Structure of PDB 4v67 Chain BN Binding Site BS01

Receptor Information

>4v67 Chain BN (length=137) Species: 274 (Thermus thermophilus)

KTYVPKQVEPRWVLIDAEGKTLGRLATKIATLLRGKHRPDWTPNVAMGDF
VVVVNADKIRVTGKKLEQKIYTRYSGYPGGLKKIPLEKMLATHPERVLEH
AVKGMLPKGPLGRRLFKRLKVYAGPDHPHQAQRPEKL

Ligand information

>4v67 Chain BA (length=2879)

agaugguaagggcccacgguggaugccucggcacccgagccgaugaagga
cguggcuaccugcgauaagccagggggagccgguagcgggcguggauccc
uggauguccgaaugggggaacccggccggcgggaacgccggucaccgcgc
uuuuugcgcggggggaaccuggggaacugaaacaucucaguacccagagg
agaggaaagagaaaucgacucccugaguagcggcgagcgaaaggggacca
gccuaaaccguccggcuuguccgggcggggucguggggcccucggacacc
gaauccccagccuagccgaagcuguugggaagcagcgccagagaggguga
aagccccguaggcgaaagguggggggauaggugaggguacccgaguaccc
cgugguucguggagccaugggggaaucugggcggaccaccgccuaaggcu
aaguacuccgggugaccgauagcgcaccaguaccgugagggaaaggugaa
aagaaccccgggaggggagugaaauagagccugaaaccgugggcuuacaa
gcagucacggccccgcaagggguuguggcgugccuauugaagcaugagcc
ggcgacucacggucgugggcgagcuuaagccguugaggcggaggcguagg
gaaaccgaguccgaacagggcgucuaguccgcggccguggacccgaaacc
gggcgagcuagcccuggccagggugaagcuggggugagacccaguggagg
cccgaaccggugggggaugcaaaccccucggaugagcuggggcuaggagu
gaaaagcuaaccgagcccggagauagcugguucuccccgaaaugacuuua
gggucagccucaggcgcugacuggggccuguagagcacugauagggcuag
ggggcccaccagccuaccaaacccugucaaacuccgaagggucccaggug
gagccugggagugagggcgcgagcgauaacguccgcguccgagcgcggga
acaaccgagaccgccagcuaaggcccccaagucugggcuaagugguaaag
gauguggcgccgcgaagacagccaggagguuggcuuagaagcagccaucc
uuuaaagagugcguaauagcucacuggucgaguggcgccgcgccgaaaau
gaucggggcuuaagcccagcgccgaagcugcgggucugggggaugacccc
aggcgguaggggagcguucccgaugccgaugaaggccgacccgcgagggc
ggcuggagguaagggaagugcgaaugccggcaugaguaacgauaaagagg
gugagaaucccucucgccguaagcccaaggguuccuacgcaauggucguc
agcguaggguuaggcgggaccuaaggugaagccgaaaggcguagccgaag
ggcagccgguuaauauuccggcccuucccgcaggugcgauggggggacgc
ucuaggcuagggggaccggagccauggacgagcccggccagaagcgcagg
gugggagguaggcaaauccgccucccaaaagcucugcgugguggggaagc
ccguacgggugacaaccccccgaagccagggagccaagaaaagccucuaa
gcacaaccugcgggaacccguaccgcaaaccgacacaggugggcgggugc
aagagcacucaggcgcgcgggagaacccucgccaaggaacucugcaaguu
ggccccguaacuucgggagaaggggugcucccuggggugaugagcuccgg
ggagccgcagugaacaggcucuggcgacuguuuaccaaaaacacagcucu
cugcgaacucguaagaggagguauagggagcgacgcuugcccggugccgg
aaggucaaggggaggggugcaagccccgaaccgaagccccggugaacggc
ggccguaacuauaacgguccuaagguagcgaaauuccuugucggguaagu
uccgaccugcacgaaaagcguaacgaccggagcgcugucucggcgaggga
cccggugaaauugaacuggccgugaagaugcggccuacccguggcaggac
gaaaagaccccguggagcuuuacugcagccugguguuggcucuuggucgc
gccugcguaggauaggugggagccugugaacccccgccuccggguggggg
ggaggcgccggugaaauaccacccuggcgcggcugggggccuaacccucg
gauggggggacagcgcuuggcgggcaguuugacuggggcggucgccuccu
aaaagguaacggaggcgcccaaagguccccucaggcgggacggaaauccg
ccggagagcgcaaggguagaagggggccugacugcgaggccugcaagccg
agcaggggcgaaagccgggccuagugaaccgguggucccguguggaaggg
ccaucgaucaacggauaaaaguuaccccggggauaacaggcugaucuccc
ccgagcguccacagcggcggggagguuuggcaccucgaugucggcucguc
gcauccuggggcugaagaaggucccaaggguugggcuguucgcccauuaa
agcggcacgcgagcuggguucagaacgucgugagacaguucggucucuau
ccgccacgggcgcaggaggcuugaggggggcucuuccuaguacgagagga
ccggaagggacgcaccucugguuucccagcugucccuccaggggcauaag
cuggguagccaugugcggaagggauaaccgcugaaagcaucuaagcggga
agcccgccccaagaugaggccucccacggcgucaagccgguaaggacccg
ggaagacuacccgguggaugggccggggguguaagcgccgcgaggcguug
agccgaccggucccaaucguccgaggucu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4v67 Crystal structure of a translation termination complex formed with release factor RF2.
• Resolution: 3.0 Å
• Binding residue (original residue number in PDB): K25 T26 V28 W36 G47 R48 T51 R58 K60 N68 F74 T86 K88 K89 Q92 K93 T96 R97 Y98 S99 Y101 P102 G103 L105 K106 K112 E123 A125 G128 M129 P131 G133 P134 L135 R137 K141
• Binding residue (residue number reindexed from 1): K1 T2 V4 W12 G23 R24 T27 R34 K36 N44 F50 T62 K64 K65 Q68 K69 T72 R73 Y74 S75 Y77 P78 G79 L81 K82 K88 E99 A101 G104 M105 P107 G109 P110 L111 R113 K117

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:4v67, PDBe:4v67, PDBj:4v67
• PDBsum: 4v67
• PubMed: 19064930
• UniProt: P60488|RL13_THET8 Large ribosomal subunit protein uL13 (Gene Name=rplM)