Structure of PDB 6woo Chain P Binding Site BS01

Receptor Information

>6woo Chain P (length=180) Species: 4932 (Saccharomyces cerevisiae)

RYGATSTNPAKSASARGSYLRVSFKNTRETAQAINGWELTKAQKYLEQVL
DHQRAIPFRRFNSSIGRTAQGKEFGVTKARWPAKSVKFVQGLLQNAAANA
EAKGLDATKLYVSHIQVNQAPKQRRRTYRAHGRINKYESSPSHIELVVTE
KEEAVAKAAEKKVVRLTSRQRGRIAAQKRI

Ligand information

>6woo Chain 5 (length=3271)

guuugaccucaaaucagguaggaguacccgcugaacuuaagcauaucaau
aagcggaggaaaagaaaccaaccgggauugccuuaguaacggcgagugaa
gcggcaaaagcucaaauuugaaaucugguaccuucggugcccgaguugua
auuuggagagggcaacuuuggggccguuccuugucuauguuccuuggaac
aggacgucauagagggugagaaucccguguggcgaggagugcgguucuuu
guaaagugccuucgaagagucgaguuguuugggaaugcagcucuaagugg
gugguaaauuccaucuaaagcuaaauauuggcgagagaccgauagcgaac
aaguacagugauggaaagaugaaaagaacuuugaaaagagagugaaaaag
uacgugaaauuguugaaagggaagggcauuugaucagacgccagcaucag
uuuugguggcaggauaaauccauaggaauguagcuugccucgguaaguau
uauagccugugggaauacugccagcugggacugaggacugcgacguaagu
caaggaugcuggcauaaugguuauaugccgcccgucuugaaacacggacc
aaggagucuaacgucuaugcgaguguuuggguguaaaacccauacgcgua
augaaagugaacguagguuggggccucgcaagaggugcacaaucgaccga
uccugaugucuucggauggauuugaguaagagcauagcuguugggacccg
aaagauggugaacuaugccugaauagggugaagccagaggaaacucuggu
ggaggcucguagcgguucugacgugcaaaucgaucgucgaauuuggguau
aggggcgaaagacuaaucgaaccaucuaguagcugguuccugccgaaguu
ucccucaggauagcagaagcucguaucaguuuuaugagguaaagcgaaug
auuagagguuccggggucgaaaugaccuugaccuauucucaaacuuuaaa
uauguaagaaguccuuguuacuuaauugaacguggacauuugaaugaaga
gcuuuuagugggccauuuuugguaagcagaacuggcgaugcgggaugaac
cgaacguagaguuaaggugccggaauacacgcucaucagacaccacaaaa
gguguuaguucaucuagacagccggacgguggccauggaagucggaaucc
gcuaaggaguguguaacaacucaccggccgaaugaacuagcccugaaaau
ggauggcgcucaagcguguuaccuauacucuaccgucaggguugauauga
ugcccugacgaguaggcaggcguggaggucagugacgaagccuagaccgu
aaggucgggucgaacggccucuagugcagaucuuggugguaguagcaaau
auucaaaugagaacuuugaagacugaaguggggaaagguuccacgucaac
agcaguuggacguggguuagucgauccuaagagauggggaagcuccguuu
caaaggccugauuuuaugcaggccaccaucgaaagggaauccgguuaaga
uuccggaaccuggauauggauucuucacgguaacguaacugaauguggag
acgucggcgcgagcccugggaggaguuaucuuuucuucuuaacagcuuau
caccccggaauugguuuauccggagauggggucuuauggcuggaagaggc
cagcaccuuugcuggcuccggugcgcuugugacggcccgugaaaauccac
aggaaggaauaguuuucaugccaggucguacugauaaccgcagcaggucu
ccaaggugaacagccucuaguugauagaauaauguagauaagggaagucg
gcaaaauagauccguaacuucgggauaaggauuggcucuaagggucgggu
agugagggccuuggucagacgcagcguuguagacggccuugguaggucuc
uuguagaugcuacaauuacgaucaacuuagaacugguacggacaagggga
aucugacugucuaauuaaaacauagcauugcgauggucagaaagugaugu
ugacgcaaugugauuucugcccagugcucugaaugucaaagugaagaaau
ucaaccaagcgcggguaaacggcgggaguaacuaugacucucuuaaggua
