Structure of PDB 5it7 Chain cc Binding Site BS01

Receptor Information

>5it7 Chain cc (length=97) Species: 28985 (Kluyveromyces lactis)

NINQKLALVVKSGKYSLGYKSTVKSLRQGKAKLIIIAANTPVLRKSELEY
YAMLSKTKVYYFQGGNNELGTAVGKLFRVGVVTILDAGDSDILTALA

Ligand information

>5it7 Chain 5 (length=3270)

uugaccucaaaucagguaggaauacccgcugaacuuaagcauaucaauaa
gcggaggaaaagaaaccaaccgggauugccuuaguaacggcgagugaagc
ggcaaaagcucaaauuugaaaucuggcgucuucgacguccgaguuguaau
uugaagaaggcaacuuuguagcugguccuugucuauguuccuuggaacag
gacgucauagagggugagaaucccguguggcgaggaucccaguuauuugu
aaagugcuuucgacgagucgaguuguuugggaaugcagcucuaagugggu
gguaaauuccaucuaaagcuaaauauuggcgagagaccgauagcgaacaa
guacagugauggaaagaugaaaagaacuuugaaaagagagugaaaaagua
cgugaaauuguugaaagggaagggcauuugaucagacaugggccagcauc
aguuuuagcgguuggauaaauccucgggaauguggcucugcuucgguaga
guguuauagcccgugggaauacagccagcugggacugaggauugcgacuu
uugucaaggaugcuggcguaaugguuaaaugccgcccgucuugaaacacg
gaccaaggagucuaacgucuaugcgaguguuuggguguaaaacccguacg
cguaaugaaagugaacguaggugagggcccgcaagggugcaucaucgacc
gauccugaugucuucggauggauuugaguaagagcauagcuguugggacc
cgaaagauggugaacuaugccugaauagggugaagccagaggaaacucug
guggaggcucguagcgguucugacgugcaaaucgaucgucgaauuugggu
auaggggcgaaagacuaaucgaaccaucuaguagcugguuccugccgaag
uuucccucaggauagcagaagcucguaucaguuuuaugagguaaagcgaa
ugauuagagguaccgggguugaaaugaccuugaccuauucucaaacuuua
aauauguaagaaguccuuguugcuuaauugaacguggacauuugaaugaa
gagcuuuuagugggccauuuuugguaagcagaacuggcgaugcgggauga
accgaacguggaguuaaggugccggaauacacgcucaucagacaccacaa
aagguguuaguucaucuagacagccggacgguggccauggaagucggaau
ccgcuaaggaguguguaacaacucaccggccgaaugaacuagcccugaaa
auggauggcgcucaagcguguuaccuauacuccaccgucaggguuaauau
gaugcccugacgaguaggcaggcguggaggucagugacgaagccuaggcu
guaaagcuggguagaacggccucuagugcagaucuuggugguaguagcaa
auauucaaaugagaacuuugaagacugaaguggggaaagguuccacguca
acagcaguuggacguggguuagucgauccuaagagauggggaagcuccgu
uucaaaggccuaauuuucuaggccaccaucgaaagggaauccgguuaaua
uuccggaaccuggauauggauucuucacgguaacguaacugaauguggag
acgucggcgcgagcccugggaggaguuaucuuuucuucuuaacagcuuau
caccccggaauugguuuauccggagagggggucuuauggcuggaagagcc
cagcccuugugcuggguccggugcgcccgcgacggcccuugaaaauccac
aggaaggaauaguuuucaugccaggucguacugauaaccgcagcaggucu
ccaaggugaacagccucuaguugauagaauaauguagauaagggaagucg
gcaaaauagauccguaacuucgggauaaggauuggcucuaaggaucgggc
gugagggccuuggucagacgcggcguuguagacggccuugguaggucucu
uguagaugcugcaauuaacgaucaacuuagaacugguacggacaagggga
aucugacugucuaauuaaaacauagcauugcgauggucagaaagugaugu
ugacgcaaugugauuucugcccagugcucugaaugucaaagugaagaaau
ucaaccaagcgcggguaaacggcgggaguaacuaugacucucuuaaggua
gccaaaugccucgucaucuaauuagugacgcgcaugaauggauuaacgag
auucccacugucccuaucuacuaucuagcgaaaccacagccaagggaacg
ggcuuggcagaaucagcggggaaagaagacccuguugagcuugacucuag
uuugacauugugaagagacauagaggguguagcauaagugggagcuucgg
cgccagugaaauaccacuaccuuuauaguuucuuuacuuauucaauuaag
cggagcuggaauucauuuuccacguucuagcauucaaaguccuauacggg
cugauccggguugaagacauugucagguggggaguuuggcuggggcggca
caucuguuaaacgauaacgcagauguccuaagggggacucauggagaaca
gaaaucuccaguagaacaaaaggguaaaaguccccuugauuuugauuuuc
agugugaauacaaaccaugaaaguguggccuaucgauccuuuagguccuc
ggaauuugaggcuagaggugccagaaaaguuaccacagggauaacuggcu
uguggcagucaagcguucauagcgacauugcuuuuugauucuucgauguc
ggcucuuccuaucauaccgaagcagaauucgguaagcguuggauuguuca
cccacuaauagggaacgugagcuggguuuagaccgucgugagacagguua
guuuuacccuacugaugaauguuaucgcaauaguaauugaacuuaguacg
agaggaacaguucauucggauaauugguuuuugcggcugucugaucaggc
auugccgcgaagcuaccauccgcuggauuauggcugaacgccucuaaguc
agaauccaugcuagaacgcgaugauuucuuugccuugcacaauauagaag
gauaagaauaaggcgucuuuuuggcgucgcugaaccauagcaggcuggca
acggugcucuuagcggaaaggcuuugggugcuugccggcgaauugcaaug
ucauuuugcgcaaggauaaaucauuuguauacgacuuaaauguacaacag
gguauuguaagcaguagaguagccuuguuguuacgaucugcugagauuaa
gccuucguugucugauuugu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5it7 Structural characterization of ribosome recruitment and translocation by type IV IRES.
• Resolution: 3.6 Å
• Binding residue (original residue number in PDB): L25 G26 Y27 K28 S29 N47 T48 P49 V50 R52 K53 S54 E57 L84 F85 R86 V87 G88
• Binding residue (residue number reindexed from 1): L17 G18 Y19 K20 S21 N39 T40 P41 V42 R44 K45 S46 E49 L76 F77 R78 V79 G80

Gene Ontology

Molecular Function

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

Cellular Component

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

External links

• PDB: RCSB:5it7, PDBe:5it7, PDBj:5it7
• PDBsum: 5it7
• PubMed: 27159451
• UniProt: P38664|RL30_KLULA Large ribosomal subunit protein eL30 (Gene Name=RPL30)