<..<<<.......
..>>>..<<<<<<<.....<<<....>>>.......>>>>>>>.<<<<<.
<<<..<<<<<<<..<<<...<<...<<<<<....>>>>>...>>...>>>
>>>>>..>>>>><<<<<<.......>>>>>>........<..........
.<<<<<<.....>>>>>>.....>....>>>>>..>>.>>>>>>>..>..
>>.>>>>>>>>.>>>>>>.....>.....<<<<<........>>>>>..<
<<<<<<<.<<<.........<<<<.<<<<<<..<<<<<.<<<.<<<<<.<
<<<<<<<<<<<<<<<...........<<<<<...<<......<<<<<<<<
....>>>>>>>>...>>.............>>>>>..>>>>>>>>>>>>>
>>>...<<<<<....>>>>>....>>>>>.>>>..>>>>>..<<<<....
.>>>><<<<<<...........>>>>>>..<<...<<<<<<<...<<<<<
<.......>>>>>>.....<<...(((>>....>>>>>>>...<<<<..<
<<......>>>..>>>>.<<<....>>>.>>))).......<<<<<<<.<
<..))))..>>>>>>>>>.............>>>>..>>>>>>.......
<<<<...<<<<<<...<<.......>>...>>>>>>....>>>.>.....
..<<<<<.<<<<<<..<<<<<<<<<......>>>>>>>..>>.<<<<<..
...>>>>>.....>>>>>..>...>>>.>>....<<<<<<<....>>>.>
>>>........>>>>>>>>>>>....<<<<<<<...<<<<..<<<<<<<.
..............>>>>>>>.<<<<<...<<<<...<<<<<<<<<<<]]
]]>>>>>>...>>>>>...>>>>.>>>>>...<<<....<<<<<......
.....>>>>>....>>>.>>>>.......>>>>>>>..<<<<.....>>>
>....<<<<<<<<<.......>>>>>....<<<<<<<<.<<<....<<<<
<....>>>>>...>>>..>>>>>.>>>...>>>>....>>>
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB4yzv Defining the mRNA recognition signature of a bacterial toxin protein.
Resolution3.1 Å
Binding residue
(original residue number in PDB)		R2 K8 K9 S17 G18 K19 V30 P32 I44 K46 K47 V49 V51 F60 H68 S70 K71 R73 R84
Binding residue
(residue number reindexed from 1)		R1 K7 K8 S16 G17 K18 V29 P31 I43 K45 K46 V48 V50 F59 H67 S69 K70 R72 R83
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0003723 RNA binding
GO:0003735 structural constituent of ribosome
GO:0019843 rRNA binding
Biological Process
GO:0006412 translation
Cellular Component
GO:0005840 ribosome
GO:1990904 ribonucleoprotein complex

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:4yzv, PDBe:4yzv, PDBj:4yzv
PDBsum4yzv
PubMed26508639
UniProtQ5SHP9|RL24_THET8 Large ribosomal subunit protein uL24 (Gene Name=rplX)

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