Structure of PDB 7bl3 Chain E Binding Site BS01

Receptor Information

>7bl3 Chain E (length=201) Species: 83333 (Escherichia coli K-12)

MELVLKDAQSALTVSETTFGRDFNEALVHQVVVAYAAGARQGTRAQKTRA
EVTGSGKKPWRQKGTGRARSGSIKSPIWRSGGVTFAARPQDHSQKVNKKM
YRGALKSILSELVRQDRLIVVEKFSVEAPKTKLLAQKLKDMALEDVLIIT
GELDENLFLAARNLHKVDVRDATGIDPVSLIAFDKVVMTADAVKQVEEML
A

Ligand information

>7bl3 Chain A (length=2902)

guuguaagguuaagcgacuaagcguacacgguggaugcccuggcagucag
aggcgaugaaggacgugcuaaucugcgauaagcgucgguaaggugauaug
aaccguuauaaccggcgauuuccgaauggggaaacccaguguguuucgac
acacuaucauuaacugaauccauagguuaaugaggcgaaccgggggaacu
gaaacaucuaaguaccccgaggaaaagaaaucaaccgagauucccccagu
agcggcgagcgaacggggagcagcccagagccugaaucaguguguguguu
aguggaagcgucuggaaaggcgcgcgauacagggugacagccccguacac
aaaaaugcacaugcugugagcucgaugaguagggcgggacacgugguauc
cugucugaauauggggggaccauccuccaaggcuaaauacuccugacuga
ccgauagugaaccaguaccgugagggaaaggcgaaaagaaccccggcgag
gggagugaaaaagaaccugaaaccguguacguacaagcagugggagcacg
cuuaggcgugugacugcguaccuuuuguauaaugggucagcgacuuauau
ucuguagcaagguuaaccgaauaggggagccgaagggaaaccgagucuua
acugggcguuaaguugcaggguauagacccgaaacccggugaucuagcca
ugggcagguugaagguuggguaacacuaacuggaggaccgaaccgacuaa
uguugaaaaauuagcggaugacuuguggcugggggugaaaggccaaucaa
accgggagauagcugguucuccccgaaagcuauuuagguagcgccucgug
aauucaucuccggggguagagcacuguuucggcaagggggucacuuacca
acccgaugcaaacugcgaauaccggagaauguuaucacgggagacacacg
gcgggugcuaacguccgucgugaagagggaaacaacccagaccgccagcu
aaggucccaaagucaugguuaagugggaaacgaugugggaaggcccagac
agccaggauguuggcuuagaagcagccaucauuuaaagaaagcguaauag
cucacuggucgagucggccugcgcggaagauguaacggggcuaaaccaug
caccgaagcugcggcagcgacgcuuaugcguuguuggguaggggagcguu
cuguaagccugcgaaggugugcugugaggcaugcuggagguaucagaagu
gcgaaugcugacauaaguaacgauaaagcgggugaaaagcccgcucgccg
gaagaccaaggguuccuguccaacguuaaucggggcagggugagucgacc
ccuaaggcgaggccgaaaggcguagucgaugggaaacagguuaauauucc
uguacuugguguuacugcgaaggggggacggagaaggcuauguuggccgg
gcgacgguugucccgguuuaagcguguaggcugguuuuccaggcaaaucc
ggaaaaucaaggcugaggcgugaugacgaggcacuacggugcugaagcaa
caaaugcccugcuuccaggaaaagccucuaagcaucagguaacaucaaau
cguaccccaaaccgacacagguggucagguagagaauaccaaggcgcuug
agagaacucgggugaaggaacuaggcaaaauggugccguaacuucgggag
aaggcacgcugauauguaggugaggucccucgcggauggagcugaaauca
gucgaagauaccagcuggcugcaacuguuuauuaaaaacacagcacugug
caaacacgaaaguggacguauacggugugacgccugcccggugccggaag
guuaauugaugggguuagcgcaagcgaagcucuugaucgaagccccggua
aacggcggccguaacuauaacgguccuaagguagcgaaauuccuugucgg
guaaguuccgaccugcacgaauggcguaaugauggccaggcugucuccac
ccgagacucagugaaauugaacucgcugugaagaugcaguguacccgcgg
caagacggaaagaccccgugaaccuuuacuauagcuugacacugaacauu
gagccuugauguguaggauaggugggaggcuuugaaguguggacgccagu
cugcauggagccgaccuugaaauaccacccuuuaauguuugauguucuaa
cguugacccguaauccggguugcggacagugucugguggguaguuugacu
ggggcggucuccuccuaaagaguaacggaggagcacgaagguuggcuaau
ccuggucggacaucaggagguuagugcaauggcauaagccagcuugacug
cgagcgugacggcgcgagcaggugcgaaagcaggucauagugauccggug
guucugaauggaagggccaucgcucaacggauaaaagguacuccggggau
aacaggcugauaccgcccaagaguucauaucgacggcgguguuugucggc
ucaucacauccuggggcugaaguaggucccaaggguauggcuguucgcca
uuuaaagugguacgcgagcuggguuuagaacgucgugagacaguucgguc
ccuaucugccgugggcgcuggagaacugaggggggcugcuccuaguacga
gaggaccggaguggacgcaucacugguguucggguugucaugccaauggc
acugcccgguagcuaaaugcggaagagauaagugcugaaagcaucuaagc
acgaaacuugccccgagaugaguucucccugacccuuuaaggguccugaa
ggaacguugaagacgacgacguugauaggccggguguguaagcgcagcga
ugcguugagcuaaccgguacuaaugaaccgugaggcuuaaccuuacaacg
cc

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7bl3 Snapshots of native pre-50S ribosomes reveal a biogenesis factor network and evolutionary specialization.
• Resolution: 3.5 Å
• Binding residue (original residue number in PDB): N24 A26 H29 Q30 V33 Y35 A36 A37 G38 A39 R40 Q41 T43 R44 Q46 T48 R49 A50 V52 G54 S55 K57 K58 Q62 K63 G64 G66 R67 A68 R69 G71 P76 I77 W78 R79 S80 V83 F85 Q94 K95 N97 K98 K99 Y101 R102 P129 K130 T131 K132 L159 R162 N163 H165 K166 T173
• Binding residue (residue number reindexed from 1): N24 A26 H29 Q30 V33 Y35 A36 A37 G38 A39 R40 Q41 T43 R44 Q46 T48 R49 A50 V52 G54 S55 K57 K58 Q62 K63 G64 G66 R67 A68 R69 G71 P76 I77 W78 R79 S80 V83 F85 Q94 K95 N97 K98 K99 Y101 R102 P129 K130 T131 K132 L159 R162 N163 H165 K166 T173

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:7bl3, PDBe:7bl3, PDBj:7bl3
• PDBsum: 7bl3
• PubMed: 33639093
• UniProt: P60723|RL4_ECOLI Large ribosomal subunit protein uL4 (Gene Name=rplD)