Structure of PDB 5njt Chain X Binding Site BS01

Receptor Information

>5njt Chain X (length=207) Species: 224308 (Bacillus subtilis subsp. subtilis str. 168)

TKGILGRKIGMTQVFAENGDLIPVTVIEAAPNVVLQKKTAENDGYEAIQL
GFDDKREKLSNKPEKGHVAKAETAPKRFVKELRGVEMDAYEVGQEVKVEI
FSAGEIVDVTGVSKGKGFQGAIKRHGQSRGPMSHGSRYHRRPGSMGPVDP
NRVFKGKLLPGRMGGEQITVQNLEIVKVDAERNLLLIKGNVPGAKKSLIT
VKSAVKS

Ligand information

>5njt Chain U (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: 5njt Structure of the Bacillus subtilis hibernating 100S ribosome reveals the basis for 70S dimerization.
• Resolution: 3.8 Å
• Binding residue (original residue number in PDB): M12 Q14 P24 Q37 Y46 R57 L60 N62 K63 P64 G67 H68 R78 V80 K81 E82 R84 K115 G116 K117 G118 F119 G121 K124 R125 Q128 S129 R130 M133 S134 H135 G136 S137 R138 Y139 H140 R141 S145 M146 P148 V149 D150 P151 N152 R153 V154 F155 K156 G157 K158 L160 P161 R163 E167 I169 T170 Q172 N173 K189 N191 P193 V206 K207 S208
• Binding residue (residue number reindexed from 1): M11 Q13 P23 Q36 Y45 R56 L59 N61 K62 P63 G66 H67 R77 V79 K80 E81 R83 K114 G115 K116 G117 F118 G120 K123 R124 Q127 S128 R129 M132 S133 H134 G135 S136 R137 Y138 H139 R140 S144 M145 P147 V148 D149 P150 N151 R152 V153 F154 K155 G156 K157 L159 P160 R162 E166 I168 T169 Q171 N172 K188 N190 P192 V205 K206 S207

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:5njt, PDBe:5njt, PDBj:5njt
• PDBsum: 5njt
• PubMed: 28468753
• UniProt: P42920|RL3_BACSU Large ribosomal subunit protein uL3 (Gene Name=rplC)