Structure of PDB 3j9w Chain BW Binding Site BS01

Receptor Information

>3j9w Chain BW (length=93) Species: 224308 (Bacillus subtilis subsp. subtilis str. 168)

MKDPRDVLKRPVITERSADLMTEKKYTFEVDVRANKTEVKDAVESIFGVK
VDKVNIMNYKGKSKRVGRYTGMTSRRRKAIVKLTADSKEIEIF

Ligand information

>3j9w Chain BA (length=2923)

uuaaguuagaaagggcgcacgguggaugccuuggcacuaggagccgauga
aggacgggacgaacaccgauaugcuucggggagcuguaagcaagcuuuga
uccggagauuuccgaauggggaaacccaccacucguaauggagugguauc
cauaucugaauucauaggauaugagaaggcagacccggggaacugaaaca
ucuaaguacccggaggaagagaaagcaaaugcgauucccugaguagcggc
gagcgaaacgggaucagcccaaaccaagaggcuugccucuugggguugua
ggacacucuguacggaguuacaaaggaacgagguagaugaagaggucugg
aaaggcccgccauaggagguaacagcccuguagucaaaacuucguucucu
ccugaguggauccugaguacggcggaacacgugaaauuccgucggaaucc
gggaggaccaucucccaaggcuaaauacucccuagugaccgauagugaac
caguaccgugagggaaaggugaaaagcaccccggaaggggagugaaagag
auccugaaaccgugugccuacaaguagucagagcccguuaacgggugaug
gcgugccuuuuguagaaugaaccggcgaguuacgaucucgugcaagguua
agcagaagaugcggagccgcagcgaaagcgagucugaauagggcgcauga
guacguggucguagacccgaaaccaggugaucuacccauguccaggguga
aguucagguaacacugaauggaggcccgaacccacgcacguugaaaagug
cggggaugagguguggguaggggugaaaugccaaucgaaccuggagauag
cugguucucuccgaaauagcuuuagggcuagccucaagguaagagucuug
gagguagagcacugauuggacuaggggccccuaccggguuaccgaauuca
gucaaacuccgaaugccaaugacuuauccuugggagucagacugcgagug
auaagauccguagucgaaagggaaacagcccagaccgccagcuaaggucc
caaaguauacguuaaguggaaaaggauguggaguugcuuagacaaccagg
auguuggcuuagaagcagccaccauuuaaagagugcguaauagcucacug
gucgagugacucugcgccgaaaauguaccggggcuaaacguaucaccgaa
gcugcggacuguucuucgaacagugguaggagagcguucuaagggcugug
aagccagaccggaaggacugguggagcgcuuagaagugagaaugccggua
ugaguagcgaaagaggggugagaauccccuccaccgaaugccuaagguuu
ccugaggaaggcucguccgcucaggguuagucgggaccuaagccgaggcc
gaaaggcguaggcgauggacaacagguugauauuccuguaccaccuccuc
accauuugagcaauggggggacgcaggaggauaggguaagcgcgguauug
gauauccgcguccaagcaguuaggcugggaaauaggcaaauccguuuccc
auaagccugagcugugauggcgagcgaaauauaguagcgaaguuccugau
uccacacugccaagaaaagccucuagcgaggugagaggugcccguaccgc
aaaccgacacagguaggcgaggagagaauccuaaggugaucgagagaacu
cucguuaaggaacucggcaaaaugaccccguaacuucgggagaaggggug
cucuguuagggugcaagcccgagagagccgcagugaauaggcccaggcga
cuguuuagcaaaaacacaggucucugcgaagccguaaggcgaaguauagg
ggcugacgccugcccggugcuggaagguuaagaggagcgcuuagcguaag
cgaaggugcgaauugaagccccaguaaacggcggccguaacuauaacggu
ccuaagguagcgaaauuccuugucggguaaguuccgacccgcacgaaagg
cgcaacgaucugggcacugucucaacgagagacucggugaaauuauagua
ccugugaagaugcagguuacccgcgacaggacggaaagaccccguggagc
uuuacugcagccugauauugaauguugguacagcuuguacaggauaggua
ggagccuuggaaaccggagcgccagcuucgguggaggcaucggugggaua
cuacccuggcuguauugaccuucuaacccgccgcccuuaucgggcgggga
gacagugucaggugggcaguuugacuggggcggucgccuccuaaaaggua
acggaggcgcccaaagguucccucagaaugguuggaaaucauucgcagag
uguaaaggcacaagggagcuugacugcgagaccuacaagucgagcaggga
cgaaagucgggcuuagugauccggugguuccgcauggaagggccaucgcu
caacggauaaaagcuaccccggggauaacaggcuuaucucccccaagagu
ccacaucgacggggagguuuggcaccucgaugucggcucaucgcauccug
gggcuguagucggucccaaggguugggcuguucgcccauuaaagcgguac
gcgagcuggguucagaacgucgugagacaguucggucccuauccgucgcg
ggcgcaggaaauuugagaggagcuguccuuaguacgagaggaccgggaug
gacgcaccgcugguguaccaguuguucugccaagggcaucgcuggguagc
uaugugcggacgggauaagugcugaaagcaucuaagcaugaagccccccu
caagaugagauuucccauuccgcaaggaaguaagaucccugaaagaugau
cagguugauaggucugagguggaaguguggcgacacauggagcugacaga
uacuaaucgaucgaggacuuaac

