Structure of PDB 4v83 Chain DL Binding Site BS01

Receptor Information

>4v83 Chain DL (length=146) Species: 262724 (Thermus thermophilus HB27)

DLRPNPGANKRRKRVGRGPGSGHGKTATRGHKGQKSRSGGLKDPRRFEGG
RSTTLMRLPKRGMQGQVPGEIKRPRYQGVNLKDLARFEGEVTPELLVRAG
LLKKGYRLKILGEGEAKPLKVVAHAFSKSALEKLKAAGGEPVLLEA

Ligand information

>4v83 Chain DA (length=2760)

agaugguaagggcccacgguggaugccucggcacccgagccgaugaagga
cguggcuaccugcgauaagccagggggagccgguagcgggcguggauccc
uggauguccgaaugggggaacccggccggcgggaacgccggucaccgcgc
uuuuugcgcggggggaaccuggggaacugaaacaucucaguacccagagg
agaggaaagagaaaucgacucccugaguagcggcgagcgaaaggggacca
gccuaaaccguccggcuuguccgggcggggucguggggcccucggacacc
gaauccccagccuagccgaagcuguugggaagcagcgccagagaggguga
aagccccguaggcgaaagguggggggauaggugaggguacccgaguaccc
cgugguucguggagccaugggggaaucugggcggaccaccgccuaaggcu
aaguacuccgggugaccgauagcgcaccaguaccgugagggaaaggugaa
aagaaccccgggaggggagugaaauagagccugaaaccgugggcuuacaa
gcagucacggccccgcaagggguuguggcgugccuauugaagcaugagcc
ggcgacucacggucgugggcgagcuuaagccguugaggcggaggcguagg
gaaaccgaguccgaacagggcgucuaguccgcggccguggacccgaaacc
gggcgagcuagcccuggccagggugaagcuggggugagacccaguggagg
cccgaaccggugggggaugcaaaccccucggaugagcuggggcuaggagu
gaaaagcuaaccgagcccggagauagcugguucuccccgaaaugacuuua
gggucagccucaggcgcugacuggggccuguagagcacugauagggcuag
ggggcccaccagccuaccaaacccugucaaacuccgaagggucccaggug
gagccugggagugagggcgcgagcgauaacguccgcguccgagcgcggga
acaaccgagaccgccagcuaaggcccccaagucugggcuaagugguaaag
gauguggcgccgcgaagacagccaggcuggucgaguggcgccgcgccgaa
aaugaucggggcuuaagcccagcgccgaagcugcgggucugggggaugac
cccaggcgguaggggagcguucccgaugccgaugaaggccgacccgcgag
ggcggcuggagguaagggaagugcgaaugccggcaugaguaacgauaaag
agggugagaaucccucucgccguaagcccaaggguuccuacgcaaugguc
gucagcguaggguuaggcgggaccuaaggugaagccgaaaggcguagccg
aagggcagccgguuaauauuccggcccuucccgcaggugcgaugggggga
cgcucuaggcuagggggaccggagccauggacgagcccggccagaagcgc
agggugggagguaggcaaauccgccucccaaaagcucugcguggugggga
agcccguacgggugacaaccccccgaagccagggagccaagaaaagccuc
uaagcacaaccugcgggaacccguaccgcaaaccgacacaggugggcggg
ugcaagagcacucaggcgcgcgggagaacccucgccaaggaacucugcaa
guuggccccguaacuucgggagaaggggugcucccuggggugaugagcuc
cggggagccgcagugaacaggcucuggcgacuguuuaccaaaaacacagc
ucucugcgaacucguaagaggagguauagggagcgacgcuugcccggugc
cggaaggucaaggggaggggugcaagccccgaaccgaagccccggugaac
ggcggccguaacuauaacgguccuaagguagcgaaauuccuugucgggua
aguuccgaccugcacgaaaagcguaacgaccggagcgcugucucggcgag
ggacccggugaaauugaacuggccgugaagaugcggccuacccguggcag
gacgaaaagaccccguggagcuuuacugcagccugguguuggcucuuggu
cgcgccggcgcggcugggggccuaacccucggauggggggacagcgcuug
gcgggcaguuugacuggggcggucgccuccuaaaagguaacggaggcgcc
caaagguccccucaggcgggacggaaauccgccggagagcgcaaggguag
aagggggccugacugcgaggccugcaagccgagcaggggcgaaagccggg
ccuagugaaccgguggucccguguggaagggccaucgaucaacggauaaa
aguuaccccggggauaacaggcugaucucccccgagcguccacagcggcg
gggagguuuggcaccucgaugucggcucgucgcauccuggggcugaagaa
ggucccaaggguugggcuguucgcccauuaaagcggcacgcgagcugggu
ucagaacgucgugagacaguucggucucuauccgccacgggcgcaggagg
cuugaggggggcucuuccuaguacgagaggaccggaagggacgcaccucu
gguuucccagcugucccuccaggggcauaagcuggguagccaugugcgga
agggauaaccgcugaaagcaucuaagcgggaagcccgccccaagaugagg
ccucccacggcgucaagccgguaaggacccgggaagacuacccgguggau
gggccggggguguaagcgccgcgaggcguugagccgaccggucccaaucg
uccgaggucu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4v83 Crystal structures of complexes containing domains from two viral internal ribosome entry site (IRES) RNAs bound to the 70S ribosome.
• Resolution: 3.5 Å
• Binding residue (original residue number in PDB): R7 P8 N9 N13 R15 R16 K17 R18 G20 R21 G24 S25 H27 T30 A31 T32 R33 G34 H35 K36 Q38 K39 S40 S42 G43 L45 K46 D47 P48 R49 R50 F51 E52 G53 G54 R55 S56 M60 L62 P63 K64 G66 M67 Q70 V71 P72 G73 E74 R77 R90 L105 K113 L115 G116 E117 S131 K132 S133
• Binding residue (residue number reindexed from 1): R3 P4 N5 N9 R11 R12 K13 R14 G16 R17 G20 S21 H23 T26 A27 T28 R29 G30 H31 K32 Q34 K35 S36 S38 G39 L41 K42 D43 P44 R45 R46 F47 E48 G49 G50 R51 S52 M56 L58 P59 K60 G62 M63 Q66 V67 P68 G69 E70 R73 R86 L101 K109 L111 G112 E113 S127 K128 S129

Gene Ontology

Molecular Function

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

Biological Process

• GO:0006412 translation

Cellular Component

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

External links

• PDB: RCSB:4v83, PDBe:4v83, PDBj:4v83
• PDBsum: 4v83
• PubMed: 21245352
• UniProt: Q72I23|RL15_THET2 Large ribosomal subunit protein uL15 (Gene Name=rplO)