Structure of PDB 6by1 Chain CE Binding Site BS01

Receptor Information

>6by1 Chain CE (length=181) Species: 83333 (Escherichia coli K-12)

RDFNEALVHQVVVAYAAGARQGTRAQKTRAEVTGSGKKPWRQKGTGRARS
GSIKSPIWRSGGVTFAARPQDHSQKVNKKMYRGALKSILSELVRQDRLIV
VEKFSVEAPKTKLLAQKLKDMALEDVLIITGELDENLFLAARNLHKVDVR
DATGIDPVSLIAFDKVVMTADAVKQVEEMLA

Ligand information

>6by1 Chain CA (length=2867)

gguuaagcgacuaagcguacacgguggaugcccuggcagucagaggcgau
gaaggacgugcuaaucugcgauaagcgucgguaaggugauaugaaccguu
auaaccggcgauuuccgaauggggaaacccaguguguuucgacacacuau
cauuaacugaauccauagguuaaugaggcgaaccgggggaacugaaacau
cuaaguaccccgaggaaaagaaaucaaccgagauucccccaguagcggcg
agcgaacggggagcagcccagagccugaaucaguguguguguuaguggaa
gcgucuggaaaggcgcgcgauacagggugacagccccguacacaaaaaug
cacaugcugugagcucgaugaguagggcgggacacgugguauccugucug
aauauggggggaccauccuccaaggcuaaauacuccugacugaccgauag
ugaaccaguaccgugagggaaaggcgaaaagaaccccggcgaggggagug
aaaaagaaccugaaaccguguacguacaagcagugggagcacgcuuaggc
gugugacugcguaccuuuuguauaaugggucagcgacuuauauucuguag
caagguuaaccgaauaggggagccgaagggaaaccgagucuuaacugggc
guuaaguugcaggguauagacccgaaacccggugaucuagccaugggcag
guugaagguuggguaacacuaacuggaggaccgaaccgacuaauguugaa
aaauuagcggaugacuuguggcugggggugaaaggccaaucaaaccggga
gauagcugguucuccccgaaagcuauuuagguagcgccucgugaauucau
cuccggggguagagcacuguuucggcaagggggucaucccgacuuaccaa
cccgaugcaaacugcgaauaccggagaauguuaucacgggagacacacgg
cgggugcuaacguccgucgugaagagggaaacaacccagaccgccagcua
aggucccaaagucaugguuaagugggaaacgaugugggaaggcccagaca
gccaggauguuggcuuagaagcagccaucauuuaaagaaagcguaauagc
ucacuggucgagucggccugcgcggaagauguaacggggcuaaaccaugc
accgaagcugcggcagcgacgcuuaugcguuguuggguaggggagcguuc
uguaagccugcgaaggugugcugugaggcaugcuggagguaucagaagug
cgaaugcugacauaaguaacgauaaagcgggugaaaagcccgcucgccgg
aagaccaaggguuccuguccaacguuaaucggggcagggugagucgaccc
cuaaggcgaggccgaaaggcguagucgaugggaaacagguuaauauuccu
guacuugguguuacugcgaaggggggacggagaaggcuauguuggccggg
cgacgguugucccgguuuaagcguguaggcugguuuuccaggcaaauccg
gaaaaucaaggcugaggcgugaugacgaggcacuacggugcugaagcaac
aaaugcccugcuuccaggaaaagccucuaagcaucagguaacaucaaauc
guaccccaaaccgacacagguggucagguagagaauaccaaggcgcuuga
gagaacucgggugaaggaacuaggcaaaauggugccguaacuucgggaga
aggcacgcugauauguaggugaggucccucgcggauggagcugaaaucag
ucgaagauaccagcuggcugcaacuguuuauuaaaaacacagcacugugc
aaacacgaaaguggacguauacggugugacgccugcccggugccggaagg
uuaauugaugggguuagcgcaagcgaagcucuugaucgaagccccgguaa
acggcggccguaacuauaacgguccuaagguagcgaaauuccuugucggg
uaaguuccgaccugcacgaauggcguaaugauggccaggcugucuccacc
cgagacucagugaaauugaacucgcugugaagaugcaguguacccgcggc
aagacggaaagaccccgugaaccuuuacuauagcuugacacugaacauug
agccuugaugggugggaggcuuguguauggagccgaaccacccuuuaaug
uuugauguucuaacguugacccguaauccggguugcggacagugucuggu
ggguaguuugacuggggcggucuccuccuaaagaguaacggaggagcacg
aagguuggcuaauccuggucggacaucaggagguuagugcaauggcauaa
gccagcuugacugcgagcgugacggcgcgagcaggugcgaaagcagguca
uagugauccggugguucugaauggaagggccaucgcucaacggauaaaag
guacuccggggauaacaggcugauaccgcccaagaguucauaucgacggc
gguguuuggcaccucgaugucggcucaucacauccuggggcugaaguagg
ucccaaggguauggcuguucgccauuuaaagugguacgcgagcuggguuu
agaacgucgugagacaguucggucccuaucugccgugggcgcuggagaac
ugaggggggcugcuccuaguacgagaggaccggaguggacgcaucacugg
uguucggguugucaugccaauggcacugcccgguagcuaaaugcggaaga
gauaagugcugaaagcaucuaagcacgaaacuugccccgagaugaguucu
cccugacccuuuaaggguccugaaggaacguugaagacgacgacguugau
aggccggguguguaagcgcagcgaugcguugagcuaaccgguacuaauga
accgugaggcuuaaccu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6by1 Structural evidence for product stabilization by the ribosomal mRNA helicase.
• Resolution: 3.94 Å
• Binding residue (original residue number in PDB): N24 H29 Q30 Y35 A39 R40 Q41 T43 R44 A45 Q46 K47 T48 R49 A50 V52 G54 S55 K58 Q62 K63 G64 T65 G66 R67 A68 R69 G71 I77 W78 R79 S80 V83 T84 F85 Q90 Q94 K95 N97 K98 M100 Y101 P129 K130 T131 L159 R162 N163 H165 T173
• Binding residue (residue number reindexed from 1): N4 H9 Q10 Y15 A19 R20 Q21 T23 R24 A25 Q26 K27 T28 R29 A30 V32 G34 S35 K38 Q42 K43 G44 T45 G46 R47 A48 R49 G51 I57 W58 R59 S60 V63 T64 F65 Q70 Q74 K75 N77 K78 M80 Y81 P109 K110 T111 L139 R142 N143 H145 T153

Gene Ontology

Molecular Function

• GO:0001070 RNA-binding transcription regulator activity
• GO:0003677 DNA binding
• GO:0003735 structural constituent of ribosome
• GO:0005515 protein binding
• GO:0019843 rRNA binding
• GO:0030371 translation repressor activity
• GO:0048027 mRNA 5'-UTR binding
• GO:0060698 endoribonuclease inhibitor activity

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006353 DNA-templated transcription termination
• GO:0006412 translation
• GO:0006417 regulation of translation
• GO:0017148 negative regulation of translation
• GO:0031555 transcriptional attenuation
• GO:0042255 ribosome assembly
• GO:0045892 negative regulation of DNA-templated transcription
• GO:0046677 response to antibiotic
• GO:2000766 negative regulation of cytoplasmic translation

Cellular Component

• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0015934 large ribosomal subunit
• GO:0022625 cytosolic large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:6by1, PDBe:6by1, PDBj:6by1
• PDBsum: 6by1
• PubMed: 30552154
• UniProt: P60723|RL4_ECOLI Large ribosomal subunit protein uL4 (Gene Name=rplD)