Structure of PDB 4v8g Chain BQ Binding Site BS01

Receptor Information

>4v8g Chain BQ (length=141) Species: 300852 (Thermus thermophilus HB8)

MLMPRRMKYRKQQRGRLKGATKGGDYVAFGDYGLVALEPAWITAQQIEAA
RVAMVRHFRRGGKIFIRIFPDKPYTKKPLEVRMGKGKGNVEGYVAVVKPG
RVMFEVAGVTEEQAMEALRIAGHKLPIKTKIVRRDAYDEAQ

Ligand information

>4v8g Chain BA (length=2809)

agaugguaagggcccacgguggaugccucggcacccgagccgaugaagga
cguggcuaccugcgauaagccagggggagccgguagcgggcguggauccc
uggauguccgaaugggggaacccggccggcgggaacgccggucaccgcgc
ugcgcggggggaaccuggggaacugaaacaucucaguacccagaggagag
gaaagagaaaucgacucccugaguagcggcgagcgaaaggggaccagccu
aaaccguccggcuuguccgggcggggucguggggcccucggacaccgaau
ccccagccuagccgaagcuguugggaagcagcgccagagagggugaaagc
cccguaggcgaaagguggggggauaggugaggguacccgaguaccccgug
guucguggagccaugggggaaucugggcggaccaccgccuaaggcuaagu
acuccgggugaccgauagcgcaccaguaccgugagggaaaggugaaaaga
accccgggaggggagugaaauagagccugaaaccgugggcuuacaagcag
ucacggccccgcaagggguuguggcgugccuauugaagcaugagccggcg
acucacggucgugggcgagcuuaagccguugaggcggaggcguagggaaa
ccgaguccgaacagggcgcaagcgcgcaaaguccgcggccguggacccga
aaccgggcgagcuagcccuggccagggugaagcuggggugagacccagug
gaggcccgaaccggugggggaugcaaaccccucggaugagcuggggcuag
gagugaaaagcuaaccgagcccggagauagcugguucuccccgaaaugac
uuuagggucagccucaggcgcugacuggggccuguagagcacugauaggg
cuaggggccuaccaaacccugucaaacuccgaagggucccagguggagcc
ugggagugagggcgcgagcgauaacguccgcguccgagcgcgggaacaac
cgagaccgccagcuaaggcccccaagucugggcuaagugguaaaggaugu
ggcgccgcgaagacagcggucgaguggcgccgcgccgaaaaugaucgggg
cuuaagcccagcgccgaagcugcgggucuggggccccaggcgguagggga
gcguucccgaugccgaugaaggccgacccgcgagggcggcuggagguaag
ggaagugcgaaugccggcaugaguaacgauaaagagggugagaaucccuc
ucgccguaagcccaaggguuccuacgcaauggucgucagcguaggguuag
gcgggaccuaaggugaagccgaaaggcguagccgaagggcagccgguuaa
uauuccggcccuucccgcaggugcgauggggggacgcucuaggcuagggg
gaccggagccauggacgagcccggccagaagcgcagggugggagguaggc
aaauccgccucccaacaagcucugcgugguggggaagcccgggugacaac
cccccgaagccagggagccaagaaaagccucuaagcacaaccugcgggaa
cccguaccgcaaaccgacacaggugggcgggugcaagagcacucaggcgc
gcgggagaacccucgccaaggaacucugcaaguuggccccguaacuucgg
gagaaggggugcucccuggggugaugagccccggggagccgcagugaaca
ggcucuggcgacuguuuaccaaaaacacagcucucugcgaacucguaaga
ggagguauagggagcgacgcuugcccggugccggaaggucaaggggaggg
gugcaagccccgaaccgaagccccggugaacggcggccguaacuauaacg
guccuaagguagcgaaauuccuugucggguaaguuccgaccugcacgaaa
agcguaacgaccggagcgcugucucggcgagggacccggugaaauugaac
uggccgugaagaugcggccuacccguggcaggacgaaaagaccccgugga
gcuuuacugcagccugguguuggcucuuggucgcgccugcguaggauagg
ugggagccugugaacccccgccuccgggugggggggaggcgccggugaaa
uaccacccuggcgcggcugggggccuaacccucggauggggggacagcgc
uuggcgggcaguuugacuggggcggucgccuccuaaaagguaacggaggc
gcccaaagguccccucaggcgggacggaaauccgccggagagcgcaaggg
uagaagggggccugacugcgaggccugcaagccgagcaggggcgaaagcc
gggccuagugaaccgguggucccguguggaagggccaucgaucaacggau
aaaaguuaccccggggauaacaggcugaucucccccgagcguccacagcg
gcggggagguuuggcaccucgaugucggcucgucgcauccuggggcugaa
gaaggucccaaggguugggcuguucgcccauuaaagcggcacgcgagcug
gguucagaacgucgugagacaguucggucucuauccgccacgggcgcagg
aggcuugaggggggcucuuccuaguacgagaggaccggaagggacgcacc
ucugguuucccagcugucccuccaggggcauaagcuggguagccaugugc
ggaagggauaaccgcugaaagcaucuaagcgggaagcccgccccaagaug
aggccucccacggcagccgguaaggacccgggaagaccacccgguggaug
ggccggggguguaagcgccgcgaggcguugagccgaccggucccaaucgu
ccgaggucu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4v8g How hibernation factors RMF, HPF, and YfiA turn off protein synthesis.
• Resolution: 3.0 Å
• Binding residue (original residue number in PDB): P4 R5 R6 K8 Y9 K11 Q12 Q13 R14 G15 R16 K22 G24 F29 Q46 A49 R56 R67 F69 D71 Y74 K76 K77 E80 R82 M83 G84 K85 G86 K87 G88 R101 R119 H123 K124 L125 P126 K128
• Binding residue (residue number reindexed from 1): P4 R5 R6 K8 Y9 K11 Q12 Q13 R14 G15 R16 K22 G24 F29 Q46 A49 R56 R67 F69 D71 Y74 K76 K77 E80 R82 M83 G84 K85 G86 K87 G88 R101 R119 H123 K124 L125 P126 K128

Gene Ontology

Molecular Function

• GO:0000049 tRNA binding
• GO:0003735 structural constituent of ribosome
• GO:0019843 rRNA binding

Biological Process

• GO:0006412 translation

Cellular Component

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

External links

• PDB: RCSB:4v8g, PDBe:4v8g, PDBj:4v8g
• PDBsum: 4v8g
• PubMed: 22605777
• UniProt: P60489|RL16_THET8 Large ribosomal subunit protein uL16 (Gene Name=rplP)