Structure of PDB 4w4g Chain YT Binding Site BS02

Receptor Information

>4w4g Chain YT (length=137) Species: 300852 (Thermus thermophilus HB8)

MNRGALIKLVESRYVRTDLPEFRPGDTVRVSYKVKEGNRTRIQDFEGIVI
RIRRNGFNTTFTVRKVSYGVGVERIFPLHSPLIQKIDIVQRGRARRAKLY
FIRNLSDREIRRKLRADRKRIDQDRAAERAAKEEAQK

Ligand information

>4w4g Chain YA (length=2875)

agaugguaagggcccacgguggaugccucggcacccgagccgaugaagga
cguggcuaccugcgauaagccagggggagccgguagcgggcguggauccc
uggauguccgaaugggggaacccggccggcgggaacgccggucaccgcgc
gcgcggggggaaccuggggaacugaaacaucucaguacccagaggagagg
aaagagaaaucgacucccugaguagcggcgagcgaaaggggaccagccua
aaccguccggcuuguccgggcggggucguggggcccucggacaccgaauc
cccagccuagccgaagcuguugggaagcagcgccagagagggugaaagcc
ccguaggcgaaagguggggggauaggugaggguacccgaguaccccgugg
uucguggagccaugggggaaucugggcggaccaccgccuaaggcuaagua
cuccgggugaccgauagcgcaccaguaccgugagggaaaggugaaaagaa
ccccgggaggggagugaaauagagccugaaaccgugggcuuacaagcagu
cacggccccgcaagggguuguggcgugccuauugaagcaugagccggcga
cucacggucgugggcgagcuuaagccguugaggcggaggcguagggaaac
cgaguccgaacagggcgcaaaguccgcggccguggacccgaaaccgggcg
agcuagcccuggccagggugaagcuggggugagacccaguggaggcccga
accggugggggaugcaaaccccucggaugagcuggggcuaggagugaaaa
gcuaaccgagcccggagauagcugguucuccccgaaaugacuuuaggguc
agccucaggcgcugacuggggccuguagagcacugauagggcuagggggc
ccaccagccuaccaaacccugucaaacuccgaagggucccagguggagcc
ugggagugagggcgcgagcgauaacguccgcguccgagcgcgggaacaac
cgagaccgccagcuaaggcccccaagucugggcuaagugguaaaggaugu
ggcgccgcgaagacagccaggagguuggcuuagaagcagccauccuuuaa
agagugcguaauagcucacuggucgaguggcgccgcgccgaaaaugaucg
gggcuuaagcccagcgccgaagcugcgggucugggggaugaccccaggcg
guaggggagcguucccgaugccgaugaaggccgacccgcgagggcggcug
gagguaagggaagugcgaaugccggcaugaguaacgauaaagagggugag
aaucccucucgccguaagcccaaggguuccuacgcaauggucgucagcgu
aggguuaggcgggaccuaaggugaagccgaaaggcguagccgaagggcag
ccgguuaauauuccggcccuucccgcaggugcgauggggggacgcucuag
gcuagggggaccggagccauggacgagcccggccagaagcgcaggguggg
agguaggcaaauccgccucccaacaagcucugcgugguggggaagcccgu
acgggugacaaccccccgaagccagggagccaagaaaagccucuaagcac
aaccugcgggaacccguaccgcaaaccgacacaggugggcgggugcaaga
gcacucaggcgcgcgggagaacccucgccaaggaacucugcaaguuggcc
ccguaacuucgggagaaggggugcucccuggggugaugagccccggggag
ccgcagugaacaggcucuggcgacuguuuaccaaaaacacagcucucugc
gaacucguaagaggagguauagggagcgacgcuugcccggugccggaagg
ucaaggggaggggugcaagccccgaaccgaagccccggugaacggcggcc
guaacuauaacgguccuaagguagcgaaauuccuugucggguaaguuccg
accugcacgaaaagcguaacgaccggagcgcugucucggcgagggacccg
gugaaauugaacuggccgugaagaugcggccuacccguggcaggacgaaa
agaccccguggagcuuuacugcagccugguguuggcucuuggucgcgccu
gcguaggauaggugggagccugugaacccccgccuccgggugggggggag
gcgccggugaaauaccacccuggcgcggcugggggccuaacccucggaug
gggggacagcgcuuggcgggcaguuugacuggggcggucgccuccuaaaa
gguaacggaggcgcccaaagguccccucaggcgggacggaaauccgccgg
agagcgcaaggguagaagggggccugacugcgaggccugcaagccgagca
ggggcgaaagccgggccuagugaaccgguggucccguguggaagggccau
cgaucaacggauaaaaguuaccccggggauaacaggcugaucucccccga
gcguccacagcggcggggagguuuggcaccucgaugucggcucgucgcau
ccuggggcugaagaaggucccaaggguugggcuguucgcccauuaaagcg
gcacgcgagcuggguucagaacgucgugagacaguucggucucuauccgc
cacgggcgcaggaggcuugaggggggcucuuccuaguacgagaggaccgg
aagggacgcaccucugguuucccagcugucccuccaggggcauaagcugg
guagccaugugcggaagggauaaccgcugaaagcaucuaagcgggaagcc
cgccccaagaugaggccucccacggcgucaagccgguaaggacccgggaa
gaccacccgguggaugggccggggguguaagcgccgcgaggcguugagcc
gaccggucccaaucguccgaggucu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4w4g Defining the mRNA recognition signature of a bacterial toxin protein.
• Resolution: 3.3 Å
• Binding residue (original residue number in PDB): N2 R3 G4 A5 R23 R51 R53 R54 N55 N58 R93 R95 R96 A97 Y100 F101 K113 R115 K119
• Binding residue (residue number reindexed from 1): N2 R3 G4 A5 R23 R51 R53 R54 N55 N58 R93 R95 R96 A97 Y100 F101 K113 R115 K119

Gene Ontology

Molecular Function

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

Biological Process

• GO:0006412 translation

Cellular Component

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

External links

• PDB: RCSB:4w4g, PDBe:4w4g, PDBj:4w4g
• PDBsum: 4w4g
• PubMed: 26508639
• UniProt: P60490|RL19_THET8 Large ribosomal subunit protein bL19 (Gene Name=rplS)