Structure of PDB 5jcs Chain A Binding Site BS01

Receptor Information

>5jcs Chain A (length=252) Species: 559292 (Saccharomyces cerevisiae S288C)

GRVIRNQRKGAGSIFTSHTRLRQGAAKLRTLDYAERHGYIRGIVKQIVHD
SGRGAPLAKVVFRDPYKYRLREEIFIANEGVHTGQFIYAGKKASLNVGNV
LPLGSVPEGTIVSNVEEKPGDRGALARASGNYVIIIGHNPDENKTRVRLP
SGAKKVISSDARGVIGVIAGGGRVDKPLLKAGRAFHKYRLKRNSWPKTRG
VAMNPVDHPHGGGNHQHIGKASTISRGAVSGQKAGLIAARRTGLLRGSQK
TQ

Ligand information

>5jcs Chain x (length=3394)

uugaccucaaaucagguaggaguacccgcugaacuuaagcauaucaauaa
gcggaggaaaagaaaccaaccgggauugccuuaguaacggcgagugaagc
ggcaaaagcucaaauuugaaaucugguaccuucggugcccgaguuguaau
uuggagagggcaacuuuggggccguuccuugucuauguuccuuggaacag
gacgucauagagggugagaaucccguguggcgaggagugcgguucuuugu
aaagugccuucgaagagucgaguuguuugggaaugcagcucuaagugggu
gguaaauuccaucuaaagcuaaauauuggcgagagaccgauagcgaacaa
guacagugauggaaagaugaaaagaacuuugaaaagagagugaaaaagua
cgugaaauuguugaaagggaagggcauuugaucagacaugguguuuugug
cccucugcuccuuguggguaggggaaucucgcauuucacugggccagcau
caguuuugguggcaggauaaauccauaggaauguagcuugccucgguaag
uauuauagccugugggaauacugccagcugggacugaggacugcgacgua
agucaaggaugcuggcauaaugguuauaugccgcccgucuugaaacacgg
accaaggagucuaacgucuaugcgaguguuuggguguaaaacccauacgc
guaaugaaagugaacguagguuggggccucgcaagaggugcacaaucgac
cgauccugaugucuucggauggauuugaguaagagcauagcuguugggac
ccgaaagauggugaacuaugccugaauagggugaagccagaggaaacucu
gguggaggcucguagcgguucugacgugcaaaucgaucgucgaauuuggg
uauaggggcgaaagacuaaucgaaccaucuaguagcugguuccugccgaa
guuucccucaggauagcagaagcucguaucaguuuuaugagguaaagcga
augauuagagguuccggggucgaaaugaccuugaccuauucucaaacuuu
aaauauguaagaaguccuuguuacuuaauugaacguggacauuugaauga
agagcuuuuagugggccauuuuugguaagcagaacuggcgaugcgggaug
aaccgaacguagaguuaaggugccggaauacacgcucaucagacaccaca
aaagguguuaguucaucuagacagccggacgguggccauggaagucggaa
uccgcuaaggaguguguaacaacucaccggccgaaugaacuagcccugaa
aauggauggcgcucaagcguguuaccuauacucuaccgucaggguugaua
ugaugcccugacgaguaggcaggcguggaggucagugacgaagccuagac
cguaaggucgggucgaacggccucuagugcagaucuuggugguaguagca
aauauucaaaugagaacuuugaagacugaaguggggaaagguuccacguc
aacagcaguuggacguggguuagucgauccuaagagauggggaagcuccg
uuucaaaggccugauuuuaugcaggccaccaucgaaagggaauccgguua
agauuccggaaccuggauauggauucuucacgguaacguaacugaaugug
gagacgucggcgcgagcccugggaggaguuaucuuuucuucuuaacagcu
uaucaccccggaauugguuuauccggagauggggucuuauggcuggaaga
ggccagcaccuuugcuggcuccggugcgcuugugacggcccgugaaaauc
cacaggaaggaauaguuuucaugccaggucguacugauaaccgcagcagg
ucuccaaggugaacagccucuaguugauagaauaauguagauaagggaag
ucggcaaaauagauccguaacuucgggauaaggauuggcucuaagggucg
gguagugagggccuuggucagacgcagcgggcgugcuuguggacugcuug
guggggcuugcucugcuaggcggacuacuugcgugccuuguuguagacgg
ccuugguaggucucuuguagaccgucgcuugcuacaauuaacgaucaacu
uagaacugguacggacaaggggaaucugacugucuaauuaaaacauagca
uugcgauggucagaaagugauguugacgcaaugugauuucugcccagugc
