Structure of PDB 4xej Chain AL25 Binding Site BS01

Receptor Information

>4xej Chain AL25 (length=187) Species: 262724 (Thermus thermophilus HB27)

YRLKAYYREGEKPSALRRAGKLPGVMYNRHLNRKVYVDLVEFDKVFRQAS
IHHVIVLELPDGQSLPTLVRQVNLDKRRRRPEHVDFFVLSDEPVEMYVPL
RFVGTPAGVRAGGVLQEIHRDILVKVSPRNIPEFIEVDVSGLEIGDSLHA
SDLKLPPGVELAVSPEETIAAVVPPEDVEKLAEEAAA

Ligand information

>4xej Chain A23S (length=2876)

agaugguaagggcccacgguggaugccucggcacccgagccgaugaagga
cguggcuaccugcgauaagccagggggagccgguagcgggcguggauccc
uggauguccgaaugggggaacccggccggcgggaacgccggucaccgcgc
uuuuugcgcggggggaaccuggggaacugaaacaucucaguacccagagg
agaggaaagagaaaucgacucccugaguagcggcgagcgaaaggggacca
gccuaaaccguccggcuuguccgggcggggucguggggcccucggacacc
gaauccccagccuagccgaagcuguugggaagcagcgccagagaggguga
aagccccguaggcgaaagguggggggauaggugaggguacccgaguaccc
cgugguucguggagccaugggggaaucugggcggaccaccgccuaaggcu
aaguacuccgggugaccgauagcgcaccaguaccgugagggaaaggugaa
aagaaccccgggaggggagugaaauagagccugaaaccgugggcuuacaa
gcagucacggccccgcaagggguuguggcgugccuauugaagcaugagcc
ggcgacucacggucgugggcgagcuuaagccguugaggcggaggcguagg
gaaaccgaguccgaacagggcgucuaguccgcggccguggacccgaaacc
gggcgagcuagcccuggccagggugaagcuggggugagacccaguggagg
cccgaaccggugggggaugcaaaccccucggaugagcuggggcuaggagu
gaaaagcuaaccgagcccggagauagcugguucuccccgaaaugacuuua
gggucagccucaggcgcugacuggggccuguagagcacugauagggcuag
ggggcccaccagccuaccaaacccugucaaacuccgaagggucccaggug
gagccugggagugagggcgcgagcgauaacguccgcguccgagcgcggga
acaaccgagaccgccagcuaaggcccccaagucugggcuaagugguaaag
gauguggcgccgcgaagacagccagggguuggcuuagaagcagccauccu
uuaaagagugcguaauagcuccuggucgaguggcgccgcgccgaaaauga
ucggggcuuaagcccagcgccgaagcugcgggucugggggaugaccccag
gcgguaggggagcguucccgaugccgaugaaggccgacccgcgagggcgg
cuggagguaagggaagugcgaaugccggcaugaguaacgauaaagagggu
gagaaucccucucgccguaagcccaaggguuccuacgcaauggucgucag
cguaggguuaggcgggaccuaaggugaagccgaaaggcguagccgaaggg
cagccgguuaauauuccggcccuucccgcaggugcgauggggggacgcuc
uaggcuagggggaccggagccauggacgagcccggccagaagcgcagggu
gggagguaggcaaauccgccucccaaaagcucugcgugguggggaagccc
guacgggugacaaccccccgaagccagggagccaagaaaagccucuaagc
acaaccugcgggaacccguaccgcaaaccgacacaggugggcgggugcaa
gagcacucaggcgcgcgggagaacccucgccaaggaacucugcaaguugg
ccccguaacuucgggagaaggggugcucccuggggugaugagcuccgggg
agccgcagugaacaggcucuggcgacuguuuaccaaaaacacagcucucu
gcgaacucguaagaggagguauagggagcgacgcuugcccggugccggaa
ggucaaggggaggggugcaagccccgaaccgaagccccggugaacggcgg
ccguaacuauaacgguccuaagguagcgaaauuccuugucggguaaguuc
cgaccugcacgaaaagcguaacgaccggagcgcugucucggcgagggacc
cggugaaauugaacuggccgugaagaugcggccuacccguggcaggacga
aaagaccccguggagcuuuacugcagccugguguuggcucuuggucgcgc
cugcguaggauaggugggagccugugaacccccgccuccggguggggggg
aggcgccggugaaauaccacccuggcgcggcuggggccuaacccucggau
ggggggacagcgcuuggcgggcaguuugacuggggcggucgccuccuaaa
agguaacggaggcgcccaaagguccccucaggcgggacggaaauccgccg
gagagcgcaaggguagaagggggccugacugcgaggccugcaagccgagc
aggggcgaaagccgggccuagugaaccgguggucccguguggaagggcca
ucgaucaacggauaaaaguuaccccggggauaacaggcugaucucccccg
agcguccacagcggcggggagguuuggcaccucgaugucggcucgucgca
uccuggggcugaagaaggucccaaggguugggcuguucgcccauuaaagc
ggcacgcgagcuggguucagaacgucgugagacaguucggucucuauccg
ccacgggcgcaggaggcuugaggggggcucuuccuaguacgagaggaccg
gaagggacgcaccucugguuucccagcugucccuccaggggcauaagcug
gguagccaugugcggaagggauaaccgcugaaagcaucuaagcgggaagc
ccgccccaagaugaggccucccacggcgucaagccgguaaggacccggga
agacuacccgguggaugggccggggguguaagcgccgcgaggcguugagc
cgaccggucccaaucguccgaggucu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4xej Initiation of translation in bacteria by a structured eukaryotic IRES RNA.
• Resolution: 3.8 Å
• Binding residue (original residue number in PDB): I146 H151 T170 P176
• Binding residue (residue number reindexed from 1): I144 H149 T168 P174

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0008097 5S rRNA binding
• 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:4xej, PDBe:4xej, PDBj:4xej
• PDBsum: 4xej
• PubMed: 25652826
• UniProt: Q72IA7|RL25_THET2 Large ribosomal subunit protein bL25 (Gene Name=rplY)