Structure of PDB 4v8i Chain DP Binding Site BS01

Receptor Information

>4v8i Chain DP (length=149) Species: 274 (Thermus thermophilus)

MKLSDLRPNPGANKRRKRVGRGPGSGHGKTATRGHKGQKSRSGGLKDPRR
FEGGRSTTLMRLPKRGMQGQVPGEIKRPRYQGVNLKDLARFEGEVTPELL
VRAGLLKKGYRLKILGEGEAKPLKVVAHAFSKSALEKLKAAGGEPVLLE

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): L3 S4 R7 P8 N9 P10 A12 N13 K14 R16 K17 R18 V19 G20 R21 G22 P23 G24 G28 K29 T30 A31 T32 R33 G34 H35 K36 G37 Q38 K39 S40 R41 S42 G43 L45 K46 R50 F51 E52 G53 G54 R55 S56 M60 R61 P63 K64 R65 G66 M67 Q70 V71 P72 G73 E74 I75 R77 N84 R90 G104 L105 K107 K108 K113 L115 G116 E117 S131 K132 S133
• Binding residue (residue number reindexed from 1): L3 S4 R7 P8 N9 P10 A12 N13 K14 R16 K17 R18 V19 G20 R21 G22 P23 G24 G28 K29 T30 A31 T32 R33 G34 H35 K36 G37 Q38 K39 S40 R41 S42 G43 L45 K46 R50 F51 E52 G53 G54 R55 S56 M60 R61 P63 K64 R65 G66 M67 Q70 V71 P72 G73 E74 I75 R77 N84 R90 G104 L105 K107 K108 K113 L115 G116 E117 S131 K132 S133

Gene Ontology

Molecular Function

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

Biological Process

• GO:0006412 translation

Cellular Component

• GO:0005840 ribosome
• GO:0015934 large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:4v8i, PDBe:4v8i, PDBj:4v8i
• PDBsum: 4v8i
• PubMed: 22605777
• UniProt: Q5SHQ7|RL15_THET8 Large ribosomal subunit protein uL15 (Gene Name=rplO)