ucugaaugucaaagugaagaaauucaaccaagcgcggguaaacggcggga
guaacuaugacucucuuaagguagccaaaugccucgucaucuaauuagug
acgcgcaugaauggauuaacgagauucccacugucccuaucuacuaucua
gcgaaaccacagccaagggaacgggcuuggcagaaucagcggggaaagaa
gacccuguugagcuugacucuaguuugacauugugaagagacauagaggg
uguagaauaagugggagcuucggcgccagugaaauaccacuaccuuuaua
guuucuuuacuuauucaaugaagcggagcuggaauucauuuuccacguuc
uagcauucaaggucccauucggggcugauccggguugaagacauugucag
guggggaguuuggcuggggcggcacaucuguuaaacgauaacgcagaugu
ccuaaggggggcucauggagaacagaaaucuccaguagaacaaaagggua
aaagcccccuugauuuugauuuucagugugaauacaaaccaugaaagugu
ggccuaucgauccuuuagucccucggaauuugaggcuagaggugccagaa
aaguuaccacagggauaacuggcuuguggcagucaagcguucauagcgac
auugcuuuuugauucuucgaugucggcucuuccuaucauaccgaagcaga
auucgguaagcguuggauuguucacccacuaauagggaacgugagcuggg
uuuagaccgucgugagacagguuaguuuuacccuacugaugaauguuacc
gcaauaguaauugaacuuaguacgagaggaacaguucauucggauaauug
guuuuugcggcugucugaucaggcauugccgcgaagcuaccauccgcugg
auuauggcugaacgccucuaagucagaauccaugcuagaacgcggugauu
ucuuugcuccacacaauauagauggauacgaauaaggcguccuuguggcg
ucgcugaaccauagcaggcuagcaacggugcacuuggcggaaaggccuug
ggugcuugcuggcgaauugcaaugucauuuugcguggggauaaaucauuu
guauacgacuuagauguacaacgggguauuguaagcaguagaguagccuu
guuguuacgaucugcugagauuaagccuuuguugucugauuugu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5jcs Architecture of the Rix1-Rea1 checkpoint machinery during pre-60S-ribosome remodeling
• Resolution: 9.5 Å
• Binding residue (original residue number in PDB): G2 V4 I5 Q8 R9 K10 G11 A12 G13 F16 T20 L22 Q24 G25 D33 Y40 I41 R42 G53 Y67 Y69 R70 L71 G85 Y89 A90 P120 G121 R128 A129 S130 G131 N132 K177 P178 L179 G183 R184 A185 H187 K188 W196 K198 T199 R200 G201 N205 P206 V207 D208 H209 G212 G213 G214 N215 I219 G220 T224 S226 A229 V230 G232 A235 G236 I238 A239 A240 R241 R242 T243 G244
• Binding residue (residue number reindexed from 1): G1 V3 I4 Q7 R8 K9 G10 A11 G12 F15 T19 L21 Q23 G24 D32 Y39 I40 R41 G52 Y66 Y68 R69 L70 G84 Y88 A89 P119 G120 R127 A128 S129 G130 N131 K176 P177 L178 G182 R183 A184 H186 K187 W195 K197 T198 R199 G200 N204 P205 V206 D207 H208 G211 G212 G213 N214 I218 G219 T223 S225 A228 V229 G231 A234 G235 I237 A238 A239 R240 R241 T242 G243

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0019843 rRNA binding

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006412 translation
• GO:0042273 ribosomal large subunit biogenesis
• GO:1990145 maintenance of translational fidelity

Cellular Component

• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0022625 cytosolic large ribosomal subunit
• GO:0022626 cytosolic ribosome
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:5jcs, PDBe:5jcs, PDBj:5jcs
• PDBsum: 5jcs
• PubMed: 26619264
• UniProt: P0CX45|RL2A_YEAST Large ribosomal subunit protein uL2A (Gene Name=RPL2A)