Structure of PDB 7yla Chain M Binding Site BS01

Receptor Information

>7yla Chain M (length=201) Species: 562 (Escherichia coli)

MELVLKDAQSALTVSETTFGRDFNEALVHQVVVAYAAGARQGTRAQKTRA
EVTGSGKKPWRQKGTGRARSGSIKSPIWRSGGVTFAARPQDHSQKVNKKM
YRGALKSILSELVRQDRLIVVEKFSVEAPKTKLLAQKLKDMALEDVLIIT
GELDENLFLAARNLHKVDVRDATGIDPVSLIAFDKVVMTADAVKQVEEML
A

Ligand information

>7yla Chain I (length=2876)

gguuaagcgacuaagcguacacgguggaugcccuggcagucagaggcgau
gaaggacgugcuaaucugcgauaagcgucgguaaggugauaugaaccguu
auaaccggcgauuuccgaauggggaaacccaguguguuucgacacacuau
cauuaacugaauccauagguuaaugaggcgaaccgggggaacugaaacau
cuaaguaccccgaggaaaagaaaucaaccgagauucccccaguagcggcg
agcgaacggggagcagcccagagccugaaucaguguguguguuaguggaa
gcgucuggaaaggcgcgcgauacagggugacagccccguacacaaaaaug
cacaugcugugagcucgaugaguagggcgggacacgugguauccugucug
aauauggggggaccauccuccaaggcuaaauacuccugacugaccgauag
ugaaccaguaccgugagggaaaggcgaaaagaaccccggcgaggggagug
aaaaagaaccugaaaccguguacguacaagcagugggagcacgcugcgug
ugacugcguaccuuuuguauaaugggucagcgacuuauauucuguagcaa
gguuaaccgaauaggggagccgaagggaaaccgagucuuaacugggcguu
aaguugcaggguauagacccgaaacccggugaucuagccaugggcagguu
gaagguuggguaacacuaacuggaggaccgaaccgacuaauguugaaaaa
uuagcggaugacuuguggcugggggugaaaggccaaucaaaccgggagau
agcugguucuccccgaaagcuauuuagguagcgccucgugaauucaucuc
cggggguagagcacuguuucggcaagggggucacuuaccaacccgaugca
aacugcgaauaccggagaauguuaucacgggagacacacggcgggugcua
acguccgucgugaagagggaaacaacccagaccgccagcuaaggucccaa
agucaugguuaagugggaaacgaugugggaaggcccagacagccaggaug
uuggcaagcagccaucauuuaaagaaagcguaauagcucacuggucgagu
cggccugcgcggaagauguaacggggcuaaaccaugcaccgaagcugcgg
cagcgacgcuuaugcguuguuggguaggggagcguucuguaagccugcga
aggugugcugugaggcaugcuggagguaucagaagugcgaaugcugacau
aaguaacgauaaagcgggugaaaagcccgcucgccggaagaccaaggguu
ccuguccaacguuaaucggggcagggugagucgaccccuaaggcgaggcc
gaaaggcguagucgaugggaaacagguuaauauuccuguacuugguguua
cugcgaaggggggacggagaaggcuauguuggccgggcgacgguuguccc
gguuuaagcguguaggcugguuuuccaggcaaauccggaaaaucaaggcu
gaggcgugaugacgaggcacuacggugcugaagcaacaaaugcccugcuu
ccaggaaaagccucuaagcaucagguaacaucaaaucguaccccaaaccg
acacagguggucagguagagaauaccaaggcgcuugagagaacucgggug
aaggaacuaggcaaaauggugccguaacuucgggagaaggcacgcugaua
uguaggugaggucccucgcggauggagcugaaaucagucgaagauaccag
cuggcugcaacuguuuauuaaaaacacagcacugugcaaacacgaaagug
gacguauacggugugacgccugcccggugccggaagguuaauugaugggg
uuagcgcaagcgaagcucuugaucgaagccccgguaaacggcggccgguc
cuaagguagcgaaauuccuugucggguaaguuccgaccugcacgaauggc
guaaugauggccaggcugucuccacccgagacucagugaaauugaacucg
cugugaagaugcaguguacccgcggcaagacggaaagaccccgugaaccu
uuacuauagcuugacacugaacauugagccuugauguguaggauaggugg
gaggcuuugaaguguggacgccagucugcauggagccgaccuugaaauac
cacccuuuaauguuugauguucuaacguugacccguaauccggguugcgg
acagugucugguggguaguuugacuggggcggucuccuccuaaagaguaa
cggaggagcacgaagguuggcuaauccuggucggacaucaggagguuagu
gcaauggcauaagccagcuugacugcgagcgugacggcgcgagcaggugc
gaaagcaggucauagugauccggugguucugaauggaagggccaucgcuc
aacggauaaaagguacuccggggauaacaggcugauaccgcccaagaguu
cauaucgacggcgguguuuggcaccucgaugucggcucaucacauccugg
ggcugaaguaggucccaaggguauggcuguucgccauuuaaagugguacg
cgagcuggguuuagaacgucgugagacaguucggucccuaucugccgugg
gcgcuggagaacugaggggggcugcuccuaguacgagaggaccggagugg
acgcaucacugguguucggguugucaugccaauggcacugcccgguagcu
aaaugcggaagagauaagugcugaaagcaucuaagcacgaaacuugcccc
gagaugaguucucccugacccuuuaaggguccugaaggaacguugaagac
gacgacguugauaggccggguguguaagcgcagcgaugcguugagcuaac
cgguacuaaugaaccgugaggcuuaa

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7yla Cryo-EM structure of 50S-HflX complex
• Resolution: 2.52 Å
• Binding residue (original residue number in PDB): N24 H29 Q30 Y35 A36 A39 R40 Q41 T43 R44 A45 Q46 K47 T48 R49 A50 V52 T53 G54 S55 K57 K58 Q62 K63 G64 T65 G66 R67 A68 R69 G71 S75 I77 W78 R79 S80 V83 T84 F85 P89 Q90 K95 N97 K98 K99 M100 R102 P129 K130 T131 L159 R162 N163 L164 H165
• Binding residue (residue number reindexed from 1): N24 H29 Q30 Y35 A36 A39 R40 Q41 T43 R44 A45 Q46 K47 T48 R49 A50 V52 T53 G54 S55 K57 K58 Q62 K63 G64 T65 G66 R67 A68 R69 G71 S75 I77 W78 R79 S80 V83 T84 F85 P89 Q90 K95 N97 K98 K99 M100 R102 P129 K130 T131 L159 R162 N163 L164 H165

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:7yla, PDBe:7yla, PDBj:7yla
• PDBsum: 7yla
• UniProt: P60723|RL4_ECOLI Large ribosomal subunit protein uL4 (Gene Name=rplD)