Structure of PDB 4v8p Chain HU Binding Site BS02

Receptor Information

>4v8p Chain HU (length=203) Species: 5911 (Tetrahymena thermophila)

MKHNNQLPVAQLRKHQQFRIKTFFNQAAQKKARLHARRAQAAAVFPRPTE
KLQPVVRKQTQRYNKSTKLGRGFTLQELKAAGISAAFAQSIGIKVDHRRK
NRCQESLELNKKRLLAYVSKLVLFPRHQGKAKKGLVNDTADTSSAAQNAL
QTSVPLPSVSKREKAVSNIAELRKKKVYRIIRQEKTNQKWDGKRKAKAQA
AAE

Ligand information

>4v8p Chain H1 (length=3119)

cuacaccugaaacaagcaagauuacccgcugaacuuaagcauaucaguaa
gcggaggaaaagaaacuaacuaggauagccccaguaauggcgaaugaaca
ggcuaaagcucaaagugaaaaucugaaguggucaacacaacagaauugua
aucuaaagggucaaccugaaacuaagcuccucucauaaguuccuuggaac
aggacgucaaagagggugacaaccccguagucggagaggaaggcuggugu
aagggagauuucaaagagucggguuguuugggauugcagcccuaaguggg
agauaaacuucuucuaaagcuaaauauacacgggagaccgauagcgaaca
aguacugcgaaggaaagaugaaaagaacuuugaaaagagggcuaaaagac
uugaaaccguugagaaggaagcuguagaagagcaauaaacuggacggcgc
auaagggggaaguacuaaucacugcagagucgauacguaaaaggucgaug
aguaaggaaaugguacagaacuugcuacgccggucagaagacaaaauggg
uucagauugaaggagucaccugagaucgggcagcaaugcagaucaaaagg
aaaacuucaaacuggacugaggggccuaagggcgauuuugucaaaauggc
uucuacugacccgucuugaaacacggaccaaggagucuaucaauuaagcg
agugauaggguggaaaaacccguccgcgaaacgaaagugaguacaaggug
ccaagccgcaagguagcagcaucacccgaccuugagucuccgacgaaggg
uucgaggaagagcuuaauuguuaggacccgaaagauggugaacuacgcuu
gaauagggugaagccaggggaaacucugguggaagcucguagcgauacug
acgugcaaaucguucgucaaauuugaguguaggggcgaaagacuaaucga
accaucuaguagcugguucccuccgaaguuucucucaggauagcaagagc
aaguacgcaguuuuauuagguaaagcgaaugauuagaggacucgggguuc
caagaaucucgaccuauucucaaacuuuaaauugguaagagccgcggagu
uuacuuaaaugaacucucgggaagaaugcagugcucuuagugggccauuu
uugguaagcagaacuggcgaugagggaugaaccuaacguugagauaaggc
gcccaaaugcacgcucaucagauaccacaaaagguguugguucauacgga
cagcaggccugccgaaugaacuagcccugaaaauggauggcgcugaagcg
uguugccgauacucaaccaucagagcaaaugcgaggcuuugaugaguagg
agggcgugaucguugccuagaaguauugggcgugagccuauauggagcag
cgauuagugcagaucuuggugguaguagcaaauauucaaaugagaacuuu
gaagaccgaaguggagaaggguuccaugagaacagcaauuguucaugggu
uacucgauccuaagacauagguuaacuccuugcaauacaagaagacauuc
guuuucguugucaaaagggaaugagguuaauauuccucaagcuggacgug
guauagagcgguaacgcaaagaaacccggagacgucagcaggugucacug
gaagaguuaucuuuucuuuuuaacauacuauggccaugaaauuggauuau
ccagagauaucggcuguauguauggcagagcagcucagagcugucaguug
cgcaccugaugacccuugaaaaucugggggagacauaauuucacgccagu
ucguacccauaaccgcaucaggucuccaagguuagcagccucugguccau
agaacaauguagauaagggaagucggcaaauuggauccguaacuucggga
uaaggauuggcucugaggaucucagaacugaagcggacaaagguaauccg
acuguuuaauaaaaacaaagcauugugacggccucaacaggugaugacac
aaugugauuucugcccagugcucugaaugucaaagugacgcaauucaacc
aagcgcggguaaacggcgggaguaacuaugacucucuuaagguagccaaa
ugccucgucaucuaauuagugacgcgcaugaauggauuaaugagauuacc
acugucccuaucuacuaucuagcgaacccacagcuaagggaacgggcuua
gaauaaucagcggggaaagaagacccuguugagcuugacucuagucuaac
uuugugaaauggcagucauuuugcuuauuucgugaagaaaagacuggugc
aaaccaguucuaaaguuaaggucauuuauugacugauuuuugcgaaagac
augguuagggggggaguuugucuggggcggaaugccuguuaaaccauaac
gcaggcguccuaaguguagcucagugagaacggaaaucucacguagaaca
aaaggguaaaagcuacauugauuuugauuuucaguaggaauacaaaccgc
gaaagcguggccuaucgauccuuuaacuuuacaaguuuuaagcuagaggu
gucagaaaaguuaccacagggauaacuggcuuguggcagccaagaguuca
uaucgacguugcuuuuugauccuucgaugucggcucuuccuaucauugug
aagcagaauucacaacgugucggauuguucacccgcuaauagggaacgug
agcuggguuuagaccgucgugagacagguuaguuuuacccuacugaugaa
acgauguugcgacaguaauuuaaguuaguacgagaggaacacuuaaauca
gauaauugguaaauacgguugucugaaaagacaaugccgugaagcuacca
ucuguuggauuaugacugaaggccucuaagucagaauccaugcuggaaag
caaugucuaagugugaugauaaacgaaaaaaaauaaaaauuaaguucgaa
agguagagcggggaagagcgaaaaagcuugaccuuaacugcuaaucguaa
uuccaaauuaucaucuacguaaaucuuuuguagacgacuuaacauggaac
ggguauuguaagcaugagaguagaauuuccuacgaucugcugagauucag
cccgucuccuuagauuuau

