Structure of PDB 5j8b Chain V Binding Site BS01

Receptor Information

>5j8b Chain V (length=101) Species: 300852 (Thermus thermophilus HB8)

MFAIVKTGGKQYRVEPGLKLRVEKLDAEPGATVELPVLLLGGEKTVVGTP
VVEGASVVAEVLGHGRGKKILVSKFKAKVQYRRKKGHRQPYTELLIKEIR
G

Ligand information

>5j8b Chain A (length=2874)

agaugguaagggcccacgguggaugccucggcacccgagccgaugaagga
cguggcuaccugcgauaagccagggggagccgguagcgggcguggauccc
uggauguccgaaugggggaacccggccggcgggaacgccggucaccgcgc
gcgcggggggaaccuggggaacugaaacaucucaguacccagaggagagg
aaagagaaaucgacucccugaguagcggcgagcgaaaggggaccagccua
aaccguccggcuuguccgggcggggucguggggcccucggaccgaauccc
cagccuagccgaagcuguugggaagcagcgccagagagggugaaagcccc
guaggcgaaagguggggggauaggugaggguacccgaguaccccgugguu
cguggagccaugggggaaucugggcggaccaccgccuaaggcuaaguacu
ccgggugaccgauagcgcaccaguaccgugagggaaaggugaaaagaacc
ccgggaggggagugaaauagagccugaaaccgugggcuuacaagcaguca
cggccccgcagggguuguggcgugccuauugaagcaugagccggcgacuc
acggucgugggcgagcuuaagccguugaggcggaggcguagggaaaccga
guccgaacagggcgcaagcggccgcaaaguccgcggccguggacccgaaa
ccgggcgagcuagcccuggccagggugaagcuggggugagacccagugga
ggcccgaaccggugggggaugcaaaccccucggaugagcuggggcuagga
gugaaaagcuaaccgagcccggagauagcugguucuccccgaaaugacuu
uagggucagccucaggcgcugacuggggccuguagagcacugauagggcu
agggggcccaccagccuaccaaacccugucaaacuccgaagggucccagg
uggagccugggagugagggcgcgagcgauaacguccgcguccgagcgcgg
gaacaaccgagaccgccagcuaaggcccccaagucugggcuaagugguaa
aggauguggcgccgcgaagacagccaggagguuggcuuagaagcagccau
ccuuuaaagagugcguaauagcucacuggucgaguggcgccgcgccgaaa
augaucggggcuuaagcccagcgccgaagcugcgggucugggggaugacc
ccaggcgguaggggagcguucccgaugccgaugaaggccgacccgcgagg
gcggcuggagguaagggaagugcgaaugccggcaugaguaacgauaaaga
gggugagaaucccucucgccguaagcccaaggguuccuacgcaauggucg
ucagcguaggguuaggcgggaccuaaggugaagccgaaaggcguagccga
agggcagccgguuaauauuccggcccuucccgcaggugcgauggggggac
gcucuaggcuagggggaccggagccauggacgagcccggccagaagcgca
gggugggagguaggcaaauccgccucccaacaagcucugcguggugggga
agcccgggugacaaccccccgaagccagggagccaagaaaagccucuaag
cacaaccugcgggaacccguaccgcaaaccgacacaggugggcgggugca
agagcacucaggcgcgcgggagaacccucgccaaggaacucugcaaguug
gccccguaacuucgggagaaggggugcucccuggggugaugagccccggg
gagccgcagugaacaggcucuggcgacuguuuaccaaaaacacagcucuc
ugcgaacucguaagaggagguauagggagcgacgcuugcccggugccgga
aggucaaggggaggggugcaagccccgaaccgaagccccggugaacggcg
gccguaacuauaacgguccuaagguagcgaaauuccuugucggguaaguu
ccgaccugcacgaaaagcguaacgaccggagcgcugucucggcgagggac
ccggugaaauugaacuggccgugaagaugcggccuacccguggcaggacg
aaaagaccccguggagcuuuacugcagccugguguuggcucuuggucgcg
ccugcguaggauaggugggagccugugaacccccgccuccgggugggggg
gaggcgccggugaaauaccacccuggcgcggcugggggccuaacccucgg
auggggggacagcgcuuggcgggcaguuugacuggggcggucgccuccua
aaagguaacggaggcgcccaaagguccccucaggcgggacggaaauccgc
cggagagcgcaaggguagaagggggccugacugcgaggccugcaagccga
gcaggggcgaaagccgggccuagugaaccgguggucccguguggaagggc
caucgaucaacggauaaaaguuaccccggggauaacaggcugaucucccc
cgagcguccacagcggcggggagguuuggcaccucgaugucggcucgucg
cauccuggggcugaagaaggucccaaggguugggcuguucgcccauuaaa
gcggcacgcgagcuggguucagaacgucgugagacaguucggucucuauc
cgccacgggcgcaggaggcuugaggggggcucuuccuaguacgagaggac
cggaagggacgcaccucugguuucccagcugucccuccaggggcauaagc
uggguagccaugugcggaagggauaaccgcugaaagcaucuaagcgggaa
gcccgccccaagaugaggccucccacggcagccgguaaggacccgggaag
accacccgguggaugggccggggguguaagcgccgcgaggcguugagccg
accggucccaaucguccgaggucu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5j8b Elongation factor 4 remodels the A-site tRNA on the ribosome.
• Resolution: 2.6 Å
• Binding residue (original residue number in PDB): G8 G9 K10 L18 K19 E23 K24 R66 K69 K74 F75 K76 A77 K78 V79 Q80 Y81 R83 K84 K85 G86 H87 Q89 P90
• Binding residue (residue number reindexed from 1): G8 G9 K10 L18 K19 E23 K24 R66 K69 K74 F75 K76 A77 K78 V79 Q80 Y81 R83 K84 K85 G86 H87 Q89 P90

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0019843 rRNA binding

Biological Process

• GO:0006412 translation

Cellular Component

• GO:0005737 cytoplasm
• GO:0005840 ribosome
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:5j8b, PDBe:5j8b, PDBj:5j8b
• PDBsum: 5j8b
• PubMed: 27092003
• UniProt: P60492|RL21_THET8 Large ribosomal subunit protein bL21 (Gene Name=rplU)