Structure of PDB 4v6f Chain AU Binding Site BS01

Receptor Information

>4v6f Chain AU (length=102) Species: 300852 (Thermus thermophilus HB8)

RVKMHVKKGDTVLVASGKYKGRVGKVKEVLPKKYAVIVEGVNIVKKAVRV
SPKYPQGGFIEKEAPLHASKVRPICPACGKPTRVRKKFLENGKKIRVCAK
CG

Ligand information

>4v6f Chain AA (length=2909)

ggucaagaugguaagggcccacgguggaugccucggcacccgagccgaug
aaggacguggcuaccugcgauaagccagggggagccgguagcgggcgugg
aucccuggauguccgaaugggggaacccggccggcgggaacgccggucac
cgcgcuugcgcggggggaaccuggggaacugaaacaucucaguacccaga
ggagaggaaagagaaaucgacucccugaguagcggcgagcgaaaggggac
cagccuaaaccguccggcuuguccgggcggggucguggggcccucggaca
ccgaauccccagccuagccgaagcuguugggaagcagcgccagagagggu
gaaagccccguaggcgaaagguggggggauaggugaggguacccgaguac
cccgugguucguggagccaugggggaaucugggcggaccaccgccuaagg
cuaaguacuccgggugaccgauagcgcaccaguaccgugagggaaaggug
aaaagaaccccgggaggggagugaaauagagccugaaaccgugggcuuac
aagcagucacggccccgcaagggguuguggcgugccuauugaagcaugag
ccggcgacucacggucgugggcgagcuuaagccguugaggcggaggcgua
gggaaaccgaguccgaacagggcgcaaacggcccgcacgcgggccgaaaa
guccgcggccguggacccgaaaccgggcgagcuagcccuggccaggguga
agcuggggugagacccaguggaggcccgaaccggugggggaugcaaaccc
cucggaugagcuggggcuaggagugaaaagcuaaccgagcccggagauag
cugguucuccccgaaaugacuuuagggucagccucaggcgcugacugggg
ccuguagagcacugauagggcuagggggcccaccagccuaccaaacccug
ucaaacuccgaagggucccagguggagccugggagugagggcgcgagcga
uaacguccgcguccgagcgcgggaacaaccgagaccgccagcuaaggccc
ccaagucugggcuaagugguaaaggauguggcgccgcgaagacagccagg
auguuggcuuagaagcagccaucauuuaaagagugcguaauagcucacug
gucgaguggcgccgcgccgaaaaugaucggggcuuaagcccagcgccgaa
gcugcgggucugggggaugaccccaggcgguaggggagcguucccgaugc
cgaugaaggccgacccgcgagggcggcuggagguaagggaagugcgaaug
ccggcaugaguaacgauaaagagggugagaaucccucucgccguaagccc
aaggguuccuacgcaauggucgucagcguaggguuaggcgggaccuaagg
ugaagccgaaaggcguagccgaagggcagccgguuaauauuccggcccuu
cccgcaggugcgauggggggacgcucuaggcuagggggaccggagccaug
gacgagcccggccagaagcgcagggugggagguaggcaaauccgccuccc
aacaagcucugcgugguggggaagcccguacgggugacaaccccccgaag
ccagggagccaagaaaagccucuaagcacaaccugcgggaacccguaccg
caaaccgacacaggugggcgggugcaagagcacucaggcgcgcgggagaa
cccucgccaaggaacucugcaaguuggccccguaacuucgggagaagggg
ugcucccuggggugaugagccccggggagccgcagugaacaggcucuggc
gacuguuuaccaaaaacacagcucucugcgaacucguaagaggagguaua
gggagcgacgcuugcccggugccggaaggucaaggggaggggugcaagcc
ccgaaccgaagccccggugaacggcggccguaacuauaacgguccuaagg
uagcgaaauuccuugucggguaaguuccgaccugcacgaaaagcguaacg
accggagcgcugucucggcgagggacccggugaaauugaacuggccguga
agaugcggccuacccguggcaggacgaaaagaccccguggagcuuuacug
cagccugguguuggcucuuggucgcgccugcguaggauaggugggagccu
gugaacccccgccuccgggugggggggaggcgccggugaaauaccacccu
ggcgcggcugggggccuaacccucggauggggggacagcgcuuggcgggc
aguuugacuggggcggucgccuccuaaaagguaacggaggcgcccaaagg
uccccucaggcgggacggaaauccgccggagagcgcaaggguagaagggg
gccugacugcgaggccugcaagccgagcaggggcgaaagccgggccuagu
gaaccgguggucccguguggaagggccaucgaucaacggauaaaaguuac
cccggggauaacaggcugaucucccccgagcguccacagcggcggggagg
uuuggcaccucgaugucggcucgucgcauccuggggcugaagaagguccc
aaggguugggcuguucgcccauuaaagcggcacgcgagcuggguucagaa
cgucgugagacaguucggucucuauccgccacgggcgcaggaggcuugag
gggggcucuuccuaguacgagaggaccggaagggacgcaccucugguuuc
ccagcugucccuccaggggcauaagcuggguagccaugugcggaagggau
aaccgcugaaagcaucuaagcgggaagcccgccccaagaugaggccuccc
acggcgucaagccgguaaggacccgggaagaccacccgguggaugggccg
gggguguaagcgccgcgaggcguugagccgaccggucccaaucguccgag
gucuugacc

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4v6f Structural aspects of messenger RNA reading frame maintenance by the ribosome.
• Resolution: 3.1 Å
• Binding residue (original residue number in PDB): R2 K4 H6 K8 K9 S17 G18 K19 V30 P32 Y35 I44 K46 K47 V49 V51 K54 H68 S70 K71 R73 R84 V85 E91
• Binding residue (residue number reindexed from 1): R1 K3 H5 K7 K8 S16 G17 K18 V29 P31 Y34 I43 K45 K46 V48 V50 K53 H67 S69 K70 R72 R83 V84 E90

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0019843 rRNA binding

Biological Process

• GO:0006412 translation

Cellular Component

• GO:0005840 ribosome
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:4v6f, PDBe:4v6f, PDBj:4v6f
• PDBsum: 4v6f
• PubMed: 20400952
• UniProt: Q5SHP9|RL24_THET8 Large ribosomal subunit protein uL24 (Gene Name=rplX)