Structure of PDB 4v8h Chain BN Binding Site BS01

Receptor Information

>4v8h Chain BN (length=140) Species: 300852 (Thermus thermophilus HB8)

MKTYVPKQVEPRWVLIDAEGKTLGRLATKIATLLRGKHRPDWTPNVAMGD
FVVVVNADKIRVTGKKLEQKIYTRYSGYPGGLKKIPLEKMLATHPERVLE
HAVKGMLPKGPLGRRLFKRLKVYAGPDHPHQAQRPEKLEV

Ligand information

>4v8h Chain BA (length=2837)

agaugguaagggcccacgguggaugccucggcacccgagccgaugaagga
cguggcuaccugcgauaagccagggggagccgguagcgggcguggauccc
uggauguccgaaugggggaacccggccggcgggaacgccggucaccgcgc
ugcgcggggggaaccuggggaacugaaacaucucaguacccagaggagag
gaaagagaaaucgacucccugaguagcggcgagcgaaaggggaccagccu
aaaccguccggcuuguccgggcggggucguggggcccucggacaccgaau
ccccagccuagccgaagcuguugggaagcagcgccagagagggugaaagc
cccguaggcgaaagguggggggauaggugaggguacccgaguaccccgug
guucguggagccaugggggaaucugggcggaccaccgccuaaggcuaagu
acuccgggugaccgauagcgcaccaguaccgugagggaaaggugaaaaga
accccgggaggggagugaaauagagccugaaaccgugggcuuacaagcag
ucacggccccgcaagggguuguggcgugccuauugaagcaugagccggcg
acucacggucgugggcgagcuuaagccguugaggcggaggcguagggaaa
ccgaguccgaacagggcgcaagcgggccgcggcccgcaaaguccgcggcc
guggacccgaaaccgggcgagcuagcccuggccagggugaagcuggggug
agacccaguggaggcccgaaccggugggggaugcaaaccccucggaugag
cuggggcuaggagugaaaagcuaaccgagcccggagauagcugguucucc
ccgaaaugacuuuagggucagccucaggcgcugacuggggccuguagagc
acugauagggcuagggggcccaccagccuaccaaacccugucaaacuccg
aagggucccagguggagccugggagugagggcgcgagcgauaacguccgc
guccgagcgcgggaacaaccgagaccgccagcuaaggcccccaagucugg
gcuaagugguaaaggauguggcgccgcgaagacagcggucgaguggcgcc
gcgccgaaaaugaucggggcuuaagcccagcgccgaagcugcgggucugg
gggaugaccccaggcgguaggggagcguucccgaugccgaugaaggccga
cccgcgagggcggcuggagguaagggaagugcgaaugccggcaugaguaa
cgauaaagagggugagaaucccucucgccguaagcccaaggguuccuacg
caauggucgucagcguaggguuaggcgggaccuaaggugaagccgaaagg
cguagccgaagggcagccgguuaauauuccggcccuucccgcaggugcga
uggggggacgcucuaggcuagggggaccggagccauggacgagcccggcc
agaagcgcagggugggagguaggcaaauccgccucccaacaagcucugcg
ugguggggaagcccguacgggugacaaccccccgaagccagggagccaag
aaaagccucuaagcacaaccugcgggaacccguaccgcaaaccgacacag
gugggcgggugcaagagcacucaggcgcgcgggagaacccucgccaagga
acucugcaaguuggccccguaacuucgggagaaggggugcucccuggggu
gaugagccccggggagccgcagugaacaggcucuggcgacuguuuaccaa
aaacacagcucucugcgaacucguaagaggagguauagggagcgacgcuu
gcccggugccggaaggucaaggggaggggugcaagccccgaaccgaagcc
ccggugaacggcggccguaacuauaacgguccuaagguagcgaaauuccu
ugucggguaaguuccgaccugcacgaaaagcguaacgaccggagcgcugu
cucggcgagggacccggugaaauugaacuggccgugaagaugcggccuac
ccguggcaggacgaaaagaccccguggagcuuuacugcagccugguguug
gcucuuggucgcgccugcguaggauaggugggagccugugaacccccgcc
uccgggugggggggaggcgccggugaaauaccacccuggcgcggcugggg
gccuaacccucggauggggggacagcgcuuggcgggcaguuugacugggg
cggucgccuccuaaaagguaacggaggcgcccaaagguccccucaggcgg
gacggaaauccgccggagagcgcaaggguagaagggggccugacugcgag
gccugcaagccgagcaggggcgaaagccgggccuagugaaccgguggucc
cguguggaagggccaucgaucaacggauaaaaguuaccccggggauaaca
ggcugaucucccccgagcguccacagcggcggggagguuuggcaccucga
ugucggcucgucgcauccuggggcugaagaaggucccaaggguugggcug
uucgcccauuaaagcggcacgcgagcuggguucagaacgucgugagacag
uucggucucuauccgccacgggcgcaggaggcuugaggggggcucuuccu
aguacgagaggaccggaagggacgcaccucugguuucccagcugucccuc
caggggcauaagcuggguagccaugugcggaagggauaaccgcugaaagc
aucuaagcgggaagcccgccccaagaugaggccucccacggcagccggua
aggacccgggaagaccacccgguggaugggccggggguguaagcgccgcg
aggcguugagccgaccggucccaaucguccgaggucu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4v8h How Hibernation Factors RMF, HPF, and YfiA Turn Off Protein Synthesis.
• Resolution: 3.1 Å
• Binding residue (original residue number in PDB): K2 T3 W13 L23 G24 R25 T28 R35 K37 N45 F51 T63 K66 K70 R74 Y75 S76 Y78 P79 G80 L82 K83 H94 R97 E100 H101 A102 G105 M106 P108 K109 P111 L112 R114 K118 K121 H130 Q133
• Binding residue (residue number reindexed from 1): K2 T3 W13 L23 G24 R25 T28 R35 K37 N45 F51 T63 K66 K70 R74 Y75 S76 Y78 P79 G80 L82 K83 H94 R97 E100 H101 A102 G105 M106 P108 K109 P111 L112 R114 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:4v8h, PDBe:4v8h, PDBj:4v8h
• PDBsum: 4v8h
• PubMed: 22605777
• UniProt: P60488|RL13_THET8 Large ribosomal subunit protein uL13 (Gene Name=rplM)