Structure of PDB 6hrm Chain Q Binding Site BS01

Receptor Information

>6hrm Chain Q (length=117) Species: 562 (Escherichia coli)

ARVKRGVIARARHKKILKQAKGYYGARSRVYRVAFQAVIKAGQYAYRDRR
QRKRQFRQLWIARINAAARQNGISYSKFINGLKKASVEIDRKILADIAVF
DKVAFTALVEKAKAALA

Ligand information

>6hrm Chain 1 (length=4450)

aaauugaagaguuugaucauggcucagauugaacgcuggcggcaggccua
acacaugcaagucgaacgguaacaggaagaagcuugcuucuuugcugacg
aguggcggacgggugaguaaugucugggaaacugccugauggagggggau
aacuacuggaaacgguagcuaauaccgcauaacgucgcaagaccaaagag
ggggaccuucgggccucuugccaucggaugugcccagaugggauuagcua
guaggugggguaacggcucaccuaggcgacgaucccuagcuggucugaga
ggaugaccagccacacuggaacugagacacgguccagacuccuacgggag
gcagcaguggggaauauugcacaaugggcgcaagccugaugcagccaugc
cgcguguaugaagaaggccuucggguuguaaaguacuuucagcggggagg
aagggaguaaaguuaauaccuuugcucauugacguuacccgcagaagaag
caccggcuaacuccgugccagcagccgcgguaauacggagggugcaagcg
uuaaucggaauuacugggcguaaagcgcacgcaggcgguuuguuaaguca
gaugugaaauccccgggcucaaccugggaacugcaucugauacuggcaag
cuugagucucguagagggggguagaauuccagguguagcggugaaaugcg
uagagaucuggaggaauaccgguggcgaaggcggcccccuggacgaagac
ugacgcucaggugcgaaagcguggggagcaaacaggauuagauacccugg
uaguccacgccguaaacgaugucgacuuggagguugugcccuugaggcgu
ggcuuccggagcuaacgcguuaagucgaccgccuggggaguacggccgca
agguuaaaacucaaaugaauugacgggggcccgcacaagcgguggagcau
gugguuuaauucgaugcaacgcgaagaaccuuaccuggucuugacaucca
cggaaguuuucagagaugagaaugugccuucgggaaccgugagacaggug
cugcauggcugucgucagcucguguugugaaauguuggguuaagucccgc
aacgagcgcaacccuuauccuuuguugccagcgguccggccgggaacuca
aaggagacugccagugauaaacuggaggaagguggggaugacgucaaguc
aucauggcccuuacgaccagggcuacacacgugcuacaauggcgcauaca
aagagaagcgaccucgcgagagcaagcggaccucauaaagugcgucguag
uccggauuggagucugcaacucgacuccaugaagucggaaucgcuaguaa
ucguggaucagaaugccacggugaauacguucccgggccuuguacacacc
gcccgucacaccaugggaguggguugcaaaagaaguagguagcuuaaccg
gucaacagccguuugagcuaaccgguacuaaugaaccgugaggcuuaacc
uugagagguuaagcgacuaagcguacacgguggaugcccuggcagucaga
ggcgaugaaggacgugcuaaucugcgauaagcgucgguaaggugauauga
accguuauaaccggcgauuuccgaauggggaaacccaguguguuucgaca
cacuaucauuaacugaauccauagguuaaugaggcgaaccgggggaacug
aaacaucuaaguaccccgaggaaaagaaaucaaccgagauucccccagua
gcggcgagcgaacggggagcagcccagagccugaaucaguguguguguua
guggaagcgucuggaaaggcgcgcgauacagggugacagccccguacaca
aaaaugcacaugcugugagcucgaugaguagggcgggacacgugguaucc
ugucugaauauggggggaccauccuccaaggcuaaauacuccugacugac
cgauagugaaccaguaccgugagggaaaggcgaaaagaaccccggcgagg
ggagugaaaaagaaccugaaaccguguacguacaagcagugggagcacgc
uuaggcgugugacugcguaccuuuuguauaaugggucagcgacuuauauu
cuguagcaagguuaaccgaauaggggagccgaagggaaaccgagucuuaa
cugggcguuaaguugcaggguauagacccgaaacccggugaucuagccau
gggcagguugaagguuggguaacacuaacuggaggaccgaaccgacuaau
guugaaaaauuagcggaugacuuguggcugggggugaaaggccaaucaaa
ccgggagauagcugguucuccccgaaagcuauuuagguagcgccucguga
auucaucuccggggguagagcacuguuucggcaagggggucaucccgacu
uaccaacccgaugcaaacugcgaauaccggagaauguuaucacgggagac
acacggcgggugcuaacguccgucgugaagagggaaacaacccagaccgc
cagcuaaggucccaaagucaugguuaagugggaaacgaugugggaaggcc
cagacagccaggauguuggcuuagaagcagccaucauuuaaagaaagcgu
aauagcucacuggucgagucggccugcgcggaagauguaacggggcuaaa
ccaugcaccgaagcugcggcagcgacgcuuaugcguuguuggguagggga
gcguucuguaagccugcgaaggugugcugugaggcaugcuggagguauca
gaagugcgaaugcugacauaaguaacgauaaagcgggugaaaagcccgcu
cgccggaagaccaaggguuccuguccaacguuaaucggggcagggugagu
cgaccccuaaggcgaggccgaaaggcguagucgaugggaaacagguuaau
auuccuguacuugguguuacugcgaaggggggacggagaaggcuauguug
gccgggcgacgguugucccgguuuaagcguguaggcugguuuuccaggca
aauccggaaaaucaaggcugaggcgugaugacgaggcacuacggugcuga
agcaacaaaugcccugcuuccaggaaaagccucuaagcaucagguaacau
caaaucguaccccaaaccgacacagguggucagguagagaauaccaaggc
gcuugagagaacucgggugaaggaacuaggcaaaauggugccguaacuuc
gggagaaggcacgcugauauguaggugaggucccucgcggauggagcuga
aaucagucgaagauaccagcuggcugcaacuguuuauuaaaaacacagca
cugugcaaacacgaaaguggacguauacggugugacgccugcccggugcc
ggaagguuaauugaugggguuagcgcaagcgaagcucuugaucgaagccc
cgguaaacggcggccguaacuauaacgguccuaagguagcgaaauuccuu
gucggguaaguuccgaccugcacgaauggcguaaugauggccaggcuguc
uccacccgagacucagugaaauugaacucgcugugaagaugcaguguacc
cgcggcaagacggaaagaccccgugaaccuuuacuauagcuugacacuga
acauugagccuugauguguaggauaggugggaggcuuugaaguguggacg
ccagucugcauggagccgaccuugaaauaccacccuuuaauguuugaugu
ucuaacguugacccguaauccggguugcggacagugucugguggguaguu
ugacuggggcggucuccuccuaaagaguaacggaggagcacgaagguugg
cuaauccuggucggacaucaggagguuagugcaauggcauaagccagcuu
gacugcgagcgugacggcgcgagcaggugcgaaagcaggucauagugauc
cggugguucugaauggaagggccaucgcucaacggauaaaagguacuccg
gggauaacaggcugauaccgcccaagaguucauaucgacggcgguguuug
gcaccucgaugucggcucaucacauccuggggcugaaguaggucccaagg
guauggcuguucgccauuuaaagugguacgcgagcuggguuuagaacguc
gugagacaguucggucccuaucugccgugggcgcuggagaacugaggggg
gcugcuccuaguacgagaggaccggaguggacgcaucacugguguucggg
uugucaugccaauggcacugcccgguagcuaaaugcggaagagauaagug
cugaaagcaucuaagcacgaaacuugccccgagaugaguucucccugacc
cuuuaaggguccugaaggaacguugaagacgacgacguugauaggccggg
uguguaaacggacaugguuggagggcgcuuaccacuuugugauucaugac
uggggugaagucguaacaagguaaccguaggggaaccugcgguuggauca

