Structure of PDB 4v8i Chain DN Binding Site BS01

Receptor Information

>4v8i Chain DN (length=140) Species: 274 (Thermus thermophilus)

MKTYVPKQVEPRWVLIDAEGKTLGRLATKIATLLRGKHRPDWTPNVAMGD
FVVVVNADKIRVTGKKLEQKIYTRYSGYPGGLKKIPLEKMLATHPERVLE
HAVKGMLPKGPLGRRLFKRLKVYAGPDHPHQAQRPEKLEV

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): K2 T3 V5 W13 L23 R25 T28 R35 K37 N45 F51 T63 K66 Q69 K70 R74 Y75 S76 Y78 P79 G80 L82 K89 R97 E100 H101 A102 G105 M106 P108 P111 L112 R114 R115 F117 K118 K121 H130 Q133
• Binding residue (residue number reindexed from 1): K2 T3 V5 W13 L23 R25 T28 R35 K37 N45 F51 T63 K66 Q69 K70 R74 Y75 S76 Y78 P79 G80 L82 K89 R97 E100 H101 A102 G105 M106 P108 P111 L112 R114 R115 F117 K118 K121 H130 Q133

Gene Ontology

Molecular Function

• GO:0003729 mRNA binding
• GO:0003735 structural constituent of ribosome

Biological Process

• GO:0006412 translation
• GO:0017148 negative regulation of translation

Cellular Component

• GO:0005737 cytoplasm
• GO:0005840 ribosome
• GO:0022625 cytosolic large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:4v8i, PDBe:4v8i, PDBj:4v8i
• PDBsum: 4v8i
• PubMed: 22605777
• UniProt: P60488|RL13_THET8 Large ribosomal subunit protein uL13 (Gene Name=rplM)