Structure of PDB 4v8i Chain DY Binding Site BS01

Receptor Information

>4v8i Chain DY (length=107) Species: 274 (Thermus thermophilus)

MRVKMHVKKGDTVLVASGKYKGRVGKVKEVLPKKYAVIVEGVNIVKKAVR
VSPKYPQGGFIEKEAPLHASKVRPICPACGKPTRVRKKFLENGKKIRVCA
KCGGALD

Ligand information

>4v8i Chain DA (length=2798)

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
agccugguguuggcucuuggucgcgccugcguaggauaggugggagccug
ugaacccccgccuccgggugggggggaggcgccggugaaauaccacccug
gcgcggcugggggccuaacccucggauggggggacagcgcuuggcgggca
guuugacuggggcggucgccuccuaaaagguaacggaggcgcccaaaggu
ccccucaggcgggacggaaauccgccggagagcgcaaggguagaaggggg
ccugacugcgaggccugcaagccgagcaggggcgaaagccgggccuagug
aaccgguggucccguguggaagggccaucgaucaacggauaaaaguuacc
ccggggauaacaggcugaucucccccgagcguccacagcggcggggaggu
uuggcaccucgaugucggcucgucgcauccuggggcugaagaagguccca
aggguugggcuguucgcccauuaaagcggcacgcgagcuggguucagaac
gucgugagacaguucggucucuauccgccacgggcgcaggaggcuugagg
ggggcucuuccuaguacgagaggaccggaagggacgcaccucugguuucc
cagcugucccuccaggggcauaagcuggguagccaugugcggaagggaua
accgcugaaagcaucuaagcgggaagcccgccccaagaugaggccuccca
cggcagccgguaaggacccgggaagaccacccgguggaugggccgggggu
guaagcgccgcgaggcguugagccgaccggucccaaucguccgagucu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4v8i How hibernation factors RMF, HPF, and YfiA turn off protein synthesis.
• Resolution: 2.7 Å
• Binding residue (original residue number in PDB): M1 R2 K4 H6 K8 K9 S17 G18 K19 V30 Y35 K46 K47 A48 V49 R50 V51 G58 G59 F60 H68 S70 K71 R73 R84 R86 K87 K94 K95
• Binding residue (residue number reindexed from 1): M1 R2 K4 H6 K8 K9 S17 G18 K19 V30 Y35 K46 K47 A48 V49 R50 V51 G58 G59 F60 H68 S70 K71 R73 R84 R86 K87 K94 K95

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:4v8i, PDBe:4v8i, PDBj:4v8i
• PDBsum: 4v8i
• PubMed: 22605777
• UniProt: Q56435|RL24_THETH Large ribosomal subunit protein uL24 (Gene Name=rplX)