........................<<<<<<.....<......>......>
>>>>.>...{.....<<....>>..<<<<<......<<.....>>.....
>>>>>..[[[...........<<<<..<<<.....>>>..>>>>......
.......<<<<<..<<<...<<<.<<<<<<<<<<......<<<<......
>>>>.((......<<<.....))>>>.......>>>>>>>..>>>>>>..
.>>>..>>>>.>........<<<<<<<........>>>>>>>.....(((
((..<<<<<<)))))..]]]....}.........................
....<<....>>...............<<<<....>>>>...........
.....................<.<<<<<<<....<<...<<<<.<<<<<.
....<<<....<<<<<.<<..<<<<...<<<<<<.<......>>>>>>>.
.>>.>>...>>>>>>>....>>>....>>>>>.>>>>..<<<<<<<<.<<
<<<<<.<<<<<<......<<<..<<<<..<<<....>>>.>>>>...>>>
....>>>>>>.>>>>>>>.....<<<....>>>.>>>>>>>>...>>..>
>>>>>>.>..<<<<........>>>><<<<<<...<<<<.<<<<<<<<<.
.<<<...<<<<......>>>>...>>>...<<....>>........<<<<
<...<<<....>>>....>>>>>.<<<<<<<....<<<...>>>....>>
.>>>.>>....>>>>>>>>>.>>>>.<<.<...<<<<<<.....<<<<<<
<<<..<<<....<<<<<<<....>>>>>>>.....>>>...<<<<.<<.<
<........>>>>>>>>....>>>>>>>>>...<<.......>>......
>>>>>>......>.>>..<<<<<<....<.<<<....>>>.><<<<<<<<
<.....<<<.<<<<<<<<<...<<<....<<<....<<<..<<<<<<<<<
...>>>>>>>>>>>>....>>>..>.>>...>>>>>>>...<<<.<<<<<
<..........>>>>>>>>>....>>>>>..>>>>>>>.>>..<<<<.<<
<<<.....>>>>>.>>>>....<<<......>>>...<<<<<<....<<<
(((.....<<<<<<......<..........<<<.<<<<<<<<<......
..<<<<..>>>>....>>>>>>>>>>>>..........))).>....>>>
>>>.>>>....>>>>>><<<<<<<<<.........>>>>>>>>>....>>
>>>><.<<<<<<<<<<......<<<<.<<<<....>>>>>>>>...>>>>
>>>>>>..>.....>>>>>><<.....<<.....<<<<<<.......>>>
>>><<<<.....<<<<<.<<...<<<<<<...<<.....>>.>>>>>>..
..((<<<<<<...<<<..<<<......>>>..........<<<<<<....
>>>>>>...>>>....>>>..<<<<<........>>>>>))<<<<.<<<<
..<<...<<<....>>>.......<<<<<<...<<<<.<<<<<<<<<<<<
<<<<<<.......>>>>>><...<<<<<...<<<<<<<....<<<<...>
>>>....>>>.>>>>....>>>>>....><<<<<<<.>>>>>>>>>>>.>
.>>>>>>>.>>>>.........>>>>>>.........>>..>>>>>>>>.
>>>..>>.....<<......>>>>>>>.<<<<.....>>>>..>>>>..<
<<<.....<<<<<<<.<<...............<<<<<............
...>>>>><<.<<<<<<...>>>>>>.>>............<<<<<<<<<
..<<<.........>>>..<<<<<<<....<<<<....>>>>......>>
>>>>>...<<..<<<..<<<<<<....<<<.....<<<......>>>...
..>>>.>>>>..>>>>><<<<<<.......>>>>>>........<.....
......<<<<<.......>>>>>.....>.....>>....>>.>>>>>>>
.....>>.>>>>>>>..>>>>>>....>>....<<<<<........>>>>
>....(((((..{{{.{{......[[[[.{{[[[[..<<<<<..<<<<<<
<..<<<<<<<<<<.>>>>>>>>>>...<<<<<.....<<<<..<<<<<..
..>>>>>............<<<<<.....>>>>>..>>>>..>>>>>...
..>>>>>>>...>>>>>...<<<.....>>>..<<<<<<...........
>>>>>>..<<...<<<<<<<...<<<<<<.......>>>>>>.....<<.
..(((>>....>>>>>>>...<<<.<<<<<.......>>>>.>>>>.<<<
....>>>.>>))).......(((((.[.(((.>>>>>>)))].)))))..
........]]]]..}}]]]].......<<.<...<<<<<<...<<.....
..>>...>>>>>>....>.>.>.......<<<<<.<<<<<<..<<<<<<<
<<......>>>>>>>..>>.<<<.........>>>.....>>>>>..>..
.>>>.>>....<<<<<<<....>>>.>>>>....}}..}}}.)))))...
..<<<<<<<<..<<<<.<<<<<<<<...............>>>>>>>><<
<<<...<<<<....<<<<<<<<<<....>>>>>..>>>>>...>>>>..>
>>>>.<<<<...<<<<<...........>>>>>...>>>>.>>>>....>
>>>>>>>.....<<<<<<<<......<<................>>....
..<<<<...<<<...<<<<......>>>>..>>>...>>>>.........
......>>>>>>>>....<<<<<<<<<.............>....<<<<<
<<<.<<<....<<<.<<..<<<<......>>>>..>>>>>...>>>....
>>>>>.>>>..>>>>>>>>

