Structure of PDB 7xam Chain T Binding Site BS01

Receptor Information

>7xam Chain T (length=114) Species: 246196 (Mycolicibacterium smegmatis MC2 155)

EFPSATAKARYVRVSATKARRVIDLVRGKSVEEALDILRWAPQAASEPVA
KVIASAAANAQNNEGLDPSTLVVATVYADEGPTAKRIRPRAQGRAFRIRK
RTSHITVIVESRPP

Ligand information

>7xam Chain A (length=3062)

aaguguuuaagggcgcaugguggaugccuuggcacugggagccgaugaag
gacguaggaggcugcgauaagccucggggagcugucaaccgagcguugau
ccgaggauguccgaauggggaaacccggcacgagugaugucgugucacca
ggcgcugaauauauaggcgucuggggggaacgcggggaagugaaacaucu
caguacccguaggaagagaaaacaaaaugugauuccgugaguaguggcga
gcgaaagcggaggauggcuaaaccguaugcaugugauaccggguaggggu
ugugugugcgggguugugggaccuaucuuuccggcucuaccuggcuggag
ggcagugagaaaauguugugguuagcggaaauggcuugggauggccugcc
guagacggugagagcccgguacgugaaaacccgacgucugucuugauggu
guucccgaguagcagcgggcccguggaaucugcugugaaucugccgggac
cacccgguaagccugaauacuucccagugaccgauagcggauuaguaccg
ugagggaauggugaaaaguaccccgggaggggagugaaagaguaccugaa
accgugcgcuuacaauccgucagagcccucgacgugucguggggugaugg
cgugccuuuugaagaaugagccugcgagucagggacaugucgcgagguua
acccgggugggguagccgcagcgaaagcgagucugaauagggcguaucca
cacaagagugugugguguagugguguguucuggacccgaagcggagugau
cuacccauggccagggugaagcgcggguaagaccgcguggaggcccgaac
ccacuuagguugaagacugaggggaugagcuguggguaggggugaaaggc
caaucaaacuccgugauagcugguucuccccgaaaugcauuuaggugcag
cgucgcauguuucuugccggagguagagcuacuggauggccgaugggccc
cacaggguuacugacgucagccaaacuccgaaugccgguaaguccaagag
ugcggcagugagacggcgggggauaagcuccgugcgucgagagggaaaca
gcccagaucgccggcuaaggccccuaagcgugugcuaaguggaaaaggau
gugcagucgcgaagacaaccaggagguuggcuuagaagcagccacccuug
aaagagugcguaauagcucacuggucaagugauugugcgccgauaaugua
gcggggcucaagcacaccgccgaagccgcggcagccaacguguuggcugg
guaggggagcguccugcauccggugaagccgccgagugaucgaguggugg
agggugugggagugagaaugcaggcaugaguagcgauuaggcaagugaga
accuugcccgccgaaagaccaaggguuccugggccaggccaguccgccca
gggugagucgggaccuaaggcgaggccgacaggcguagucgauggacaac
ggguugauauucccguacccguguaugugcguccaugaugaaucagcggu
acuaaccauccaugggaccuucguugguaguagucaagcgauggggugac
gcaggaagguagccguaccggucagugguaauaccgggguaagccuguag
ggagucagauagguaaauccgucuggcauauauccugagaggugaugcau
agccgagugaggcgaauucggugauccuaugcugccgagaaaagccucua
gcgaggacauacacggcccguaccccaaaccaacacagguggucagguag
agaauacuaaggcguacgagugaacuaugguuaaggaacucggcaaaaug
cccccguaacuucgggagaagggggacccacauggcguguaagccuuuac
ggcccaagcgugaguggguggcacaaaccagugagaagcgacuguuuacu
aaaaacacagguccgugcgaagucgcaagacgauguauacggacugacgc
cugcccggugcuggaagguuaagaggacccguuaacucccuuugggggug
aagcggagaauuuaagccccaguaaacggcgguggucauccuaagguagc
gaaauuccuugucggguaaguuccgaccugcacgaauggcguaacgacuu
cucaacugucucaaccauagacucggcgaaauugcacuacgaguaaagau
gcucguuacgcgcggcaggacgaaaagaccccgggaccuucacuacaacu
ugguauuggugcucgauacgguuuguguaggauaggugggagacugugaa
gcucacacgccaguguggguggagucguuguugaaauaccacucugaucg
uauugggccucuaaccucggaccguauauccgguucagggacagugccug
guggguaguuuaacuggggcgguugccuccuaaaauguaacggaggcgcc
caaagguucccucaaccuggacggcaaucagguguugaguguaagugcac
aagggagcuugacugcgagacggacaugucgagcagggacgaaagucggg
acuagugauccggcaccucugaguggaaggggugucgcucaacggauaaa
agguaccccggggauaacaggcugaucuuccccaagaguccauaucgacg
ggaugguuuggcaccucgaugucggcucgucgcauccuggggcuggagca
ggucccaaggguugggcuguucgcccauuaaagcggcacgcgagcugggu
uuagaacgucgugagacaguucggucucuauccgccgcgcgcgucagaag
cuugaggaaaccugucccuaguacgagaggaccgggacggacgaaccucu
gguauaccaguugucccaccaggggcacggcuggauagccacguucggac
aggauaaccgcugaaagcaucuaagcgggaaaccucuuccaagaccaggc
uucucacccucuaggagggauaaggccccccgcagaccacgggauugaua
gaccagaccuggaagccuaguaauaggugcagggaacuggcacuaaccgg
ccgaaaacuuac

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7xam Cryo-EM structures reveal a unique conformational dynamics of the Mycobacterium 23S rRNA helices
• Resolution: 3.5 Å
• Binding residue (original residue number in PDB): T11 K13 A14 R15 Y16 R18 S20 T22 K23 R25 R32 P47 A49 K56 A63 N64 N67 N68 D84 E85 K90 R91 P94 R95 A96 Q97 G98 R99 A100 F101 R102 I103 R104
• Binding residue (residue number reindexed from 1): T6 K8 A9 R10 Y11 R13 S15 T17 K18 R20 R27 P42 A44 K51 A58 N59 N62 N63 D79 E80 K85 R86 P89 R90 A91 Q92 G93 R94 A95 F96 R97 I98 R99

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:0015934 large ribosomal subunit
• GO:0022625 cytosolic large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:7xam, PDBe:7xam, PDBj:7xam
• PDBsum: 7xam
• PubMed: 37709237
• UniProt: A0QSD6|RL22_MYCS2 Large ribosomal subunit protein uL22 (Gene Name=rplV)