Structure of PDB 6o9k Chain L Binding Site BS01

Receptor Information

>6o9k Chain L (length=143) Species: 562 (Escherichia coli)

RLNTLSPAEGSKKAGKRLGRGIGSGLGKTGGRGHKGQKSRSGGGVRRGFE
GGQMPLYRRLPKFGFTSRKAAITAEIRLSDLAKVEGGVVDLNTLKAANII
GIQIEFAKVILAGEVTTPVTVRGLRVTKGARAAIEAAGGKIEE

Ligand information

>6o9k Chain A (length=2854)

gguuaagcgacuaagcguacacgguggaugcccuggcagucagaggcgau
gaaggacgugcuaaucugcgauaagcgucgguaaggugauaugaaccguu
auaaccggcgauuuccgaauggggaaacccaguguguuucgacacacuau
cauuaacugaauccauagguuaaugaggcgaaccgggggaacugaaacau
cuaaguaccccgaggaaaagaaaucaaccgagauucccccaguagcggcg
agcgaacggggagcagcccagagccugaaucaguguguguguuaguggaa
gcgucuggaaaggcgcgcgauacagggugacagccccguacacaaaaaug
cacaugcugugagcucgaugaguagggcgggacacgugguauccugucug
aauauggggggaccauccuccaaggcuaaauacuccugacugaccgauag
ugaaccaguaccgugagggaaaggcgaaaagaaccccggcgaggggagug
aaaaagaaccugaaaccguguacguacaagcagugggagcacgcuuaggc
gugugacugcguaccuuuuguauaaugggucagcgacuuauauucuguag
caagguuaaccgaauaggggagccgaagggaaaccgagucuuaacugggc
guuaaguugcaggguauagacccgaaacccggugaucuagccaugggcag
guugaagguuggguaacacuaacuggaggaccgaaccgacuaauguugaa
aaauuagcggaugacuuguggcugggggugaaaggccaaucaaaccggga
gauagcugguucuccccgaaagcuauuuagguagcgccucgugaauucau
cuccggggguagagcacuguuucggcaagggggucacuuaccaacccgau
gcaaacugcgaauaccggagaauguuaucacgggagacacacggcgggug
cuaacguccgucgugaagagggaaacaacccagaccgccagcuaaggucc
caaagucaugguuaagugggaaacgaugugggaaggcccagacagccagg
auguuggcuuagaagcagccaucauuuaaagaaagcguaauagcucacug
gucgagucggccugcgcggaagauguaacggggcuaaaccaugcaccgaa
gcugcggcagcgacgcuuaugcguuguuggguaggggagcguucuguaag
ccugcgaaggugugcugugaggcaugcuggagguaucagaagugcgaaug
cugacauaaguaacgauaaagcgggugaaaagcccgcucgccggaagacc
aaggguuccuguccaacguuaaucggggcagggugagucgaccccuaagg
cgaggccgaaaggcguagucgaugggaaacagguuaauauuccuguacuu
gguguuacugcgaaggggggacggagaaggcuauguuggccgggcgacgg
uugucccgguuuaagcguguaggcugguuuuccaggcaaauccggaaaau
caaggcugaggcgugaugacgaggcacuacggugcugaagcaacaaaugc
ccugcuuccaggaaaagccucuaagcaucagguaacaucaaaucguaccc
caaaccgacacagguggucagguagagaauaccaaggcgcuugagagaac
ucgggugaaggaacuaggcaaaauggugccguaacuucgggagaaggcac
gcugauauguaggugaggucccucgcggauggagcugaaaucagucgaag
auaccagcuggcugcaacuguuuauuaaaaacacagcacugugcaaacac
gaaaguggacguauacggugugacgccugcccggugccggaagguuaauu
gaugggguuagcgcaagcgaagcucuugaucgaagccccgguaaacggcg
gccguaacuauaacgguccuaagguagcgaaauuccuugucggguaaguu
ccgaccugcacgaauggcguaaugauggccaggcugucuccacccgagac
ucagugaaauugaacucgcugugaagaugcaguguacccgcggcaagacg
gaaagaccccgugaaccuuuacuauagcuugacacugaacauugagccuu
gauggaaguguggacgccagucugcauggcuuuaauguuugauguucuaa
cguugacccguaauccggguugcggacagugucugguggguaguuugacu
ggggcggucuccuccuaaagaguaacggaggagcacgaagguuggcuaau
ccuggucggacaucaggagguuagugcaauggcauaagccagcuugacug
cgagcgugacggcgcgagcaggugcgaaagcaggucauagugauccggug
guucugaauggaagggccaucgcucaacggauaaaagguacuccggggau
aacaggcugauaccgcccaagaguucauaucgacggcgguguuuggcacc
ucgaugucggcucaucacauccuggggcugaaguaggucccaaggguaug
gcuguucgccauuuaaagugguacgcgagcuggguuuagaacgucgugag
acaguucggucccuaucugccgugggcgcuggagaacugaggggggcugc
uccuaguacgagaggaccggaguggacgcaucacugguguucggguuguc
augccaauggcacugcccgguagcuaaaugcggaagagauaagugcugaa
agcaucuaagcacgaaacuugccccgagaugaguucucccugacccuuua
aggguccugaaggaacguugaagacgacgacguugauaggccgggugugu
aagcgcagcgaugcguugagcuaaccgguacuaaugaaccgugaggcuua
accu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6o9k Late steps in bacterial translation initiation visualized using time-resolved cryo-EM.
• Resolution: 4.0 Å
• Binding residue (original residue number in PDB): R2 N4 S12 K13 K14 K17 R18 L19 G20 R21 G22 I23 G24 G28 K29 T30 G31 R33 H35 K36 G37 Q38 K39 R41 S42 G43 R47 R48 F50 E51 G52 Q54 Y58 R59 R60 P62 K63 F64 G65 F66 T67 S68 R69 K70 E76 R78 N99 K109 I111 L112 R126 T128 K129 G130
• Binding residue (residue number reindexed from 1): R1 N3 S11 K12 K13 K16 R17 L18 G19 R20 G21 I22 G23 G27 K28 T29 G30 R32 H34 K35 G36 Q37 K38 R40 S41 G42 R46 R47 F49 E50 G51 Q53 Y57 R58 R59 P61 K62 F63 G64 F65 T66 S67 R68 K69 E75 R77 N98 K108 I110 L111 R125 T127 K128 G129

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome
• GO:0005515 protein binding
• GO:0019843 rRNA binding

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006412 translation

Cellular Component

• GO:0005737 cytoplasm
• GO:0005840 ribosome
• GO:0015934 large ribosomal subunit
• GO:0022625 cytosolic large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:6o9k, PDBe:6o9k, PDBj:6o9k
• PDBsum: 6o9k
• PubMed: 31108498
• UniProt: P02413|RL15_ECOLI Large ribosomal subunit protein uL15 (Gene Name=rplO)