Structure of PDB 4v4w Chain BO Binding Site BS01

Receptor Information

>4v4w Chain BO (length=115) Species: 562 (Escherichia coli)

RVKRGVIARARHKKILKQAKGYYGARSRVYRVAFQAVIKAGQYAYRDRRQ
RKRQFRQLWIARINAAARQNGISYSKFINGLKKASVEIDRKILADIAVFD
KVAFTALVEKAKAAL

Ligand information

>4v4w Chain B0 (length=2740)

cguacacgguggaugcccuggcagucaaggcgaugaaggacgugcuaauc
ugcgauaagcgucgguaaggugauaugaaccguuuaaccggcgauuuccg
aauggggaaccccgaucauuauccaaaugaggcgaaccgggggaacugaa
acaucuaaguaccccgaggaaaagaaaucaaccgagauucccccaguagc
ggcgagcgaacggggagcagcccgagccuaaucaguguguguguugugga
agcgucuggaaaggcgcgcgauacagggugacagccccguacacaaugca
caugcuguagcucgaugaguagggcgggccgugguaccugucugaauaug
gggggaccauccuccaaggcuaaauacucugacugaccgauagugaacca
guaccgugagggaaaggcgaaaagaaccccggcgaggggagugaaaaaga
accugaaaccguguacguacaagcagugggaggcaccuuaugcguguuau
ggcgugccuuuuguauaaugggucagcgacuuauauucuguagcaagguu
aaccggggagccgaagggaaaccgagucuuaacgggcguuaaguugcagg
guauagacccgaaacccggugaucuagccaugggcagguugaagguuggg
uaacacuaacuggaggaccgaaccgacuaauguugaaaaauuagcggaug
acuuguggcugggggugaaaggccaaucaaaccgggagauagcugguucu
ccccgaaagcuauuuagguagcgccucgugaaucaucuccggggguagag
cacuguuucggcaagggggucgacuuccaacccgaugcaaacugcgaaua
ccggagauguuaucacgggagacacacggcggguguaacguccgucguga
agagggaaacaacccagaccgcagcuaaggucccaaagucaugguuaagu
gggaaacgaugugggaaggcccagacagccaggauguuggcuuagaagca
gccaucauuuaaagaaagcguaauagcucacuggucgagucggccugcgc
ggaagauguacggggcuaaaccaugcaccgaagcugcggcagcgacguua
ugcguuguuggguaggggagcguucuguagccugcgaaggugugcuguga
ggcaugcuggagguaucagaagugcgaaugcugacauaaguaacgauaaa
gcgggugaaaagcccgcucgccggaagaccaaggguuccuguccaacguu
aaucggggcagggugagucgacccuaaggcgaggccgaaaggcguagucg
augggaaacagguuaauauuccuguacuuggugugugggugauggaggga
cggagaaggcuauguuaugccaagcuauggcugcugguugguacgcucaa
gggcgaucgggucagaaaaucuaccggucacaugccucagacguaucggg
agcuuccucggaagcgaaguaacaaagcccucuuccaggaaaagcuucua
aacguugaaacaugucaaaucguaccccaaaccgacacagguggucaggu
agagaauaccaggcgcuugagagaacucgggugaaggaacuaggcaaaau
ggugccguaacuucgggagaaggcacgcugauuagcucgccugaucaguc
gaagauaccagcuggcugcaacuguuuauuaaaaacacagcacugugcaa
acacgaaaguggacguauacggugugacgccugcccggugccggaagguu
aaugggguugcaaagcucucgaagccccgguaaacggcggccguaacuau
aacgguccuaagguagcgaaauuccuugucggguaaguuccgaccugcac
gaauggcguaaugauggccaggcugucuccacccgagacucagugaaauu
gaacucgcugugaagaugcaguguacccgcggcaagacggaaagaccccg
ugaaccuuuacuauagcuugacacugaacauugagccuugauguguagga
uaggugggaggcuuugaaguguggacgccagucugcauggagccggccuu
gaaauaccacccuuuaauguuugauguucuaacccgaauccggggacagu
gucugguggguaguuugacuggggcggucuccuccuaaagaguaacggag
gagcacgaagguuggcuaauccuggcaucaggagguuagugcaauggcau
aagccagcuugacugcgagcgugacggcgcgagcaggugcgaaagcaggu
cauagugauccgguggucugaauggaagggccaucgucaacggaaaaggu
acuccggggauaacaggcugauaccgcccaagaguucauaucgacggcgg
uguuuggcaccucgaugucggcucaucacauccuggggcugaaguagguc
ccaaggguauggcuguucgccauuuaaagugguacgcgagcuggguuuag
aacgucgugagacaguucggucccuaucugccgugggcggagaacugagg
ggggcugcuccuaguacgagaggaccggaguggacgcaucacugguguuc
ggguugucagccauggcacugcccgguagcuaaaugcggagagauaagug
cugaaagcaucuaagcacgaaacuugccccgagaugaguucucccgaagg
aacguugaagacgacgacguugauaggccggguguguaagcgcagcaaug
cguugagcuaaccgguacuaaugaaccgaggucuugacca

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4v4w Elongation arrest by SecM via a cascade of ribosomal RNA rearrangements
• Resolution: 15.0 Å
• Binding residue (original residue number in PDB): R2 K4 R5 V7 I8 R10 K14 Y23 Y24 G25 R29 Y31 R32 Q36 Y44 Y46 R47 D48 R49 R50 Q51 R52 K53 R54 Q55 R57 Q58 I61 A62 N65 Y75 R91 K92
• Binding residue (residue number reindexed from 1): R1 K3 R4 V6 I7 R9 K13 Y22 Y23 G24 R28 Y30 R31 Q35 Y43 Y45 R46 D47 R48 R49 Q50 R51 K52 R53 Q54 R56 Q57 I60 A61 N64 Y74 R90 K91

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:4v4w, PDBe:4v4w, PDBj:4v4w
• PDBsum: 4v4w
• PubMed: 16713583
• UniProt: P0A7L3|RL20_ECOLI Large ribosomal subunit protein bL20 (Gene Name=rplT)