Structure of PDB 3j3v Chain L Binding Site BS01

Receptor Information

>3j3v Chain L (length=146) Species: 224308 (Bacillus subtilis subsp. subtilis str. 168)

MKLHELKPSEGSRKTRNRVGRGIGSGNGKTAGKGHKGQNARSGGGVRPGF
EGGQMPLFQRLPKRGFTNINRKEYAVVNLDKLNGFAEGTEVTPELLLETG
VISKLNAGVKILGNGKLEKKLTVKANKFSASAKEAVEAAGGTAEVI

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): L3 H4 K7 P8 S9 E10 G11 R13 K14 T15 R16 N17 R18 G20 R21 I23 S25 N27 G28 K29 T30 A31 K33 G34 H35 K36 G37 Q38 A40 R41 S42 G43 R47 P48 F50 E51 G52 G53 Q54 M55 P56 L57 F58 Q59 R60 P62 K63 R64 G65 F66 N68 R71 K72 Y74 V76 N78 K81 G100 V101 I102 K104 K110 L112 G113 N114 S129 S131
• Binding residue (residue number reindexed from 1): L3 H4 K7 P8 S9 E10 G11 R13 K14 T15 R16 N17 R18 G20 R21 I23 S25 N27 G28 K29 T30 A31 K33 G34 H35 K36 G37 Q38 A40 R41 S42 G43 R47 P48 F50 E51 G52 G53 Q54 M55 P56 L57 F58 Q59 R60 P62 K63 R64 G65 F66 N68 R71 K72 Y74 V76 N78 K81 G100 V101 I102 K104 K110 L112 G113 N114 S129 S131

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:3j3v, PDBe:3j3v, PDBj:3j3v
• PDBsum: 3j3v
• PubMed: 23700310
• UniProt: P19946|RL15_BACSU Large ribosomal subunit protein uL15 (Gene Name=rplO)