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6hrm Controlling orthogonal ribosome subunit interactions enables evolution of new function.
• Resolution: 2.96 Å
• Binding residue (original residue number in PDB): A2 R3 V4 K5 R6 G7 V8 I9 R11 R13 H14 K15 G23 Y24 Y25 G26 A27 R28 R30 V31 R33 V34 Q37 K41 A42 Y45 Y47 R48 D49 R50 R51 R53 K54 R55 Q56 F57 R58 Q59 W61 I62 N66 R70 S75 Y76 S77 N81 K84 D91 R92 K93
• Binding residue (residue number reindexed from 1): A1 R2 V3 K4 R5 G6 V7 I8 R10 R12 H13 K14 G22 Y23 Y24 G25 A26 R27 R29 V30 R32 V33 Q36 K40 A41 Y44 Y46 R47 D48 R49 R50 R52 K53 R54 Q55 F56 R57 Q58 W60 I61 N65 R69 S74 Y75 S76 N80 K83 D90 R91 K92

Gene Ontology

Molecular Function

• GO:0000900 mRNA regulatory element binding translation repressor activity
• GO:0003729 mRNA binding
• GO:0003735 structural constituent of ribosome
• GO:0019843 rRNA binding
• GO:0070180 large ribosomal subunit rRNA binding

Biological Process

• GO:0000027 ribosomal large subunit assembly
• GO:0002181 cytoplasmic translation
• GO:0006412 translation
• GO:0017148 negative regulation of translation

Cellular Component

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

External links

• PDB: RCSB:6hrm, PDBe:6hrm, PDBj:6hrm
• PDBsum: 6hrm
• PubMed: 30518861
• UniProt: P0A7L3|RL20_ECOLI Large ribosomal subunit protein bL20 (Gene Name=rplT)