Structure of PDB 3j3w Chain D Binding Site BS01

Receptor Information

>3j3w Chain D (length=206) Species: 224308 (Bacillus subtilis subsp. subtilis str. 168)

KGILGRKIGMTQVFAENGDLIPVTVIEAAPNVVLQKKTAENDGYEAIQLG
FDDKREKLSNKPEKGHVAKAETAPKRFVKELRGVEMDAYEVGQEVKVEIF
SAGEIVDVTGVSKGKGFQGAIKRHGQSRGPMSHGSRYHRRPGSMGPVDPN
RVFKGKLLPGRMGGEQITVQNLEIVKVDAERNLLLIKGNVPGAKKSLITV
KSAVKS

Ligand information

>3j3w Chain A (length=2685)

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
ggggcugacgccugcgcggccguaacuauaacgguccuaagguagcgaaa
ggcgcaacgaucugggcacugucucaacgagagacucggugaaauuauag
uaccugugaagaugcagguuacccgcgacaggacggaaagaccccgugga
gcuuuacugcagccugauauugaauguugguacagcuuguacaggauagg
uaggagccuuggaaaccggagcgccagcuucgguggaggcaucgguggga
uacuacccuggcuguauugaccuucuaacccgccgcccuuaucgggcggg
gagacagugucaggugggcaguuuggugauccggugguuccgcauggaag
ggccaucgcucaacggauaaaagcuaccccggggauaacaggcuuaucuc
ccccaagaguccacaucgacggggagguuuggcaccucgaugucggcuca
ucgcauccuggggcuguagucagucccaaggguugggcuguucgcccauu
aaagcgguacgcgagcuggguucagaacgucgugagacaguucggucccu
auccgucgcgggcgcaggaaauuugagaggagcuguccuuaguacgagag
gaccgggauggacgcaccgcugguguaccaguuguucugccaagggcauc
gcuggguagcuaugugcggacgggauaagugcugaaagcaucuaagcaug
aagccccccucaagaugagauuucccauuccgcaaggaaguaagaucccu
gaaagaugaucagguugauaggucugagguggaaguguggcgacacaugg
agcugacagauacuaaucgaucgaggacuuaacca

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3j3w Cryo-EM structures of the late-stage assembly intermediates of the bacterial 50S ribosomal subunit
• Resolution: 10.7 Å
• Binding residue (original residue number in PDB): M12 T13 Q14 P24 N43 D44 Y46 R57 K59 L60 N62 K63 P64 G67 H68 K71 R78 V80 E82 R84 S114 K115 G116 F119 G121 R125 Q128 S129 R130 G131 M133 S134 H135 G136 S137 R138 Y139 R141 R142 P143 G144 S145 M146 G147 P148 V149 D150 P151 N152 R153 V154 F155 K156 G157 K158 L160 P161 R163 Q168 I169 T170 V171 Q172 N173 K189 N191 V192 P193 G194 K196 V206 K207 S208
• Binding residue (residue number reindexed from 1): M10 T11 Q12 P22 N41 D42 Y44 R55 K57 L58 N60 K61 P62 G65 H66 K69 R76 V78 E80 R82 S112 K113 G114 F117 G119 R123 Q126 S127 R128 G129 M131 S132 H133 G134 S135 R136 Y137 R139 R140 P141 G142 S143 M144 G145 P146 V147 D148 P149 N150 R151 V152 F153 K154 G155 K156 L158 P159 R161 Q166 I167 T168 V169 Q170 N171 K187 N189 V190 P191 G192 K194 V204 K205 S206

Gene Ontology

Molecular Function

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

Biological Process

• GO:0006364 rRNA processing
• GO:0006412 translation
• GO:2000234 positive regulation of rRNA processing

Cellular Component

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

External links

• PDB: RCSB:3j3w, PDBe:3j3w, PDBj:3j3w
• PDBsum: 3j3w
• PubMed: 23700310
• UniProt: P42920|RL3_BACSU Large ribosomal subunit protein uL3 (Gene Name=rplC)