Structure of PDB 6wnv Chain x Binding Site BS01

Receptor Information

>6wnv Chain x (length=77) Species: 562 (Escherichia coli)

SRVCQVTGKRPVTGNNRSHALNATKRRFLPNLHSHRFWVESEKRFVTLRV
SAKGMRVIDKKGIDTVLAELRARGEKY

Ligand information

>6wnv Chain 4 (length=3025)

gguuaagcgacuaagcguacacgguggaugcccuggcagucagaggcgau
gaaggacgugcuaaucugcgauaagcgucgguaaggugauaugaaccguu
auaaccggcgauuuccgaauggggaaacccaguguguuucgacacacuau
cauuaacugaauccauagguuaaugaggcgaaccgggggaacugaaacau
cuaaguaccccgaggaaaagaaaucaaccgagauucccccaguagcggcg
agcgaacggggagcagcccagagccugaaucaguguguguguuaguggaa
gcgucuggaaaggcgcgcgauacagggugacagccccguacacaaaaaug
cacaugcugugagcucgaugaguagggcgggacacgugguauccugucug
aauauggggggaccauccuccaaggcuaaauacuccugacugaccgauag
ugaaccaguaccgugagggaaaggcgaaaagaaccccggcgaggggagug
aaaaagaaccugaaaccguguacguacaagcagugggagcacgcuuaggc
gugugacugcguaccuuuuguauaaugggucagcgacuuauauucuguag
caagguuaaccgaauaggggagccgaagggaaaccgagucuuaacugggc
guuaaguugcaggguauagacccgaaacccggugaucuagccaugggcag
guugaagguuggguaacacuaacuggaggaccgaaccgacuaaugucgaa
aaauuagcggaugacuuguggcugggggugaaaggccaaucaaaccggga
gauagcugguucuccccgaaagcuauuuagguagcgccucgugaauucau
cuccggggguagagcacuguuucggcaagggggucaucccgacuuaccaa
cccgaugcaaacugcgaauaccggagaauguuaucacgggagacacacgg
cgggugcuaacguccgucgugaagagggaaacaacccagaccgccagcua
aggucccaaagucaugguuaagugggcugcuccccaugcgagaguaggga
acugccaggcauucggugccuggcggccguagcgcgguggucccaccuga
ccccaugccgaacucagaagugaaacgccguagcgccgaugguagugugg
gguaaaacgaugugggaaggcccagacagccaggauguuggcuuagaagc
agccaucauuuaaagaaagcguaauagcucacuggucgagucggccugcg
cggaagauguaacggggcuaaaccaugcaccgaagcugcggcagcgacgc
uuaugcguuguuggguaggggagcguucuguaagccugcgaaggugugcu
gugaggcaugcuggagguaucagaagugcgaaugcugacauaaguaacga
uaaagcgggugaaaagcccgcucgccggaagaccaaggguuccuguccaa
cguuaaucggggcagggugagucgaccccuaaggcgaggccgaaaggcgu
agucgaugggaaacagguuaauauuccuguacuugguguuacugcgaagg
ggggacggagaaggcuauguuggccgggcgacgguugucccgguuuaagc
guguaggcugguuuuccaggcaaauccggaaaaucaaggcugaggcguga
ugacgaggcacuacggugcugaagcaacaaaugcccugcuuccaggaaaa
gccucuaagcaucagguaacaucaaaucguaccccaaaccgacacaggug
gucagguagagaauaccaaggcgcuugagagaacucgggugaaggaacua
ggcaaaauggugccguaacuucgggagaaggcacgcugauauguagguga
ggucccucgcggauggagcugaaaucagucgaagauaccagcuggcugca
acuguuuauuaaaaacacagcacugugcaaacacgaaaguggacguauac
ggugugacgccugcccggugccggaagguuaauugaugggguuagcgcaa
gcgaagcucuugaucgaagccccgguaaacggcggccguaacuauaacgg
uccuaagguagcgaaauuccuugucggguaaguuccgaccugcacgaaug
gcguaaugauggccaggcugucuccacccgagacucagugaaauugaacu
cgcugugaagaugcaguguacccgcggcaagacggaaagaccccgugaac
cuuuacuauagcuugacacugaacauugagccuugauguguaggauaggu
gggaggcuuugaaguguggacgccagucugcauggagccgaccuugaaau
accacccuuuaauguuugauguucuaacguugacccguaauccggguugc
ggacagugucugguggguaguuugacuggggcggucuccuccuaaagagu
aacggaggagcacgaagguuggcuaauccuggucggacaucaggagguua
gugcaauggcauaagccagcuugacugcgagcgugacggcgcgagcaggu
gcgaaagcaggucauagugauccggugguucugaauggaagggccaucgc
ucaacggauaaaagguacuccggggaucugauaccgcccaagaguucaua
ucgacggcgguguuuggcaccucgaugucggcucaucacauccuggggcu
gaaguaggucccaaggguauggcuguucgccauuuaaagugguacgcgag
cuggguuuagaacgucgugagacaguucggucccuaucugccgugggcgc
uggagaacugaggggggcugcuccuaguacgagaggaccggaguggacgc
aucacugguguucggguugucaugccaauggcacugcccgguagcuaaau
gcggaagagauaagugcugaaagcaucuaagcacgaaacuugccccgaga
ugaguucucccugacccuuuaaggguccugaaggaacguugaagacgacg
acguugauaggccggguguguaagcgcagcgaugcguugagcuaaccggu
acuaaugaaccgugaggcuuaaccu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6wnv Ribosome engineering reveals the importance of 5S rRNA autonomy for ribosome assembly.
• Resolution: 3.5 Å
• Binding residue (original residue number in PDB): S1 R2 K9 T13 N15 R17 S18 L21 N22 T24 K25 R26 R27 F28 L29 P30 N31 H33 H35 R36 R49 K53 R56 K60
• Binding residue (residue number reindexed from 1): S1 R2 K9 T13 N15 R17 S18 L21 N22 T24 K25 R26 R27 F28 L29 P30 N31 H33 H35 R36 R49 K53 R56 K60

Gene Ontology

Molecular Function

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

Biological Process

• GO:0000027 ribosomal large subunit assembly
• GO:0002181 cytoplasmic translation
• GO:0006412 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:6wnv, PDBe:6wnv, PDBj:6wnv
• PDBsum: 6wnv
• PubMed: 32518240
• UniProt: P0A7M2|RL28_ECOLI Large ribosomal subunit protein bL28 (Gene Name=rpmB)