Structure of PDB 4v8q Chain AU Binding Site BS01

Receptor Information

>4v8q Chain AU (length=117) Species: 300852 (Thermus thermophilus HB8)

PRAKTGVVRRRKHKKILKLAKGYWGLRSKSFRKARETLFAAGNYAYAHRK
RRKRDFRRLWIVRINAACRQHGLNYSTFIHGLKKAGIEVDRKNLADLAVR
EPQVFAELVERAKAAQG

Ligand information

>4v8q Chain AA (length=2901)

agaugguaagggcccacgguggaugccucggcacccgagccgaugaagga
cguggcuaccugcgauaagccagggggagccgguagcgggcguggauccc
uggauguccgaaugggggaacccggccggcgggaacgccggucaccgcgc
uuuugcgcggggggaaccuggggaacugaaacaucucaguacccagagga
gaggaaagagaaaucgacucccugaguagcggcgagcgaaaggggaccag
ccuaaaccguccggcuuguccgggcggggucguggggcccucggacaccg
aauccccagccuagccgaagcuguugggaagcagcgccagagagggugaa
agccccguaggcgaaagguggggggauaggugaggguacccgaguacccc
gugguucguggagccaugggggaaucugggcggaccaccgccuaaggcua
aguacuccgggugaccgauagcgcaccaguaccgugagggaaaggugaaa
agaaccccgggaggggagugaaauagagccugaaaccgugggcuuacaag
cagucacggccccgcaagggguuguggcgugccuauugaagcaugagccg
gcgacucacggucgugggcgagcuuaagccguugaggcggaggcguaggg
aaaccgaguccgaacagggcgcaagcgggccgcacgcggcccgcaaaguc
cgcggccguggacccgaaaccgggcgagcuagcccuggccagggugaagc
uggggugagacccaguggaggcccgaaccggugggggaugcaaaccccuc
ggaugagcuggggcuaggagugaaaagcuaaccgagcccggagauagcug
guucuccccgaaaugacuuuagggucagccucaggcgcugacuggggccu
guagagcacugauagggcuagggggcccaccagccuaccaaacccuguca
aacuccgaagggucccagguggagccugggagugagggcgcgagcgauaa
cguccgcguccgagcgcgggaacaaccgagaccgccagcuaaggccccca
agucugggcuaagugguaaaggauguggcgcggcgaagacagccaggagg
uuggcuuagaagcagccauccuuuaaagagugcguaauagcucacugguc
gaguggcgccgcgccgaaaaugaucggggcuuaagcccagcgccgaagcu
gcgggucugggggaugaccccaggcgguaggggagcguucccgaugccga
ugaaggccgacccgcgagggcggcuggagguaagggaagugcgaaugccg
gcaugaguaacgauaaagagggugagaaucccucucgccguaagcccaag
gguuccuacgcaauggucgucagcguaggguuaggcgggaccuaagguga
agccgaaaggcguagccgaagggcagccgguuaauauuccggcccuuccc
gcaggugcgauggggggacgcucuaggcuagggggaccggagccauggac
gagcccggccagaagcgcagggugggagguaggcaaauccgccucccaac
aagcucugcgugguggggaagcccguacgggugacaaccccccgaagcca
gggagccaagaaaagccucuaagcacaaccugcgggaacccguaccgcaa
accgacacaggugggcgggugcaagagcacucaggcgcgcgggagaaccc
ucgccaaggaacucugcaaguuggccccguaacuucgggagaaggggugc
ucccuggggugaugagccccggggagccgcagugaacaggcucuggcgac
uguuuaccaaaaacacagcucucugcgaacucguaagaggagguauaggg
agcgacgcuugcccggugccggaaggucaaggggaggggugcaagccccg
aaccgaagccccggugaacggcggccguaaauauaacgguccuaagguag
cgaaauuccuugucggguaaguuccgaccugcacgaaaagcguaacgacc
ggagcgcugucucggcgagggacccggugaaauugaacuggccgugaaga
ugcggccuacccguggcaggacgaaaagaccccguggagcuuuacugcag
ccugguguuggcucuuggucgcgccugcguaggauaggugggagccugug
aacccccgccuccgggugggggggaggcgccggugaaauaccacccuggc
gcggcugggggccuaacccucggauggggggacagcgcuuggcgggcagu
uugacuggggcggucgccuccuaaaagguaacggaggcgcccaaaggucc
ccucaggcgggacggaaauccgccggagagcgcaaggguagaagggggcc
ugacugcgaggccugcaagccgagcaggggcgaaagccgggccuagugaa
ccgguggucccguguggaagggccaucgaucaacggauaaaaguuacccc
ggggauaacaggcugaucucccccgagcguccacagcggcggggagguuu
ggcaccucgaugucggcucgucgcauccuggggcugaagaaggucccaag
gguugggcuguucgcccauuaaagcggcacgcgagcuggguucagaacgu
cgugagacaguucggucucuauccgccacgggcgcaggaggcuugagggg
ggcucuuccuaguacgagaggaccggaagggacgcaccucugguuuccca
gcugucccuccaggggcauaagcuggguagccaugugcggaagggauaac
cgcugaaagcaucuaagcgggaagcccgccccaagaugaggccucccacg
gcgucaagccgguaaggacccgggaagaccacccgguggaugggccgggg
guguaagcgccgcgaggcguugagccgaccggucccaaucguccgagguc
u

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4v8q Decoding in the absence of a codon by tmRNA and SmpB in the ribosome.
• Resolution: 3.1 Å
• Binding residue (original residue number in PDB): P2 R3 A4 K5 T6 V8 V9 R10 R11 R12 K13 H14 K15 K16 K19 K22 G23 Y24 W25 G26 L27 K30 S31 R33 K34 E37 Y45 A46 Y47 H49 R50 K51 R52 R53 K54 R55 F57 R58 R59 W61 I62 R70 N75 Y76 S77 H81 R92 K93
• Binding residue (residue number reindexed from 1): P1 R2 A3 K4 T5 V7 V8 R9 R10 R11 K12 H13 K14 K15 K18 K21 G22 Y23 W24 G25 L26 K29 S30 R32 K33 E36 Y44 A45 Y46 H48 R49 K50 R51 R52 K53 R54 F56 R57 R58 W60 I61 R69 N74 Y75 S76 H80 R91 K92

Gene Ontology

Molecular Function

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

Biological Process

• GO:0000027 ribosomal large subunit assembly
• GO:0006412 translation

Cellular Component

• GO:0005840 ribosome
• GO:0022625 cytosolic large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:4v8q, PDBe:4v8q, PDBj:4v8q
• PDBsum: 4v8q
• PubMed: 22422985
• UniProt: P60491|RL20_THET8 Large ribosomal subunit protein bL20 (Gene Name=rplT)