Structure of PDB 4v95 Chain DU Binding Site BS01

Receptor Information

>4v95 Chain DU (length=116) Species: 300852 (Thermus thermophilus HB8)

PRAKTGVVRRRKHKKILKLAKGYWGLRSKSFRKARETLFAAGNYAYAHRK
RRKRDFRRLWIVRINAACRQHGLNYSTFIHGLKKAGIEVDRKNLADLAVR
EPQVFAELVERAKAAQ

Ligand information

>4v95 Chain DA (length=2722)

agaugguaagggcccacgguggaugccucggcacccgagccgaugaagga
cguggcuaccugcgauaagccagggggagccgguagcgggcguggauccc
uggauguccgaaugggggaacccggccggcgggaacgccggucaccgcgc
ugcgcggggggaaccuggggaacugaaacaucucaguacccagaggagag
gaaagagaaaucgacucccugaguagcggcgagcgaaaggggaccagccu
aaaccguccggcuuguccgggcggggucguggggcccucgcgaaucccca
gccuagccgaagcuguugggaagcagcgccagagagggugaaagccccgu
aggcgaaagguggggggauaggugaggguacccgaguaccccgugguucg
uggagccaugggggaaucugggcggaccaccgccuaaggcuaaguacucc
gggugaccgauagcgcaccaguaccgugagggaaaggugaaaagaacccc
gggaggggagugaaauagagccugaaaccgugggcuuacaagcagucacg
gccccgcagggguuguggcgugccuauugaagcaugagccggcgacucac
ggucgugggcgagcuuaagccguugaggcggaggcguagggaaaccgagu
ccgaacagggcgcaagcgcgcaaaguccgcggccguggacccgaaaccgg
gcgagcuagcccuggccagggugaagcuggggugagacccaguggaggcc
cgaaccggugggggaugcaaaccccucggaugagcuggggcuaggaguga
aaagcuaaccgagcccggagauagcugguucuccccgaaaugacuuuagg
gucagccucaggcgcugacuggggccuguagagcacugauagggcuaggg
ggcccaccagccuaccaaacccugucaaacuccgaagggucccaggugga
gccugggagugagggcgcgagcgauaacguccgcguccgagcgcgggaac
aaccgagaccgccagcuaaggcccccaagucugggcuaagugguaaagga
uguggcgccgcguggcgccgcgccgaaaaugaucggggcuuaagcccagc
gccgaagcugcgggucuggggccccaggcgguaggggagcguucccgaug
ccgaugaaggccgacccgcgagggcggcuggagguaagggaagugcgaau
gccggcaugaguaacgauaaagagggugagaaucccucucgccguaagcc
caaggguuccuacgcaauggucgucagcguaggguuaggcgggaccuaag
gugaagccgaaaggcguagccgaagggcagccgguuaauauuccggcccu
ucccgcaggugcgauggggggacgcucuaggcuagggggaccggagccau
ggacgagcccggccagaagcgcagggugggagguaggcaaauccgccucc
caacaagcucugcgugguggggaagcccgcgggugacaaccccccgaagc
cagggagccaagaaaagccucuaagcacaaccugcgggaacccguaccgc
aaaccgacacaggugggcgggugcaagagcacucaggcgcgcgggagaac
ccucgccaaggaacucugcaaguuggccccguaacuucgggagaaggggu
gcucccuggggugaugagccccggggagccgcagugaacaggcucuggcg
acuguuuaccaaaaacacagcucucugcgaacucguaagaggagguauag
ggagcgacgcuugcccggugccggaaggucaaggggaggggugcaagccc
cgaaccgaagccccggugaacggcggccguaacuauaacgguccuaaggu
agcgaaauuccuugucggguaaguuccgaccugcacgaaaagcguaacga
ccggagcgcugucucggcgagggacccggugaaauugaacuggccgugaa
gaugcggccuacccguggcaggacgaaaagaccccguggagcuuuacugc
agccugguguuggcucuuggucgcgcgcggcugggggccuaacccucgga
uggggggacagcgcuuggcgggcaguuugacuggggcggucgccuccuaa
aagguaacggaggcgcccaaagguccccucaggcgggacggaaauccgcc
ggagagcgcaaggguagaagggggccugacugcgaggccugcaagccgag
caggggcgaaagccgggccuagugaaccgguggucccguguggaagggcc
aucgaucaacggauaaaaguuaccccggggauaacaggcugaucuccccc
gagcguccacagcggcggggagguuuggcaccucgaugucggcucgucgc
auccuggggcugaagaaggucccaaggguugggcuguucgcccauuaaag
cggcacgcgagcuggguucagaacgucgugagacaguucggucucuaucc
gccacgggcgcaggaggcuugaggggggcucuuccuaguacgagaggacc
ggaagggacgcaccucugguuucccagcugucccuccaggggcauaagcu
ggguagccaugugcggaagggauaaccgcugaaagcaucuaagcgggaag
cccgccccaagaugaggccucccacggcagccgguaaggacccgggaaga
ccacccgguggaugggccggggguguaagcgccgcgaggcguugagccga
ccggucccaaucguccgagucu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4v95 Structural basis for the rescue of stalled ribosomes: structure of YaeJ bound to the ribosome.
• Resolution: 3.2 Å
• Binding residue (original residue number in PDB): P2 R3 A4 K5 T6 G7 V8 R10 R11 K13 H14 K15 K16 K19 K22 G23 Y24 W25 G26 L27 R28 K30 S31 F32 R33 K34 R36 E37 A42 Y45 A46 Y47 H49 R50 K51 R53 K54 R55 F57 R58 R59 W61 I62 V63 N66 R70 N75 Y76 S77 H81 D91 R92 K93
• Binding residue (residue number reindexed from 1): P1 R2 A3 K4 T5 G6 V7 R9 R10 K12 H13 K14 K15 K18 K21 G22 Y23 W24 G25 L26 R27 K29 S30 F31 R32 K33 R35 E36 A41 Y44 A45 Y46 H48 R49 K50 R52 K53 R54 F56 R57 R58 W60 I61 V62 N65 R69 N74 Y75 S76 H80 D90 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:4v95, PDBe:4v95, PDBj:4v95
• PDBsum: 4v95
• PubMed: 22422986
• UniProt: P60491|RL20_THET8 Large ribosomal subunit protein bL20 (Gene Name=rplT)