Structure of PDB 4xej Chain BL13 Binding Site BS01

Receptor Information

>4xej Chain BL13 (length=137) Species: 262724 (Thermus thermophilus HB27)

KTYVPKQVEPRWVLIDAEGKTLGRLATKIATLLRGKHRPDWTPNVAMGDF
VVVVNADKIRVTGKKLEQKIYTRYSGYPGGLKKIPLEKMLATHPERVLEH
AVKGMLPKGPLGRRLFKRLKVYAGPDHPHQAQRPEKL

Ligand information

>4xej Chain B23S (length=2876)

agaugguaagggcccacgguggaugccucggcacccgagccgaugaagga
cguggcuaccugcgauaagccagggggagccgguagcgggcguggauccc
uggauguccgaaugggggaacccggccggcgggaacgccggucaccgcgc
uuuuugcgcggggggaaccuggggaacugaaacaucucaguacccagagg
agaggaaagagaaaucgacucccugaguagcggcgagcgaaaggggacca
gccuaaaccguccggcuuguccgggcggggucguggggcccucggacacc
gaauccccagccuagccgaagcuguugggaagcagcgccagagaggguga
aagccccguaggcgaaagguggggggauaggugaggguacccgaguaccc
cgugguucguggagccaugggggaaucugggcggaccaccgccuaaggcu
aaguacuccgggugaccgauagcgcaccaguaccgugagggaaaggugaa
aagaaccccgggaggggagugaaauagagccugaaaccgugggcuuacaa
gcagucacggccccgcaagggguuguggcgugccuauugaagcaugagcc
ggcgacucacggucgugggcgagcuuaagccguugaggcggaggcguagg
gaaaccgaguccgaacagggcgucuaguccgcggccguggacccgaaacc
gggcgagcuagcccuggccagggugaagcuggggugagacccaguggagg
cccgaaccggugggggaugcaaaccccucggaugagcuggggcuaggagu
gaaaagcuaaccgagcccggagauagcugguucuccccgaaaugacuuua
gggucagccucaggcgcugacuggggccuguagagcacugauagggcuag
ggggcccaccagccuaccaaacccugucaaacuccgaagggucccaggug
gagccugggagugagggcgcgagcgauaacguccgcguccgagcgcggga
acaaccgagaccgccagcuaaggcccccaagucugggcuaagugguaaag
gauguggcgccgcgaagacagccagggguuggcuuagaagcagccauccu
uuaaagagugcguaauagcucacuggucgaguggcgccgcgccgaaaaug
aucggggcuuaagcccagcgccgaagcugcgggucugggggaugacccca
ggcgguaggggagcguucccgaugccgaugaaggccgacccgcgagggcg
gcuggagguaagggaagugcgaaugccggcaugaguaacgauaaagaggg
ugagaaucccucucgccguaagcccaaggguuccuacgcaauggucguca
gcguaggguuaggcgggaccuaaggugaagccgaaaggcguagccgaagg
gcagccgguuaauauuccggcccuucccgcaggugcgauggggggacgcu
cuaggcuagggggaccggagccauggacgagcccggccagaagcgcaggg
ugggagguaggcaaauccgccucccaaaagcucugcgugguggggaagcc
cguacgggugacaaccccccgaagccagggagccaagaaaagccucuaag
cacaaccugcgggaacccguaccgcaaaccgacacaggugggcgggugca
agagcacucaggcgcgcgggagaacccucgccaaggaacucugcaaguug
gccccguaacuucgggagaaggggugcucccuggggugaugagcuccggg
gagccgcagugaacaggcucuggcgacuguuuaccaaaaacacagcucuc
ugcgaacucguaagaggagguauagggagcgacgcuugcccggugccgga
aggucaaggggaggggugcaagccccgaaccgaagccccggugaacggcg
gccguaacuauaacgguccuaagguagcgaaauuccuugucggguaaguu
ccgaccugcacgaaaagcguaacgaccggagcgcugucucggcgagggac
ccggugaaauugaacuggccgugaagaugcggccuacccguggcaggacg
aaaagaccccguggagcuuuacugcagccugguguuggcucuggucgcgc
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): K25 T26 L46 G47 R48 T51 R58 K60 P67 N68 F74 T86 G87 K88 K89 Q92 K93 R97 Y98 S99 Y101 P102 G103 L105 K106 K112 H117 E123 A125 G128 M129 G133 P134 L135 R138 K141
• Binding residue (residue number reindexed from 1): K1 T2 L22 G23 R24 T27 R34 K36 P43 N44 F50 T62 G63 K64 K65 Q68 K69 R73 Y74 S75 Y77 P78 G79 L81 K82 K88 H93 E99 A101 G104 M105 G109 P110 L111 R114 K117

Gene Ontology

Molecular Function

• GO:0003729 mRNA binding
• GO:0003735 structural constituent of ribosome

Biological Process

• GO:0006412 translation
• GO:0017148 negative regulation of translation

Cellular Component

• GO:0005737 cytoplasm
• 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: Q72IN1|RL13_THET2 Large ribosomal subunit protein uL13 (Gene Name=rplM)