Structure of PDB 5apn Chain P Binding Site BS01

Receptor Information

>5apn Chain P (length=183) Species: 559292 (Saccharomyces cerevisiae S288C)

ARYGATSTNPAKSASARGSYLRVSFKNTRETAQAINGWELTKAQKYLEQV
LDHQRAIPFRRFNSSIGRTAQGKEFGVTKARWPAKSVKFVQGLLQNAAAN
AEAKGLDATKLYVSHIQVNQAPKQRRRTYRAHGRINKYESSPSHIELVVT
EKEEAVAKAAEKKVVRLTSRQRGRIAAQKRIAA

Ligand information

>5apn Chain 5 (length=3112)

uugaccucaaaucagguaggaguacccgcugaacuuaagcauaucaauaa
gcggaggaaaagaaaccaaccgggauugccuuaguaacggcgagugaagc
ggcaaaagcucaaauuugaaaucugguaccuucggugcccgaguuguaau
uuggagagggcaacuuuggggccguuccuugucuauguuccuuggaacag
gacgucauagagggugagaaucccguguggcgaggagugcgguucuuugu
aaagugccuucgaagagucgaguuguuugggaaugcagcucuaagugggu
gguaaauuccaucuaaagcuaaauauuggcgagagaccgauagcgaacaa
guacagugauggaaagaugaaaagaacuuugaaaagagagugaaaaagua
cgugaaauuguugaaagggaagggcauuugaucagacgggccagcaucag
uuuugguggcaggauaaauccauaggaauguagcuugccucgguaaguau
uauagccugugggaauacugccagcugggacugaggacugcgacguaagu
caaggaugcuggcauaaugguuauaugccgcccgucuugaaacacggacc
aaggagucuaacgucuaugcgaguguuuggguguaaaacccauacgcgua
augaaagugaacguagguuggggccucgcaagaggugcacaaucgaccga
uccugaugucuucggauggauuugaguaagagcauagcuguugggacccg
aaagauggugaacuaugccugaauagggugaagccagaggaaacucuggu
ggaggcucguagcgguucugacgugcaaaucgaucgucgaauuuggguau
aggggcgaaagacuaaucgaaccaucuaguagcugguuccugccgaaguu
ucccucaggauagcagaagcucguaucaguuuuaugagguaaagcgaaug
auuagagguugaccuauucucaaacuuuaaauauguaagaaguccuuguu
acuuaauugaacguggacauuugaaugaagagcuuuuagugggccauuuu
ugguaagcagaacuggcgaugcgggaugaaccgaacguagaguuaaggug
ccggaauacacgcucaucagacaccacaaaagguguuaguucaucuagac
agccggacgguggccauggaagucggaauccgcuaaggaguguguaacaa
cucaccggccgaaugaacuagcccugaaaauggauggcgcucaagcgugu
uaccuauacucuaccgucaggguugauaugaugcccugacgaguaggcag
gcguggaggucagugacgaagccuagaccguaaggucgggucgaacggcc
ucuagugcagaucuuggugguaguagcaaauauucaaaugagaacuuuga
agacugaaguggggaaagguuccacgucaacagcaguuggacguggguua
gucgauccuaagagauggggaagcuccguuucaaaggccugauuuuaugc
aggccaccaucgaaagggaauccgguuaagauuccggaaccuggauaugg
auucuucacgguaacguaacugaauguggagacgucggcgcgagcccugg
gaggaguuaucuuuucuucuuaacagcuuaucaccccggaauugguuuau
ccggagauggggucuuauggcuggaagaggccagcaccuuugcuggcucc
ggugcgcuugugacggcccgugaaaauccacaggaaggaauaguuuucau
gccaggucguacugauaaccgcagcaggucuccaaggugaacagccucua
guugauagaauaauguagauaagggaagucggcaaaauagauccguaacu
ucgggauaaggauuggcucuaagggucgguuuuuuuuuuaaaaaaaaaaa
cgaucaacuuagaacugguacggacaaggggaaucugacugucuaauuaa
aacauagcauugcgauggucagaaagugauguugacgcaaugugauuucu
gcccagugcucugaaugucaaagugaagaaauucaaccaagcgcggguaa
acggcgcuuaagguagccaaaugccucgucaucuaauuagugacgcgcau
gaauggauuaacgagauucccacugucccuaucuacuaucuagcgaaacc
acagccaagggaacgggcuuggcagaaucagcggggaaagaagacccugu
ugagcuugacucuaguuugacauugugaauuacuuauucaaugaagcgga
gcuggaauucauuuuccacguucuagcauucaaggucccauucggggcug
auccggguugaagacauugucagguggggaguuuggcuggggcggcacau
cuguuaaacgauaacgcagauguccuaaggggggcucauggagaacagaa
aucuccaguagaacaaaaggguaaaagcccccuugauuuugauuuucagu
gugaauacaaaccaugaaaguguggccuaucgauccuuuagucccucgga
auuugaggcuagaggugccagaaaaguuaccacagggauaacuggcuugu
ggcagucaagcguucauagcgacauugcuuuuugauucuucgaugucggc
ucuuccuaucauaccgaagcagaauucgguaagcguuggauuguucaccc
acuaauagggaacgugagcuggguuuagaccgucgugagacagguuaguu
uuacccuacugaugaauguuaccgcaauaguaauugaacuuaguacgaga
ggaacaguucauucggauaauugguuuuugcggcugucugaucaggcauu
gccgcgaagcuaccauccgcuggauuauggcugaacgccucuaagucaga
auccaugcuagaacgcggugauugcuccacacaauauagauggauacgaa
uaaggcguccuuguggcgucgcugaaccauagcaggcuagcaacggugca
cuuggcggaaaggccuugggugcuugcuggcgaauugcaaugucauuuug
cguggggauaaaucauuuguauacgacuuagauguacaacgggguauugu
aagcaguagaguagccuuguuguuacgaucugcugagauuaagccuuugu
ugucugauuugu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5apn Insertion of the Biogenesis Factor Rei1 Probes the Ribosomal Tunnel during 60S Maturation.
• Resolution: 3.91 Å
• Binding residue (original residue number in PDB): Y4 S16 R18 Y21 S25 K27 R30 Q34 Q55 R56 R62 F63 S65 S66 I67 G68 R69 Q72 K74 E75 K80 R82 W83 K86 N97 N101 V119 K124 R127 T129 Y130 R131 A132 H133 G134 I136 K138 Y139 E140 S141 R167 S170 R171 Q172 G174 R175 I182
• Binding residue (residue number reindexed from 1): Y3 S15 R17 Y20 S24 K26 R29 Q33 Q54 R55 R61 F62 S64 S65 I66 G67 R68 Q71 K73 E74 K79 R81 W82 K85 N96 N100 V118 K123 R126 T128 Y129 R130 A131 H132 G133 I135 K137 Y138 E139 S140 R166 S169 R170 Q171 G173 R174 I181

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:5apn, PDBe:5apn, PDBj:5apn
• PDBsum: 5apn
• PubMed: 26709046
• UniProt: P05740|RL17A_YEAST Large ribosomal subunit protein uL22A (Gene Name=RPL17A)