<<<<<<......<<<<<<<<<<<....{[[..[[<<<<<<<[[<<.....
.<<<<<<.....((.>>>.....<<<<<<<..<<<)).....>>>.....
>>>>>>>...>>>....<<<....>>><<<<<<<......>>>>>>>.<<
<<<<<<<.........>>>>>>>.>>.>>....<<<<<<.....<.....
.>......>>>>>.>.........<<....>>...<<<<......<<...
..>>.....>>>>...(((....<<<<<<<<<..>>>>>>>>>......<
<<<<<<<<.....<<<<.......<<<<<<<<<<.<<<.....<<<<...
...>>>>.((......<<<.....))>>>...>>>...>>>>>>>>>>>>
>>.>>>>>..>>>>.....<<<<<<<<.........>>>>>>>>......
<<<<<..<<<<>>>>>..)))......]].>>>>>>>.]]..........
.....<<....>>....]].........<<<<....>>>>..........
...}....>>>>>>>>>>>.......<<<<..<<<<......>>>>..>>
>>...<.<........>.>.<<<<<<....<<<<<<<.<<<<<..<<<..
.<<<.....>>>...>>>...<<....>>..<<<<.....>>>>......
>>>>>.>>>>>>>..<<.<..<<<<<<<.....<<<<<<<<<..<<<<..
.<<<<<<......>>>>>>...>.>>>...<<<.<<<<<........>>>
>>>>>....>>>>>>>>>...<<<.....>>>......>>>>>>...>..
>.>>..<<<<<<....<<<<<....>>>>><<<<<<<<<...<<<<<<<<
<.....<<<...<<<<<<<<...<<<<<<<.....>>>>>.>>...>>>>
>>>>..>>.>.....>>>>.>>>>>..>>>>>>>.>>..<<<<<<<.<<.
.....>>.>>>>>>>....<<<......>>>...<<<<.<<<...<<<((
(.....<<<<<<...........<<..<<<<<<<<<........<<<<<.
<<...<<<.........>>>...>>.........<<......>>...>>>
>>....>>>>>>>>>.>>...........))).....>>>>>>.>>>...
>>>>>>><<<<<<<...>>>>>>>....>>>>>>..<<<<<<<.<<....
..<<<<<.<<....>>.>>>>>...>>.>>>>>>>........>>>>>><
......<<....<<<<<<.......>>>>>><<<<....<<<<..<<...
<<<<<<...<<.....>>.>>>>>>....((<<<<.<<...<<<...<<<
....>>>...>>>...>>...<<<<<........>>>>>))<<<<<.<<<
<<<......<<...<<<<....<<<<..<<<..<<<.<.<<<.<.....{
....>.>>>.<<...<<<<<.<<<<.<<<<<<<.<<.....>>>>>>>>>
....>>>>..>>>>>...>><..<<...........>>...>>.>>>...
>>>...>>>>.........>>>>..>>..>>>>>>>>>>>>>>>..>>..
...<<......>>.>>>>.<<<<.....>>>>..>>>>..<<<<....<<
<<<<<<.<<...............<<<<<....<<..>>.....>>>>><
<<<<....<<<<....>>>>...>>>>>............<<<<<<<<<.
.<<<.........>>>..<<<<<<<.....<<<....>>>.......>>>
>>>>..<<<<.<<<..<<<<<<<..<<<...<<...<<<<<..<<....>
