Structure of PDB 4v71 Chain BJ Binding Site BS01

Receptor Information

>4v71 Chain BJ (length=142) Species: 83333 (Escherichia coli K-12)

MKTFTAKPETVKRDWYVVDATGKTLGRLATELARRLRGKHKAEYTPHVDT
GDYIIVLNADKVAVTGNKRTDKVYYHHTGHIGGIKQATFEEMIARRPERV
IEIAVKGMLPKGPLGRAMFRKLKVYAGNEHNHAAQQPQVLDI

Ligand information

>4v71 Chain BA (length=2903)

gguuaagcgacuaagcguacacgguggaugcccuggcagucagaggcgau
gaaggacgugcuaaucugcgauaagcgucgguaaggugauaugaaccguu
auaaccggcgauuuccgaauggggaaacccaguguguuucgacacacuau
cauuaacugaauccauagguuaaugaggcgaaccgggggaacugaaacau
cuaaguaccccgaggaaaagaaaucaaccgagauucccccaguagcggcg
agcgaacggggagcagcccagagccugaaucaguguguguguuaguggaa
gcgucuggaaaggcgcgcgauacagggugacagccccguacacaaaaaug
cacaugcugugagcucgaugaguagggcgggacacgugguauccugucug
aauauggggggaccauccuccaaggcuaaauacuccugacugaccgauag
ugaaccaguaccgugagggaaaggcgaaaagaaccccggcgaggggagug
aaaaagaaccugaaaccguguacguacaagcagugggagcacgcuuaggc
gugugacugcguaccuuuuguauaaugggucagcgacuuauauucuguag
caagguuaaccgaauaggggagccgaagggaaaccgagucuuaacugggc
guuaaguugcaggguauagacccgaaacccggugaucuagccaugggcag
guugaagguuggguaacacuaacuggaggaccgaaccgacuaauguugaa
aaauuagcggaugacuuguggcugggggugaaaggccaaucaaaccggga
gauagcugguucuccccgaaagcuauuuagguagcgccucgugaauucau
cuccggggguagagcacuguuucggcaagggggucaucccgacuuaccaa
cccgaugcaaacugcgaauaccggagaauguuaucacgggagacacacgg
cgggugcuaacguccgucgugaagagggaaacaacccagaccgccagcua
aggucccaaagucaugguuaagugggaaacgaugugggaaggcccagaca
gccaggauguuggcuuagaagcagccaucauuuaaagaaagcguaauagc
ucacuggucgagucggccugcgcggaagauguaacggggcuaaaccaugc
accgaagcugcggcagcgacgcuuaugcguuguuggguaggggagcguuc
uguaagccugcgaaggugugcugugaggcaugcuggagguaucagaagug
cgaaugcugacauaaguaacgauaaagcgggugaaaagcccgcucgccgg
aagaccaaggguuccuguccaacguuaaucggggcagggugagucgaccc
cuaaggcgaggccgaaaggcguagucgaugggaaacagguuaauauuccu
guacuugguguuacugcgaaggggggacggagaaggcuauguuggccggg
cgacgguugucccgguuuaagcguguaggcugguuuuccaggcaaauccg
gaaaaucaaggcugaggcgugaugacgaggcacuacggugcugaagcaac
aaaugcccugcuuccaggaaaagccucuaagcaucagguaacaucaaauc
guaccccaaaccgacacagguggucagguagagaauaccaaggcgcuuga
gagaacucgggugaaggaacuaggcaaaauggugccguaacuucgggaga
aggcacgcugauauguaggugaggucccucgcggauggagcugaaaucag
ucgaagauaccagcuggcugcaacuguuuauuaaaaacacagcacugugc
aaacacgaaaguggacguauacggugugacgccugcccggugccggaagg
uuaauugaugggguuagcgcaagcgaagcucuugaucgaagccccgguaa
acggcggccguaacuauaacgguccuaagguagcgaaauuccuugucggg
uaaguuccgaccugcacgaauggcguaaugauggccaggcugucuccacc
cgagacucagugaaauugaacucgcugugaagaugcaguguacccgcggc
aagacggaaagaccccgugaaccuuuacuauagcuugacacugaacauug
agccuugauguguaggauaggugggaggcuuugaaguguggacgccaguc
ugcauggagccgaccuugaaauaccacccuuuaauguuugauguucuaac
guugacccguaauccggguugcggacagugucugguggguaguuugacug
gggcggucuccuccuaaagaguaacggaggagcacgaagguuggcuaauc
cuggucggacaucaggagguuagugcaauggcauaagccagcuugacugc
gagcgugacggcgcgagcaggugcgaaagcaggucauagugauccggugg
uucugaauggaagggccaucgcucaacggauaaaagguacuccggggaua
acaggcugauaccgcccaagaguucauaucgacggcgguguuuggcaccu
cgaugucggcucaucacauccuggggcugaaguaggucccaaggguaugg
cuguucgccauuuaaagugguacgcgagcuggguuuagaacgucgugaga
caguucggucccuaucugccgugggcgcuggagaacugaggggggcugcu
ccuaguacgagaggaccggaguggacgcaucacugguguucggguuguca
ugccaauggcacugcccgguagcuaaaugcggaagagauaagugcugaaa
gcaucuaagcacgaaacuugccccgagaugaguucucccugacccuuuaa
ggguccugaaggaacguugaagacgacgacguugauaggccgggugugua
agcgcagcgaugcguugagcuaaccgguacuaaugaaccgugaggcuuaa
ccu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4v71 Energy barriers and driving forces in tRNA translocation through the ribosome.
• Resolution: 20.0 Å
• Binding residue (original residue number in PDB): M1 K7 W15 G26 R27 T30 R34 R37 H47 K68 K72 Y75 H76 T78 H80 I81 G82 R95 R96 E102 K106 G107 M108 L109 R116 R120 K123 N131 A133 A134 Q135
• Binding residue (residue number reindexed from 1): M1 K7 W15 G26 R27 T30 R34 R37 H47 K68 K72 Y75 H76 T78 H80 I81 G82 R95 R96 E102 K106 G107 M108 L109 R116 R120 K123 N131 A133 A134 Q135

Gene Ontology

Molecular Function

• GO:0003729 mRNA binding
• GO:0003735 structural constituent of ribosome
• GO:0008270 zinc ion binding
• GO:0048027 mRNA 5'-UTR binding
• GO:0070180 large ribosomal subunit rRNA binding

Biological Process

• 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:4v71, PDBe:4v71, PDBj:4v71
• PDBsum: 4v71
• PubMed: 24186064
• UniProt: P0AA10|RL13_ECOLI Large ribosomal subunit protein uL13 (Gene Name=rplM)