Structure of PDB 4v6u Chain BU Binding Site BS01

Receptor Information

>4v6u Chain BU (length=121) Species: 186497 (Pyrococcus furiosus DSM 3638)

MKISSKQPRKQRKFLYNAPLHVRQKLMSAPLSRELREKYKVRNLPVRVGD
KVRIMRGDYKGHEGKVVEVDLKRYRIYVEGATLRKTNGTEVFYPIHPSNV
MIIELNLEDEKRKKIIERRAG

Ligand information

>4v6u Chain B1 (length=3049)

gggcuaggacgcuaagccgcccgguggauggcucggcucggggcgccgac
gaagggcguggcaagcugcgauaagccccggcgaggcgcaggcagccguc
gaaccggggauucccgaaugggaccucccgcggcuuaugccgcacuccgg
gguuuauccccggagggggaacgcggggaauugaaacaucuuaguacccg
caggaaaagaaagcaaaagcgaugccgugaguaggggcgaccgaaaacgg
cagagggcaaacugaaccccgggccgacgagguucgggggaugugggguu
guagggcccccguaugagacccucgcgggugaagccgaaguccgcuggaa
cgcggcgccggagagggugauagccccguaggcguaagcccgcagggucu
cgggggacccugaguaccgucgguuggauauccggcgggaagcugggagg
caucggcucccaacccuaaauacgucccgagaccgauagcgaacuaguac
cgugagggaaagcugaaaagcaccccgggaggggggugaaaagagccuga
aaccgggcggcgauaggagggugcggcccgaaaggaaugagccuccccga
aggaaaccgcggcgacgcgggaguacgaggggaggggaccgggguugcac
cguccgucuugaaacacggggcagggaguucgcggccguggcgagguuaa
ggggguuaagccccguagccgcagggaaaccgacaugcccgcagccgggc
uuaugcccggugaggggcggggugcgaaagcgcccggagucacggccgcg
agacccgaaaccggucgaucuagcccggggcagggugaagucccucaacc
gagggauggaggcccgcuaggggugcugaugugcaguucgcucccgugac
cccgggcuaggggugaaaggccaaucgaggccggagauagcugguucccg
ccgaaucaucccgcaggauggccuccccggagguaggcggugggguagag
cacugauuggaggugcagggggcgaaagcccccggccuccugucaaacuc
cgaacccaccgccgccguagauggggggaguaggguggcgguguaagccg
uccaccgagaggggaacaacccagaccgggguuaaggccccaaagugccg
gcuaaguguuacuccaaagggugucccgggccuuagacagcggggaggua
ggcuuagaagcagccauccuuuaaagagugcguaacagcucacccgucga
gguccggggccccgaaaauggacggggcucaagccggccgccgagacccc
ggcgcacggaccgauugguccgugaucggguaggcgggcgugccgguggc
guagaagccgggccguaagguccgguggagccgccgguaucgcggauccu
gccgggaguagcagcguagucgggugagaaucccgaccgccggaggggcc
aggguuccacggcaauggucgucagccguggguuagucgguccuaacccc
gcccguaacucggcgcgggggaaagggaaacggguuuauauucccguacc
gcggggguaggugcggcaacgcaagcccggagggugacgccucgggguag
gcggaccggccgaugaggccggcuaagcguauaagcccggggagugccgu
aauggcgagaaccgggugaaagcgcgaauggcccccccguuagggggguu
ccgccgaucccuggggcccgugaaaagcccuccgggaauuccgauccccc
gcgaccguaccgagaaccgacacaggugccccugggugagaagccuaagg
cgugucgggggaaacccggccgagggaacucggcaaacuggccccguaac
uucgggagaaggggugccugcgggugcguaacccgcaggucgcagugacu
aggggggcccgacuguuuaauaaaaacacaggucccagcuagcccgaaag
gguuuguacuggggccgacgccugcccagugccgguaugugaagcccggg
uacaaccgggugaagcaccgguaaacggcggggguaacuauaacccucuu
aagguagcgaaauuccuugucgguuaaaugccgaccugcaugaauggcgu
aacgagguccccgcuguccccggccggggcccggcgaaaccucugccugg
cgcgcaugccagggacccccggugggaagcgaagaccccauggagcuuua
cugcagccugccguugccacacggcggggggugcgcagcguaggcgggag
gcgucgaagcccggccuccgggucggguggagccguccaugagacaccgc
ccacuccccgcuguguggcuaacccccgaaaggggggacagcgguaggug
ggcaguuuggcuggggcggcacgccuccgaaaagguaucggaggcgcccu
aaggucggcucaggcgggucaggaauccgccguagagugcaagggcaaaa
gccggccugacuggacccguaacagaggcggguccagccccgaaagggug
gccuagcgaaccccugugccuccccggugggggccagggaugacagaaaa
gcuacccuggggauaacagagucgucucgggcgagagcccauaucgaccc
cgaggcuugcuaccucgcugucggcucuucccauccuggcccugcagcag
gggccaaggguggggguguucacccauuaaaggggaacgugagcuggguu
uagaccgucgugagacaggucggaugcuaucuaccggggguguuggccgc
cugaggggaaggugccccuaguacgagaggaacagggugccgcggccucu
ggucuaccgguuguccucccgggcaucgccgggcagcuacgccgcagccg
auaaggccugaaagcaucuaaggccgaagcggcccccgaaaauaggcggc
cguucccuggcgcuugggccugggcgaccggcccauugccagggacgagg
gcucggguagaagacccgguugauagggcggggauguaagcgggaagggu
caaccgacccgcuuaguccgccgccccuaaucgcccgagguccugcccc

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4v6u Promiscuous behaviour of archaeal ribosomal proteins: Implications for eukaryotic ribosome evolution.
• Resolution: 6.6 Å
• Binding residue (original residue number in PDB): M1 K2 S4 S5 K6 Q7 P8 R9 K10 Q11 R12 Y16 L20 H21 Q24 K25 S28 P30 R33 R36 R42 N43 R47 R56 G57 D58 D70 L71 R73 R75 L83 K85 T86 N87 Y93 P94 H96 S98 N99 D109 K111 R112 I115 R119
• Binding residue (residue number reindexed from 1): M1 K2 S4 S5 K6 Q7 P8 R9 K10 Q11 R12 Y16 L20 H21 Q24 K25 S28 P30 R33 R36 R42 N43 R47 R56 G57 D58 D70 L71 R73 R75 L83 K85 T86 N87 Y93 P94 H96 S98 N99 D109 K111 R112 I115 R119

Gene Ontology

Molecular Function

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

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006412 translation
• GO:0042273 ribosomal large subunit biogenesis

Cellular Component

• GO:0005840 ribosome
• GO:0015934 large ribosomal subunit
• GO:0022625 cytosolic large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:4v6u, PDBe:4v6u, PDBj:4v6u
• PDBsum: 4v6u
• PubMed: 23222135
• UniProt: Q8U010|RL24_PYRFU Large ribosomal subunit protein uL24 (Gene Name=rpl24)