Structure of PDB 4v97 Chain DZ Binding Site BS01

Receptor Information

>4v97 Chain DZ (length=176) Species: 300852 (Thermus thermophilus HB8)

YRLKAYYREGEKPSALRRAGKLPGVMYNRHLNRKVYVDLVEFDKVFRQAS
IHHVIVLELPDGQSLPTLVRQVNLDKRRRRPEHVDFFVLSDEPVEMYVPL
RFVGTPAGVRAGGVLQEIHRDILVKVSPRNIPEFIEVDVSGLEIGDSLHA
SDLKLPPGVELAVSPEETIAAVVPPE

Ligand information

>4v97 Chain DA (length=2824)

agaugguaagggcccacgguggaugccucggcacccgagccgaugaagga
cguggcuaccugcgauaagccagggggagccgguagcgggcguggauccc
uggauguccgaaugggggaacccggccggcgggaacgccggucaccgcgc
gcgcggggggaaccuggggaacugaaacaucucaguacccagaggagagg
aaagagaaaucgacucccugaguagcggcgagcgaaaggggaccagccua
aaccguccggcuuguccgggcggggucguggggcccucgcgaauccccag
ccuagccgaagcuguugggaagcagcgccagagagggugaaagccccgua
ggcgaaagguggggggauaggugaggguacccgaguaccccgugguucgu
ggagccaugggggaaucugggcggaccaccgccuaaggcuaaguacuccg
ggugaccgauagcgcaccaguaccgugagggaaaggugaaaagaaccccg
ggaggggagugaaauagagccugaaaccgugggcuuacaagcagucacgg
ccccgcaagggguuguggcgugccuauugaagcaugagccggcgacucac
ggucgugggcgagcuuaagccguugaggcggaggcguagggaaaccgagu
ccgaacagggcgcaguccgcggccguggacccgaaaccgggcgagcuagc
ccuggccagggugaagcuggggugagacccaguggaggcccgaaccggug
ggggaugcaaaccccucggaugagcuggggcuaggagugaaaagcuaacc
gagcccggagauagcugguucuccccgaaaugacuuuagggucagccuca
ggcgcugacuggggccuguagagcacugauagggcuagggggcccaccag
ccuaccaaacccugucaaacuccgaagggucccagguggagccugggagu
gagggcgcgagcgauaacguccgcguccgagcgcgggaacaaccgagacc
gccagcuaaggcccccaagucugggcuaagugguaaaggauguggcgccg
cgaagacagccagauagcucacuggucgaguggcgccgcgccgaaaauga
ucggggcuuaagcccagcgccgaagcugcgggucugggggaugaccccag
gcgguaggggagcguucccgaugccgaugaaggccgacccgcgagggcgg
cuggagguaagggaagugcgaaugccggcaugaguaacgauaaagagggu
gagaaucccucucgccguaagcccaaggguuccuacgcaauggucgucag
cguaggguuaggcgggaccuaaggugaagccgaaaggcguagccgaaggg
cagccgguuaauauuccggcccuucccgcaggugcgauggggggacgcuc
uaggcuagggggaccggagccauggacgagcccggccagaagcgcagggu
gggagguaggcaaauccgccucccaacaagcucugcgugguggggaagcc
cgggugacaaccccccgaagccagggagccaagaaaagccucuaagcaca
accugcgggaacccguaccgcaaaccgacacaggugggcgggugcaagag
cacucaggcgcgcgggagaacccucgccaaggaacucugcaaguuggccc
cguaacuucgggagaaggggugcucccuggggugaugagccccggggagc
cgcagugaacaggcucuggcgacuguuuaccaaaaacacagcucucugcg
aacucguaagaggagguauagggagcgacgcuugcccggugccggaaggu
caaggggaggggugcaagccccgaaccgaagccccggugaacggcggccg
uaacuauaacgguccuaagguagcgaaauuccuugucggguaaguuccga
ccugcacgaaaagcguaacgaccggagcgcugucucggcgagggacccgg
ugaaauugaacuggccgugaagaugcggccuacccguggcaggacgaaaa
gaccccguggagcuuuacugcagccugguguuggcucuuggucgcgccug
cguaggauaggugggagccugugaacccccgccuccgggugggggggagg
cgccggugaaauaccacccuggcgcggcugggggccuaacccucggaugg
ggggacagcgcuuggcgggcaguuugacuggggcggucgccuccuaaaag
guaacggaggcgcccaaagguccccucaggcgggacggaaauccgccgga
gagcgcaaggguagaagggggccugacugcgaggccugcaagccgagcag
gggcgaaagccgggccuagugaaccgguggucccguguggaagggccauc
gaucaacggauaaaaguuaccccggggauaacaggcugaucucccccgag
cguccacagcggcggggagguuuggcaccucgaugucggcucgucgcauc
cuggggcugaagaaggucccaaggguugggcuguucgcccauuaaagcgg
cacgcgagcuggguucagaacgucgugagacaguucggucucuauccgcc
acgggcgcaggaggcuugaggggggcucuuccuaguacgagaggaccgga
agggacgcaccucugguuucccagcugucccuccaggggcauaagcuggg
uagccaugugcggaagggauaaccgcugaaagcaucuaagcgggaagccc
gccccaagaugaggccucccacggcgucaagccgguaaggacccgggaag
accacccgguggaugggccggggguguaagcgccgcgaggcguugagccg
accggucccaaucguccgaggucu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4v97 Reorganization of an intersubunit bridge induced by disparate 16S ribosomal ambiguity mutations mimics an EF-Tu-bound state.
• Resolution: 3.516 Å
• Binding residue (original residue number in PDB): A113 I146 E169
• Binding residue (residue number reindexed from 1): A111 I144 E167

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:4v97, PDBe:4v97, PDBj:4v97
• PDBsum: 4v97
• PubMed: 23630274
• UniProt: Q5SHZ1|RL25_THET8 Large ribosomal subunit protein bL25 (Gene Name=rplY)