Structure of PDB 4v6u Chain BM Binding Site BS01

Receptor Information

>4v6u Chain BM (length=194) Species: 186497 (Pyrococcus furiosus DSM 3638)

MGMYKYIREAWKSPKKSYVGELLKQRMIKWRREPVVVRIERPTRLDRARA
LGYQAKQGYVIVRVRVRKGGRKRPRWKGGRKPSKMGQVKYSPKKSLQWIA
EEKAARKFPNLEVLNSYWVGEDGMYKWFEVIMVDPHHPVIKSDPKIAWIA
LKHHKGRVFRGLTSAGKKGRGLRNKGKGAEKVRPSIRANEGKGK

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 Y4 R8 K12 P14 R31 R32 V35 R38 R41 P42 L45 R47 R49 A50 L51 Y53 Q54 A55 K56 Q57 R67 K68 G69 R71 K72 R73 R75 W76 G79 R80 K81 P82 S83 K84 M85 Q87 V88 K89 Y90 S91 P92 K93 K94 L96 R106 F108 P109 N110 L111 W118 G123 M124 H136 H137 S142 D143 K145 W148 H153 H154 K155 R157 F159 R160 L162 S164 K168 G169 R170 G171 R173 K175 G176 K177 G178 E180 K181 R183 P184 S185 I186 R187 E190 K194
• Binding residue (residue number reindexed from 1): M1 Y4 R8 K12 P14 R31 R32 V35 R38 R41 P42 L45 R47 R49 A50 L51 Y53 Q54 A55 K56 Q57 R67 K68 G69 R71 K72 R73 R75 W76 G79 R80 K81 P82 S83 K84 M85 Q87 V88 K89 Y90 S91 P92 K93 K94 L96 R106 F108 P109 N110 L111 W118 G123 M124 H136 H137 S142 D143 K145 W148 H153 H154 K155 R157 F159 R160 L162 S164 K168 G169 R170 G171 R173 K175 G176 K177 G178 E180 K181 R183 P184 S185 I186 R187 E190 K194

Gene Ontology

Molecular Function

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

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006412 translation

Cellular Component

• GO:0005840 ribosome
• GO:0022625 cytosolic large ribosomal subunit
• GO:0022626 cytosolic ribosome
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:4v6u, PDBe:4v6u, PDBj:4v6u
• PDBsum: 4v6u
• PubMed: 23222135
• UniProt: Q8U2F9|RL15E_PYRFU Large ribosomal subunit protein eL15 (Gene Name=rpl15e)