Structure of PDB 4v8d Chain DM Binding Site BS01

Receptor Information

>4v8d Chain DM (length=138) Species: 300852 (Thermus thermophilus HB8)

MKTYVPKQVEPRWVLIDAEGKTLGRLATKIATLLRGKHRPDWTPNVAMGD
FVVVVNADKIRVTGKKLEQKIYTRYSGYPGGLKKIPLEKMLATHPERVLE
HAVKGMLPKGPLGRRLFKRLKVYAGPDHPHQAQRPEKL

Ligand information

>4v8d Chain DA (length=2907)

ggucaagaugguaagggcccacgguggaugccucggcacccgagccgaug
aaggacguggcuaccugcgauaagccagggggagccgguagcgggcgugg
aucccuggauguccgaaugggggaacccggccggcgggaacgccggucac
cgcgcgcgcggggggaaccuggggaacugaaacaucucaguacccagagg
agaggaaagagaaaucgacucccugaguagcggcgagcgaaaggggacca
gccuaaaccguccggcuuguccgggcggggucguggggcccucggacacc
gaauccccagccuagccgaagcuguugggaagcagcgccagagaggguga
aagccccguaggcgaaagguggggggauaggugaggguacccgaguaccc
cgugguucguggagccaugggggaaucugggcggaccaccgccuaaggcu
aaguacuccgggugaccgauagcgcaccaguaccgugagggaaaggugaa
aagaaccccgggaggggagugaaauagagccugaaaccgugggcuuacaa
gcagucacggccccgcaagggguuguggcgugccuauugaagcaugagcc
ggcgacucacggucgugggcgagcuuaagccguugaggcggaggcguagg
gaaaccgaguccgaacagggcgcaaacggcccgcacgcgggccgaaaagu
ccgcggccguggacccgaaaccgggcgagcuagcccuggccagggugaag
cuggggugagacccaguggaggcccgaaccggugggggaugcaaaccccu
cggaugagcuggggcuaggagugaaaagcuaaccgagcccggagauagcu
gguucuccccgaaaugacuuuagggucagccucaggcgcugacuggggcc
uguagagcacugauagggcuagggggcccaccagccuaccaaacccuguc
aaacuccgaagggucccagguggagccugggagugagggcgcgagcgaua
acguccgcguccgagcgcgggaacaaccgagaccgccagcuaaggccccc
aagucugggcuaagugguaaaggauguggcgccgcgaagacagccaggau
guuggcuuagaagcagccaucauuuaaagagugcguaauagcucacuggu
cgaguggcgccgcgccgaaaaugaucggggcuuaagcccagcgccgaagc
ugcgggucugggggaugaccccaggcgguaggggagcguucccgaugccg
augaaggccgacccgcgagggcggcuggagguaagggaagugcgaaugcc
ggcaugaguaacgauaaagagggugagaaucccucucgccguaagcccaa
ggguuccuacgcaauggucgucagcguaggguuaggcgggaccuaaggug
aagccgaaaggcguagccgaagggcagccgguuaauauuccggcccuucc
cgcaggugcgauggggggacgcucuaggcuagggggaccggagccaugga
cgagcccggccagaagcgcagggugggagguaggcaaauccgccucccaa
caagcucugcgugguggggaagcccguacgggugacaaccccccgaagcc
agggagccaagaaaagccucuaagcacaaccugcgggaacccguaccgca
aaccgacacaggugggcgggugcaagagcacucaggcgcgcgggagaacc
cucgccaaggaacucugcaaguuggccccguaacuucgggagaaggggug
cucccuggggugaugagccccggggagccgcagugaacaggcucuggcga
cuguuuaccaaaaacacagcucucugcgaacucguaagaggagguauagg
gagcgacgcuugcccggugccggaaggucaaggggaggggugcaagcccc
gaaccgaagccccggugaacggcggccguaacuauaacgguccuaaggua
gcgaaauuccuugucggguaaguuccgaccugcacgaaaagcguaacgac
cggagcgcugucucggcgagggacccggugaaauugaacuggccgugaag
augcggccuacccguggcaggacgaaaagaccccguggagcuuuacugca
gccugguguuggcucuuggucgcgccugcguaggauaggugggagccugu
gaacccccgccuccgggugggggggaggcgccggugaaauaccacccugg
cgcggcugggggccuaacccucggauggggggacagcgcuuggcgggcag
uuugacuggggcggucgccuccuaaaagguaacggaggcgcccaaagguc
cccucaggcgggacggaaauccgccggagagcgcaaggguagaagggggc
cugacugcgaggccugcaagccgagcaggggcgaaagccgggccuaguga
accgguggucccguguggaagggccaucgaucaacggauaaaaguuaccc
cggggauaacaggcugaucucccccgagcguccacagcggcggggagguu
uggcaccucgaugucggcucgucgcauccuggggcugaagaaggucccaa
ggguugggcuguucgcccauuaaagcggcacgcgagcuggguucagaacg
ucgugagacaguucggucucuauccgccacgggcgcaggaggcuugaggg
gggcucuuccuaguacgagaggaccggaagggacgcaccucugguuuccc
agcugucccuccaggggcauaagcuggguagccaugugcggaagggauaa
ccgcugaaagcaucuaagcgggaagcccgccccaagaugaggccucccac
ggcgucaagccgguaaggacccgggaagaccacccgguggaugggccggg
gguguaagcgccgcgaggcguugagccgaccggucccaaucguccgaggu
cuugacc

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4v8d A new understanding of the decoding principle on the ribosome.
• Resolution: 3.0 Å
• Binding residue (original residue number in PDB): T3 G24 R25 T28 R35 K37 N45 F51 T63 G64 K65 K66 Q69 R74 Y75 S76 Y78 P79 G80 K89 R97 E100 H101 A102 G105 M106 K109 G110 P111 L112 R114 F117 K118 K121 P129 Q131
• Binding residue (residue number reindexed from 1): T3 G24 R25 T28 R35 K37 N45 F51 T63 G64 K65 K66 Q69 R74 Y75 S76 Y78 P79 G80 K89 R97 E100 H101 A102 G105 M106 K109 G110 P111 L112 R114 F117 K118 K121 P129 Q131

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:4v8d, PDBe:4v8d, PDBj:4v8d
• PDBsum: 4v8d
• PubMed: 22437501
• UniProt: P60488|RL13_THET8 Large ribosomal subunit protein uL13 (Gene Name=rplM)