gccaaaugccucgucaucuaauuagugacgcgcaugaauggauuaacgag
auucccacugucccuaucuacuaucuagcgaaaccacagccaagggaacg
ggcuuggcagaaucagcggggaaagaagacccuguugagcuugacucuag
uuugacauugugaagagacauagaggguguagaauaagugggagcuucgg
cgccagugaaauaccacuaccuuuauaguuucuuuacuuauucaaugaag
cggagcuggaauucauuuuccacguucuagcauucaaggucccauucggg
gcugauccggguugaagacauugucagguggggaguuuggcuggggcggc
acaucuguuaaacgauaacgcagauguccuaaggggggcucauggagaac
agaaaucuccaguagaacaaaaggguaaaagcccccuugauuuugauuuu
cagugugaauacaaaccaugaaaguguggccuaucgauccuuuagucccu
cggaauuugaggcuagaggugccagaaaaguuaccacagggauaacuggc
uuguggcagucaagcguucauagcgacauugcuuuuugauucuucgaugu
cggcucuuccuaucauaccgaagcagaauucgguaagcguuggauuguuc
acccacuaauagggaacgugagcuggguuuagaccgucgugagacagguu
aguuuuacccuacugaugaauguuaccgcaauaguaauugaacuuaguac
gagaggaacaguucauucggauaauugguuuuugcggcugucugaucagg
cauugccgcgaagcuaccauccgcuggauuauggcugaacgccucuaagu
cagaauccaugcuagaacgcggugauuucuuugcuccacacaauauagau
ggauacgaauaaggcguccuuguggcgucgcugaaccauagcaggcuagc
aacggugcacuuggcggaaaggccuugggugcuugcuggcgaauugcaau
gucauuuugcguggggauaaaucauuuguauacgacuuagauguacaacg
ggguauuguaagcaguagaguagccuuguuguuacgaucugcugagauua
agccuuuguugucugauuugu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6woo An active role of the eukaryotic large ribosomal subunit in translation initiation fidelity.
• Resolution: 2.9 Å
• Binding residue (original residue number in PDB): Y4 S16 A17 R18 Y21 R23 S25 F26 K27 R30 Q34 Q50 Q55 R56 R62 F63 S65 S66 G68 R69 A71 Q72 K74 E75 G77 T79 K80 R82 W83 P84 A85 K86 Q96 N97 A100 N101 K105 Q118 V119 Q121 R127 T129 Y130 R131 A132 H133 G134 R135 I136 N137 K138 Y139 E140 S141 S142 K164 R167 T169 S170 R171 Q172 R173 G174 R175 A178 I182
• Binding residue (residue number reindexed from 1): Y2 S14 A15 R16 Y19 R21 S23 F24 K25 R28 Q32 Q48 Q53 R54 R60 F61 S63 S64 G66 R67 A69 Q70 K72 E73 G75 T77 K78 R80 W81 P82 A83 K84 Q94 N95 A98 N99 K103 Q116 V117 Q119 R125 T127 Y128 R129 A130 H131 G132 R133 I134 N135 K136 Y137 E138 S139 S140 K162 R165 T167 S168 R169 Q170 R171 G172 R173 A176 I180

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome

Biological Process

• GO:0000448 cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
• GO:0002181 cytoplasmic translation
• GO:0006412 translation

Cellular Component

• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0015934 large ribosomal subunit
• GO:0022625 cytosolic large ribosomal subunit
• GO:0030687 preribosome, large subunit precursor
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:6woo, PDBe:6woo, PDBj:6woo
• PDBsum: 6woo
• UniProt: P05740|RL17A_YEAST Large ribosomal subunit protein uL22A (Gene Name=RPL17A)