>...>>>>>...>>...>>>>>>>>..>>>>><<<<<<.......>>>>>
>........<...........<<<<<<.....>>>>>>.....>....>>
>>...>>.>>>>>>>.....>>.>>>>>>>>.>>>>>>.....>.(...<
<<<<.......)>>>>>..<<<<<<<<.(((.[[......<<<<.[[<<<
<..<<<<<.<<<<<<<<<.<<<.<<<<<<<<<<<<...........<<<<
<..<<<......<<<<<<<<....>>>>>>>>...>>>............
>>>>>..>>>>>>>>>>>>.>>>....<<.<<<<<<.....>>>>>>>>.
....>>>>>>>>>..>>>>>..<<<<.....>>>><<<<<<.........
..>>>>>>..<<...<<<<<<<...<<<<<<.......>>>>>>.....<
<.[.(((>>....>>>>>>>...<<<<..<<<......>>>..>>>>.<<
<....>>>.>>)))]......<<<<<<<.((..>>>>..))>>>>>>>..
...........>>>>..]]>>>>.......<<<<...<<<<<<...<<..
.....>>...>>>>>>....>>>.>.......<<<<<.<<<<<<..<<<<
<<<<<......>>>>>>..>>>.<<<<<.....>>>>>.....>>>>>..
>...>>>.>>....<<<<<<<....>>>.>>>>....]]..)))>>>>>>
>>....<<<<<<<...<<<<..<<<<<<<...............>>>>>>
>.<<<<<...<<<<...<<<<<<<<<<<.}..>>>>>>..>>>>>...>>
>>.>>>>>...<<<....<<<<<...........>>>>>....>>>.>>>
>.......>>>>>>>..<<<<....>>>>....<<<<<<<<<.......>
>>>>....<<<<<<<<.<<<....<<<<<....>>>>>...>>>..>>>>
>.>>>...>>>>....>>>>>>.

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3j9w Structure of the Bacillus subtilis 70S ribosome reveals the basis for species-specific stalling.
• Resolution: 3.9 Å
• Binding residue (original residue number in PDB): M1 K2 T14 R16 K25 R33 N35 K36 T37 E38 K40 N55 M57 N58 Y59 K60 K62 K64 R65 V66 Y69 G71 S74 R75 R77 K82
• Binding residue (residue number reindexed from 1): M1 K2 T14 R16 K25 R33 N35 K36 T37 E38 K40 N55 M57 N58 Y59 K60 K62 K64 R65 V66 Y69 G71 S74 R75 R77 K82

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome
• GO:0019843 rRNA binding

Biological Process

• GO:0000027 ribosomal large subunit assembly
• GO:0006412 translation

Cellular Component

• GO:0005840 ribosome
• GO:0022625 cytosolic large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:3j9w, PDBe:3j9w, PDBj:3j9w
• PDBsum: 3j9w
• PubMed: 25903689
• UniProt: P42924|RL23_BACSU Large ribosomal subunit protein uL23 (Gene Name=rplW)