Structure of PDB 5apo Chain G Binding Site BS01

Receptor Information

>5apo Chain G (length=231) Species: 559292 (Saccharomyces cerevisiae S288C)

NPLTHSTPKNFGIGQAVQPKRNLSRYVKWPEYVRVQRQKKILSIRLKVPP
TIAQFQYTLDRNTAAETFKLFNKYRPETAAEKKERLTKEAAAVAEGKSKQ
DASPKPYAVKYGLNHVVALIENKKAKLVLIANDVDPIELVVFLPALCKKM
GVPYAIVKGKARLGTLVNQKTSAVAALTEVRAEDEAALAKLVSTIDANFA
DKYDEVKKHWGGGILGNKAQAKMDKRAKNSD

Ligand information

>5apo 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: 5apo Insertion of the Biogenesis Factor Rei1 Probes the Ribosomal Tunnel during 60S Maturation.
• Resolution: 3.41 Å
• Binding residue (original residue number in PDB): H28 S29 T30 P31 K32 N33 G35 I36 G37 Q38 K43 R44 L46 S47 R48 Y49 K51 E54 Y55 R57 R60 L65 R68 L69 E100 K105 R108 Q123 S126 K128 P129 K133 Y134 G135 L136 H138 A141 L142 K147 V157 D158 L162 K183 Q192 K193 T194 S195 N240 K241 A242 K245
• Binding residue (residue number reindexed from 1): H5 S6 T7 P8 K9 N10 G12 I13 G14 Q15 K20 R21 L23 S24 R25 Y26 K28 E31 Y32 R34 R37 L42 R45 L46 E77 K82 R85 Q100 S103 K105 P106 K110 Y111 G112 L113 H115 A118 L119 K124 V134 D135 L139 K160 Q169 K170 T171 S172 N217 K218 A219 K222

Gene Ontology

Molecular Function

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

Biological Process

• GO:0000470 maturation of LSU-rRNA
• GO:0002181 cytoplasmic translation
• GO:0006364 rRNA processing
• GO:0042254 ribosome biogenesis

Cellular Component

• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0022625 cytosolic large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:5apo, PDBe:5apo, PDBj:5apo
• PDBsum: 5apo
• PubMed: 26709046
• UniProt: P17076|RL8A_YEAST Large ribosomal subunit protein eL8A (Gene Name=RPL8A)