Structure of PDB 6oxi Chain YV Binding Site BS01

Receptor Information

>6oxi Chain YV (length=101) Species: 300852 (Thermus thermophilus HB8)

MFAIVKTGGKQYRVEPGLKLRVEKLDAEPGATVELPVLLLGGEKTVVGTP
VVEGASVVAEVLGHGRGKKILVSKFKAKVQYRRKKGHRQPYTELLIKEIR
G

Ligand information

>6oxi Chain YA (length=2878)

agaugguaagggcccacgguggaugccucggcacccgagccgaugaagga
cguggcuaccugcgauaagccagggggagccgguagcgggcguggauccc
uggauguccgaaugggggaacccggccggcgggaacgccggucaccgcgc
uuugcgcggggggaaccuggggaacugaaacaucucaguacccagaggag
aggaaagagaaaucgacucccugaguagcggcgagcgaaaggggaccagc
cuaaaccguccggcuuguccgggcggggucguggggcccucggacaccga
auccccagccuagccgaagcuguugggaagcagcgccagagagggugaaa
gccccguaggcgaaagguggggggauaggugaggguacccgaguaccccg
ugguucguggagccaugggggaaucugggcggaccaccgccuaaggcuaa
guacuccgggugaccgauagcgcaccaguaccgugagggaaaggugaaaa
gaaccccgggaggggagugaaauagagccugaaaccgugggcuuacaagc
agucacggccccgcaagggguuguggcgugccuauugaagcaugagccgg
cgacucacggucgugggcgagcuuaagccguugaggcggaggcguaggga
aaccgaguccgaacagggcgcaaaguccgcggccguggacccgaaaccgg
gcgagcuagcccuggccagggugaagcuggggugagacccaguggaggcc
cgaaccggugggggaugcaaaccccucggaugagcuggggcuaggaguga
aaagcuaaccgagcccggagauagcugguucuccccgaaaugacuuuagg
gucagccucaggcgcugacuggggccuguagagcacugauagggcuaggg
ggcccaccagccuaccaaacccugucaaacuccgaagggucccaggugga
gccugggagugagggcgcgagcgauaacguccgcguccgagcgcgggaac
aaccgagaccgccagcuaaggcccccaagucugggcuaagugguaaagga
uguggcgccgcgaagacagccaggagguuggcuuagaagcagccauccuu
uaaagagugcguaauagcucacuggucgaguggcgccgcgccgaaaauga
ucggggcuuaagcccagcgccgaagcugcgggucugggggaugaccccag
gcgguaggggagcguucccgaugccgaugaaggccgacccgcgagggcgg
cuggagguaagggaagugcgaaugccggcaugaguaacgauaaagagggu
gagaaucccucucgccguaagcccaaggguuccuacgcaauggucgucag
cguaggguuaggcgggaccuaaggugaagccgaaaggcguagccgaaggg
cagccgguuaauauuccggcccuucccgcaggugcgauggggggacgcuc
uaggcuagggggaccggagccauggacgagcccggccagaagcgcagggu
gggagguaggcaaauccgccucccaacaagcucugcgugguggggaagcc
cguacgggugacaaccccccgaagccagggagccaagaaaagccucuaag
cacaaccugcgggaacccguaccgcaaaccgacacaggugggcgggugca
agagcacucaggcgcgcgggagaacccucgccaaggaacucugcaaguug
gccccguaacuucgggagaaggggugcucccuggggugaugagccccggg
gagccgcagugaacaggcucuggcgacuguuuaccaaaaacacagcucuc
ugcgaacucguaagaggagguauagggagcgacgcuugcccggugccgga
aggucaaggggaggggugcaagccccgaaccgaagccccggugaacggcg
gccguaacuauaacgguccuaagguagcgaaauuccuugucggguaaguu
ccgaccugcacgaaaagcguaacgaccggagcgcugucucggcgagggac
ccggugaaauugaacuggccgugaagaugcggccuacccguggcaggacg
aaaagaccccguggagcuuuacugcagccugguguuggcucuuggucgcg
ccugcguaggauaggugggagccugugaacccccgccuccgggugggggg
gaggcgccggugaaauaccacccuggcgcggcugggggccuaacccucgg
auggggggacagcgcuuggcgggcaguuugacuggggcggucgccuccua
aaagguaacggaggcgcccaaagguccccucaggcgggacggaaauccgc
cggagagcgcaaggguagaagggggccugacugcgaggccugcaagccga
gcaggggcgaaagccgggccuagugaaccgguggucccguguggaagggc
caucgaucaacggauaaaaguuaccccggggauaacaggcugaucucccc
cgagcguccacagcggcggggagguuuggcaccucgaugucggcucgucg
cauccuggggcugaagaaggucccaaggguugggcuguucgcccauuaaa
gcggcacgcgagcuggguucagaacgucgugagacaguucggucucuauc
cgccacgggcgcaggaggcuugaggggggcucuuccuaguacgagaggac
cggaagggacgcaccucugguuucccagcugucccuccaggggcauaagc
uggguagccaugugcggaagggauaaccgcugaaagcaucuaagcgggaa
gcccgccccaagaugaggccucccacggcgucaagccgguaaggacccgg
gaagaccacccgguggaugggccggggguguaagcgccgcgaggcguuga
gccgaccggucccaaucguccgaggucu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6oxi Monomeric YoeB toxin retains RNase activity but adopts an obligate dimeric form for thermal stability.
• Resolution: 3.495 Å
• Binding residue (original residue number in PDB): G8 G9 K10 E23 R66 K69 K74 F75 K76 A77 K78 V79 Q80 Y81 R82 R83 K84 K85 G86 H87 Q89 P90
• Binding residue (residue number reindexed from 1): G8 G9 K10 E23 R66 K69 K74 F75 K76 A77 K78 V79 Q80 Y81 R82 R83 K84 K85 G86 H87 Q89 P90

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:0005737 cytoplasm
• GO:0005840 ribosome
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:6oxi, PDBe:6oxi, PDBj:6oxi
• PDBsum: 6oxi
• PubMed: 31501867
• UniProt: P60492|RL21_THET8 Large ribosomal subunit protein bL21 (Gene Name=rplU)