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4v8p Crystal Structure of the Eukaryotic 60S Ribosomal Subunit in Complex with Initiation Factor 6.
• Resolution: 3.52 Å
• Binding residue (original residue number in PDB): M1 K2 H3 N5 Q6 P8 L12 R13 K14 H15 Q26 A27 K30 R33 R37 V56 R57 K58 Q59 T60 R62 Y63 N64 K68 G70 R71 L75 K79 H97 R98 R99 K100 R102 C103 R126 K132 K161 Y178 R179 R182 Q183 K185 T186 K189 W190 G192 R194
• Binding residue (residue number reindexed from 1): M1 K2 H3 N5 Q6 P8 L12 R13 K14 H15 Q26 A27 K30 R33 R37 V56 R57 K58 Q59 T60 R62 Y63 N64 K68 G70 R71 L75 K79 H97 R98 R99 K100 R102 C103 R126 K132 K161 Y178 R179 R182 Q183 K185 T186 K189 W190 G192 R194

Gene Ontology

Molecular Function

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

Biological Process

• GO:0006412 translation

Cellular Component

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

External links

• PDB: RCSB:4v8p, PDBe:4v8p, PDBj:4v8p
• PDBsum: 4v8p
• PubMed: 22052974
• UniProt: P0DJ58|RL13_TETTS Large ribosomal subunit protein eL13 (Gene Name=RPL13)