Structure of PDB 4v8x Chain DU Binding Site BS01

Receptor Information

>4v8x Chain DU (length=117) Species: 300852 (Thermus thermophilus HB8)

PRAKTGVVRRRKHKKILKLAKGYWGLRSKSFRKARETLFAAGNYAYAHRK
RRKRDFRRLWIVRINAACRQHGLNYSTFIHGLKKAGIEVDRKNLADLAVR
EPQVFAELVERAKAAQG

Ligand information

>4v8x Chain DA (length=2848)

agaugguaagggcccacgguggaugccucggcacccgagccgaugaagga
cguggcuaccugcgauaagccagggggagccgguagcgggcguggauccc
uggauguccgaaugggggaacccggccggcgggaacgccggucaccgcgc
uuuugcgcggggggaaccuggggaacugaaacaucucaguacccagagga
gaggaaagagaaaucgacucccugaguagcggcgagcgaaaggggaccag
ccuaaaccguccggcuuguccgggcggggucgggggcccucggacaccga
auccccagccuagccgaagcuguugggaagcagcgccagagagggugaaa
gccccguaggcgaaagguggggggauaggugaggguacccgaguaccccg
ugguucguggagccaugggggaaucugggcggaccaccgccuaaggcuaa
guacuccgggugaccgauagcgcaccaguaccgugagggaaaggugaaaa
gaaccccgggaggggagugaaauagagccugaaaccgugggcuuacaagc
agucacggccccgcaagggguuguggcgugccuauugaagcaugagccgg
cgacucacggucgugggcgagcuuaagccguugaggcggaggcguaggga
aaccgaguccgaacagggcgcaagcgggccgcacgcggcccgcaaagucc
gcggccguggacccgaaaccgggcgagcuagcccuggccagggugaagcu
ggggugagacccaguggaggcccgaaccggugggggaugcaaaccccucg
gaugagcuggggcuaggagugaaaagcuaaccgagcccggagauagcugg
uucuccccgaaaugacuuuagggucagccucaggcgcugacuggggccug
uagagcacugauagggcuagggggcccaccagccuaccaaacccugucaa
acuccgaagggucccagguggagccugggagugagggcgcgagcgauaac
guccgcguccgagcgcgggaacaaccgagaccgccagcuaaggcccccaa
gucugggcuaagugguaaaggauguggcgccgcgaagacagccagucgag
uggcgccgcgccgaaaaugaucggggcuuaagcccagcgccgaagcugcg
ggucugggggaugaccccaggcgguaggggagcguucccgaugccgauga
aggccgacccgcgagggcggcuggagguaagggaagugcgaaugccggca
ugaguaacgauaaagagggugagaaucccucucgccguaagcccaagggu
uccuacgcaauggucgucagcguaggguuaggcgggaccuaaggugaagc
cgaaaggcguagccgaagggcagccgguuaauauuccggcccuucccgca
ggugcgauggggggacgcucuaggcuagggggaccggagccauggacgag
cccggccagaagcgcagggugggagguaggcaaauccgccucccaacaag
cucugcgugguggggaagcccguacgggugacaaccccccgaagccaggg
agccaagaaaagccucuaagcacaaccugcgggaacccguaccgcaaacc
gacacaggugggcgggugcaagagcacucaggcgcgcgggagaacccucg
ccaaggaacucugcaaguuggccccguaacuucgggagaaggggugcucc
cuggggugaugagccccggggagccgcagugaacaggcucuggcgacugu
uuaccaaaaacacagcucucugcgaacucguaagaggagguauagggagc
gacgcuugcccggugccggaaggucaaggggaggggugcaagccccgaac
cgaagccccggugaacggcggccguaacuauaacgguccuaagguagcga
aauuccuugucggguaaguuccgaccugcacgaaaagcguaacgaccgga
gcgcugucucggcgagggacccggugaaauugaacuggccgugaagaugc
ggccuacccguggcaggacgaaaagaccccguggagcuuuacugcagccu
gguguuggcucuuggucgcgccugcguaggauaggugggagccugugaac
ccccgccuccgggugggggggaggcgccggugaaauaccacccuggcgcg
gcugggggccuaacccucggauggggggacagcgcuuggcgggcaguuug
acuggggcggucgccuccuaaaagguaacggaggcgcccaaagguccccu
caggcgggacggaaauccgccggagagcgcaaggguagaagggggccuga
cugcgaggccugcaagccgagcaggggcgaaagccgggccuagugaaccg
guggucccguguggaagggccaucgaucaacggauaaaaguuaccccggg
gauaacaggcugaucucccccgagcguccacagcggcggggagguuuggc
accucgaugucggcucgucgcauccuggggcugaagaaggucccaagggu
ugggcuguucgcccauuaaagcggcacgcgagcuggguucagaacgucgu
gagacaguucggucucuauccgccacgggcgcaggaggcuugaggggggc
ucuuccuaguacgagaggaccggaagggacgcaccucugguuucccagcu
gucccuccaggggcauaagcuggguagccaugugcggaagggauaaccgc
ugaaagcaucuaagcgggaagcccgccccaagaugaggccucccacggcg
ucaagccgguaaggacccgggaagaccacccgguggaugggccgggggug
uaagcgccgcgaggcguugagccgaccggucccaaucguccgaggucu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4v8x Yoeb-Ribosome Structure: A Canonical Rnase that Requires the Ribosome for its Specific Activity.
• Resolution: 3.35 Å
• Binding residue (original residue number in PDB): P2 R3 A4 K5 T6 G7 V8 R10 R11 R12 K13 H14 K15 K16 K19 G23 Y24 W25 G26 L27 R28 K30 S31 R33 K34 R36 E37 A42 Y45 A46 Y47 H49 R50 K51 R52 R53 K54 R55 F57 R58 R59 W61 I62 N66 R70 N75 Y76 S77 H81 R92 K93
• Binding residue (residue number reindexed from 1): P1 R2 A3 K4 T5 G6 V7 R9 R10 R11 K12 H13 K14 K15 K18 G22 Y23 W24 G25 L26 R27 K29 S30 R32 K33 R35 E36 A41 Y44 A45 Y46 H48 R49 K50 R51 R52 K53 R54 F56 R57 R58 W60 I61 N65 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:4v8x, PDBe:4v8x, PDBj:4v8x
• PDBsum: 4v8x
• PubMed: 23945936
• UniProt: P60491|RL20_THET8 Large ribosomal subunit protein bL20 (Gene Name=rplT)