Structure of PDB 6vwm Chain N Binding Site BS01

Receptor Information

>6vwm Chain N (length=114) Species: 562 (Escherichia coli)

SNIIKQLEQEQMKQDVPSFRPGDTVEVKVWVVEGSKKRLQAFEGVVIAIR
NRGLHSAFTVRKISNGEGVERVFQTHSPVVDSISVKRRGAVRKAKLYYLR
ERTGKAARIKERLN

Ligand information

>6vwm Chain 2 (length=2833)

gguuaagcgacuaagcguacacgguggaugcccuggcagucagaggcgau
gaaggacgugcuaaucugcgauaagcgucgguaaggugauaugaaccguu
auaaccggcgauuuccgaauggggaaacccaguguguuucgacacacuau
cauuaacugaauccauagguuaaugaggcgaaccgggggaacugaaacau
cuaaguaccccgaggaaaagaaaucaaccgagauucccccaguagcggcg
agcgaacggggagcagcccagagccugaaucaguguguguguuaguggaa
gcgucuggaaaggcgcgcgauacagggugacagccccguacacaaaaaug
cacaugcugugagcucgaugaguagggcgggacacgugguauccugucug
aauauggggggaccauccuccaaggcuaaauacuccugacugaccgauag
ugaaccaguaccgugagggaaaggcgaaaagaaccccggcgaggggagug
aaaaagaaccugaaaccguguacguacaagcagugggagcacgcuuaggc
gugugacugcguaccuuuuguauaaugggucagcgacuuauauucuguag
caagguuaaccgaauaggggagccgaagggaaaccgagucuuaacugggc
guuaaguugcaggguauagacccgaaacccggugaucuagccaugggcag
guugaagguuggguaacacuaacuggaggaccgaaccgacuaaugucgaa
aaauuagcggaugacuuguggcugggggugaaaggccaaucaaaccggga
gauagcugguucuccccgaaagcuauuuagguagcgccucgugaauucau
cuccggggguagagcacuguuucggcaagggggucaucccgacuuaccaa
cccgaugcaaacugcgaauaccggagaauguuaucacgggagacacacgg
cgggugcuaacguccgucgugaagagggaaacaacccagaccgccagcua
aggucccaaagucaugguuaagugggaaacgaugugggaaggucggccug
cgcggaagauguaacggggcuaaaccaugcaccgaagcugcggcagcgac
gcuuaugcguuguuggguaggggagcguucuguaagccugcgaaggugug
cugugaggcaugcuggagguaucagaagugcgaaugcugacauaaguaac
gauaaagcgggugaaaagcccgcucgccggaagaccaaggguuccugucc
aacguuaaucggggcagggugagucgaccccuaaggcgaggccgaaaggc
guagucgaugggaaacagguuaauauuccuguacuugguguuacugcgaa
ggggggacggagaaggcuauguuggccgggcgacgguugucccgguuuaa
gcguguaggcugguuuuccaggcaaauccggaaaaucaaggcugaggcgu
gaugacgaggcacuacggugcugaagcaacaaaugcccugcuuccaggaa
aagccucuaagcaucagguaacaucaaaucguaccccaaaccgacacagg
uggucagguagagaauaccaaggcgcuugagagaacucgggugaaggaac
uaggcaaaauggugccguaacuucgggagaaggcacgcugauauguaggu
gaggucccucgcggauggagcugaaaucagucgaagauaccagcuggcug
caacuguuuauuaaaaacacagcacugugcaaacacgaaaguggacguau
acggugugacgccugcccggugccggaagguuaauugaugggguuagcgc
aagcgaagcucuugaucgaagccccgguaaacggcggccguaacuauaac
gguccuaagguagcgaaauuccuugucggguaaguuccgaccugcacgaa
uggcguaaugauggccaggcugucuccacccgagacucagugaaauugaa
cucgcugugaagaugcaguguacccgcggcaagacggaaagaccccguga
accuuuacuauagcuugacacugaacauugagccuugauguguaggauag
gugggaggcuuugaaguguggacgccagucugcauggagccgaccuugaa
auaccacccuuuaauguuugauguucuaacguugacccguaauccggguu
gcggacagugucugguggguaguuugacuggggcggucuccuccuaaaga
guaacggaggagcacgaagguuggcuaauccuggucggacaucaggaggu
uagugcaauggcauaagccagcuugacugcgagcgugacggcgcgagcag
gugcgaaagcaggucauagugauccggugguucugaauggaagggccauc
gcucaacggauaaaagguacuccggggauaacaggcugauaccgcccaag
aguucauaucgacggcgguguuuggcaccucgaugucggcucaucacauc
cuggggcugaaguaggucccaaggguauggcuguucgccauuuaaagugg
uacgcgagcuggguuuagaacgucgugagacaguucggucccuaucugcc
gugggcgcuggagaacugaggggggcugcuccuaguacgagaggaccgga
guggacgcaucacugguguucggguugucaugccaauggcacugcccggu
agcuaaaugcggaagagauaagugcugaaagcaucuaagcacgaaacuug
ccccgagaugaguucucccugacccuuuaaggguccugaaggaacguuga
agacgacgacguugauaggccggguguguaagcgcagcgaugcguugagc
uaaccgguacuaaugaaccgugaggcuuaaccu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6vwm mRNA stem-loops can pause the ribosome by hindering A-site tRNA binding.
• Resolution: 3.4 Å
• Binding residue (original residue number in PDB): S1 R20 R50 N51 R52 H55 R92 K93 A94 K95 Y97 Y98 R102
• Binding residue (residue number reindexed from 1): S1 R20 R50 N51 R52 H55 R92 K93 A94 K95 Y97 Y98 R102

Gene Ontology

Molecular Function

• 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

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:6vwm, PDBe:6vwm, PDBj:6vwm
• PDBsum: 6vwm
• PubMed: 32427100
• UniProt: P0A7K6|RL19_ECOLI Large ribosomal subunit protein bL19 (Gene Name=rplS)