Structure of PDB 3j3v Chain N Binding Site BS01

Receptor Information

>3j3v Chain N (length=120) Species: 224308 (Bacillus subtilis subsp. subtilis str. 168)

MSYRKLGRTSAQRKAMLRDLTTDLIINERIETTETRAKELRSVVEKMITL
GKRGDLHARRQAAAYIRNEVANEENNQDALQKLFSDIATRYEERQGGYTR
IMKLGPRRGDGAPMAIIELV

Ligand information

>3j3v Chain A (length=2884)

gguuaaguuagaaagggcgcacgguggaugccuuggcacuaggagccgau
gaaggacgggacgaacaccgauaugcuucggggagcuguaagcaagcuuu
gauccggagauuuccgaauggggaaacccaccacucguaauggaguggua
uccauaucugaauucauaggauaugagaaggcagacccggggaacugaaa
caucuaaguacccggaggaagagaaagcaaaugcgauucccugaguagcg
gcgagcgaaacgggauuagcccaaaccaagaggcuugccucuugggguug
uaggacacucuguacggaguuacaaaggaacgagguagaugaagaggucu
ggaaaggcccgccauaggagguaacagcccuguagucaaaacuucguucu
cuccugaguggauccugaguacggcggaacacgugaaauuccgucggaau
ccgggaggaccaucucccaaggcuaaauacucccuagugaccgauaguga
accaguaccgugagggaaaggugaaaagcaccccggaaggggagugaaag
agauccugaaaccgugugccuacaaguagucagagcccguuaacggguga
uggcgugccuuuuguagaaugaaccggcgaguuacgaucccgugcaaggu
uaagcagaagaugcggagccgcagcgaaagcgagucugaauagggcgcau
gaguacguggucguagacccgaaaccaggugaucuacccauguccagggu
gaaguucagguaacacugaauggaggcccgaacccacgcacguugaaaag
ugcggggaugagguguggguaggggugaaaugccaaucgaaccuggagau
agcugguucucuccgaaauagcuuuagggcuagccucaagguaagagucu
uggagguagagcacugauuggacuaggggccccuaccggguuaccgaauu
cagucaaacuccgaaugccaaugacuuauccuugggagucagacugcgag
ugauaagauccguagucgaaagggaaacagcccagaccgccagcuaaggu
cccaaaguauacguuaaguggaaaaggauguggaguugcuuagacaacca
ggauguuggcuuagaagcagccaccauuuaaagagugcguaauagcucac
uggucgagugacucugcgccgaaaauguaccggggcuaaacguaucaccg
aagcugcggacuguucuucgaacagugguaggagagcguucuaagggcug
ugaagccagaccggaaggacugguggagcgcuuagaagugagaaugccgg
uaugaguagcgaaagaggggugagaauccccuccaccgaaugccuaaggu
uuccugaggaaggcucguccgcucaggguuagucgggaccuaagccgagg
ccgaaaggcguaggcgauggacaacagguugauauuccuguaccaccucc
ucaccauuugagcaauggggggacgcaggaggauaggguaagcgcgguau
uggauauccgcguccaagcaguuaggcugggaaauaggcaaauccguuuc
ccauaaggcugagcugugauggcgagcgaaauauaguagcgaaguuccug
auuccacacugccaagaaaagccucuagcgaggugagaggugcccguacc
gcaaaccgacacagguaggcgaggagagaauccuaaggugaucgagagaa
cucucguuaaggaacucggcaaaaugaccccguaacuucgggagaagggg
ugcucuguuagggugcaagcccgagagagccgcagugaauaggcccaggc
gacuguuuagcaaaaacacaggucucugcgaagccguaaggcgaaguaua
ggggcugacgccugcccggugcuggaaccccaguaaacggcggccguaac
uauaacgguccuaagguagcgaaauuccuugucggguaaguuccgacccg
cacgaaaggcgcaacgaucugggcacugucucaacgagagacucggugaa
auuauaguaccugugaagaugcagguuacccgcgacaggacggaaagacc
ccguggagcuuuacugcagccugauauugaauguugguacagcuuguaca
ggauagguaggagccuuggaaaccggagcgccagcuucgguggaggcauc
ggugggauacuacccuggcuguauugaccuucuaacccgccgcccuuauc
gggcggggagacagugucaggugggcaguuugacuggggcggucgccucc
uaaaagguaacggaggcgcccaaagguucccucagaaugguuggaaauca
uucgcagaguguaaaggcacaagggagcuugacugcgagaccuacaaguc
gagcagggacgaaagucgggcuuagugauccggugguuccgcauggaagg
gccaucgcucaacggauaaaagcuaccccggggauaacaggcuuaucucc
cccaagaguccacaucgacggggagguuuggcaccucgaugucggcucau
cgcauccuggggcuguagucagucccaaggguugggcuguucgcccauua
aagcgguacgcgagcuggguucagaacgucgugagacaguucggucccua
uccgucgcgggcgcaggaaauuugagaggagcuguccuuaguacgagagg
accgggauggacgcaccgcugguguaccaguuguucugccaagggcaucg
cuggguagcuaugugcggacgggauaagugcugaaagcaucuaagcauga
agccccccucaagaugagauuucccauuccgcaaggaaguaagaucccug
aaagaugaucagguugauaggucugagguggaaguguggcgacacaugga
gcugacagauacuaaucgaucgaggacuuaacca

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3j3v Cryo-EM structures of the late-stage assembly intermediates of the bacterial 50S ribosomal subunit
• Resolution: 13.3 Å
• Binding residue (original residue number in PDB): M1 S2 Y3 R4 K5 L6 G7 R8 A11 Q12 K14 M16 R18 D19 D23 N27 E31 R36 K38 R41 S42 E45 K46 R53 L56 H57 R59 R60 R67 N68 E69 V70 A71 N72 E73 N75 N76 Q81 R94 Q95 G96 G97 R100 I101 M102 K103 R108 D110 G111 A112
• Binding residue (residue number reindexed from 1): M1 S2 Y3 R4 K5 L6 G7 R8 A11 Q12 K14 M16 R18 D19 D23 N27 E31 R36 K38 R41 S42 E45 K46 R53 L56 H57 R59 R60 R67 N68 E69 V70 A71 N72 E73 N75 N76 Q81 R94 Q95 G96 G97 R100 I101 M102 K103 R108 D110 G111 A112

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome

Biological Process

• GO:0006412 translation

Cellular Component

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

External links

• PDB: RCSB:3j3v, PDBe:3j3v, PDBj:3j3v
• PDBsum: 3j3v
• PubMed: 23700310
• UniProt: P20277|RL17_BACSU Large ribosomal subunit protein bL17 (Gene Name=rplQ)