Structure of PDB 4ypb Chain RE Binding Site BS01

Receptor Information

>4ypb Chain RE (length=205) Species: 300852 (Thermus thermophilus HB8)

MKGILGVKVGMTRIFRDDRAVPVTVILAGPCPVVQRRTPEKDGYTAVQLG
FLPQNPKRVNRPLKGHFAKAGVEPVRILREIRDFNPEGDTVTVEIFKPGE
RVDVTGTSKGRGFAGVMKRWNFAGGPDSHGAHKIHRHPGSIGNRKTPGRV
YKGKKMAGHYGAERVTVMNLEVVDVIPEENLLLVKGAVPGPNGGLVIVRE
TKKAA

Ligand information

>4ypb Chain RA (length=2891)

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

Structure summary

• PDB: 4ypb Defining the mRNA recognition signature of a bacterial toxin protein.
• Resolution: 3.4 Å
• Binding residue (original residue number in PDB): M11 T12 R13 P22 R37 K41 D42 Y44 R58 N60 R61 P62 K64 H66 L78 R79 E80 R82 S108 K109 G110 R111 G112 F113 G115 M117 K118 R119 F122 A123 S128 H129 G130 A131 H132 K133 I134 H135 R136 H137 P138 G139 S140 I141 G142 N143 R144 K145 T146 P147 G148 R149 V150 Y151 K152 G153 K154 M156 A157 H159 Y160 R164 T166 M168 N169 K185 A187 V188 P189 G190 P191 K203
• Binding residue (residue number reindexed from 1): M11 T12 R13 P22 R37 K41 D42 Y44 R58 N60 R61 P62 K64 H66 L78 R79 E80 R82 S108 K109 G110 R111 G112 F113 G115 M117 K118 R119 F122 A123 S128 H129 G130 A131 H132 K133 I134 H135 R136 H137 P138 G139 S140 I141 G142 N143 R144 K145 T146 P147 G148 R149 V150 Y151 K152 G153 K154 M156 A157 H159 Y160 R164 T166 M168 N169 K185 A187 V188 P189 G190 P191 K203

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:4ypb, PDBe:4ypb, PDBj:4ypb
• PDBsum: 4ypb
• PubMed: 26508639
• UniProt: Q5SHN8|RL3_THET8 Large ribosomal subunit protein uL3 (Gene Name=rplC)