Structure of PDB 4v6u Chain BI Binding Site BS01

Receptor Information

>4v6u Chain BI (length=142) Species: 186497 (Pyrococcus furiosus DSM 3638)

MRIINAEGLILGRLASKVAKMLLEGEEVVIVNAEKAVITGNRDVIFKKYK
QRTELRTLTNPRRGPFYPKRSDEIVRRTIRGMLPWKTDRGRKAFKRLKVY
VGIPKEFQGKELETIIEAHVSRLSRPKYVTVGEVAKFLGGKF

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): I10 G12 R13 S16 K17 K20 I38 T39 K48 K50 R52 L55 R56 L58 N60 R62 R63 G64 P65 F66 Y67 P68 K69 R70 E73 R76 T78 R80 M82 W85 K86 D88 F94 K95 V99 I116 E117 R125 K127 F137
• Binding residue (residue number reindexed from 1): I10 G12 R13 S16 K17 K20 I38 T39 K48 K50 R52 L55 R56 L58 N60 R62 R63 G64 P65 F66 Y67 P68 K69 R70 E73 R76 T78 R80 M82 W85 K86 D88 F94 K95 V99 I116 E117 R125 K127 F137

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: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: Q8U0E6|RL13_PYRFU Large ribosomal subunit protein uL13 (Gene Name=rpl13)