Structure of PDB 8p8u Chain RA Binding Site BS01

Receptor Information

>8p8u Chain RA (length=148) Species: 4932 (Saccharomyces cerevisiae)

PSRFTKTRKHRGHVSAGKGRIGKHRKHPGGRGMAGGQHHHRINMDKYHPG
YFGKVGMRYFHKQQAHFWKPVLNLDKLWTLIPEDKRDQYLKSASKETAPV
IDTLAAGYGKILGKGRIPNVPVIVKARFVSKLAEEKIRAAGGVVELIA

Ligand information

>8p8u Chain A (length=3045)

uugaccucaaaucagguaggaguacccgcugaacuuaagcauaucaauaa
gcggaggaaaagaaaccaaccgggauugccuuaguaacggcgagugaagc
ggcaaaagcucaaauuugaaaucugguaccuucggugcccgaguuguaau
uuggagagggcaacuuuggggccguuccuugucuauguuccuuggaacag
gacgucauagagggugagaaucccguguggcgaggagugcgguucuuugu
aaagugccuucgaagagucgaguuguuugggaaugcagcucuaagugggu
gguaaauuccaucuaaagcuaaauauuggcgagagaccgauagcgaacaa
guacagugauggaaagaugaaaagaacuuugaaaagagagugaaaaagua
cgugaaauuguugaaagggaagggcauuugaucagacaggccagcaucag
uuuugguggcaggauaaauccauaggaauguagcuugccucgguaaguau
uauagccugugggaauacugccagcugggacugaggacugcgacguaagu
caaggaugcuggcauaaugguuauaugccgcccgucuugaaacacggacc
aaggagucuaacgucuaugcgaguguuuggguguaaaacccauacgcgua
augaaagugaacguagguuggggccucgcaagaggugcacaaucgaccga
uccugaugucuucggauggauuugaguaagagcauagcuguugggacccg
aaagauggugaacuaugccugaauagggugaagccagaggaaacucuggu
ggaggcucguagcgguucugacgugcaaaucgaucgucgaauuuggguau
aggggcgaaagacuaaucgaaccaucuaguagcugguuccugccgaaguu
ucccucaggauagcagaagcucguaucaguuuuaugagguaaagcgaaug
auuagagguuccggggucuugaccuauucucaaacuuuaaauauguaaga
aguccuuguuacuuaauugaacguggacauuugaaugaagagcuuuuagu
gggccauuuuugguaagcagaacuggcgaugcgggaugaaccgaacguag
aguuaaggugccggaauacacgcucaucagacaccacaaaagguguuagu
ucaucuagacaggaaugaacuagcccugaaaauggauggcgcucaagcgu
guuaccuauacucuaccgucaggguugauaugaugcccugacgaguaggc
aggcguggaggucagugacgaagccuagaccguaaggucgggucgaacgg
ccucuagugcagaucuuggugguaguagcaaauauucaaaugagaacuuu
gaagacugaaguggggaaagguuccacgucaacagcaguuggacgugggu
uagucgauccuaagagauggggaagcuccguuucaaaggccugauuuuau
gcaggccaccaucgaaagggaauccgguuaagauuccggaaccuggauau
ggauucuucacgguaacguaacugaauguggagacgucggcgcgagcccu
gggaggaguuaucuuuucuucuuaacagcuuaucaccccggaauugguuu
auccggagauggggucuuauggcuggaagaggccagcaccuuugcuggcu
ccggugcgcuugugacggcccgugaaaauccacaggaaggaauaguuuuc
augccaggucguacugauaaccgcagcaggucuccaaggugaacagccuc
uaguugauagaauaauguagauaagggaagucggcaaaauagauccguaa
cuucgggauaaggauuggcucuaagggucgcgaucaacuuagaacuggua
cggacaaggggaaucugacugucuaauuaaaacauagcauugcgaugguc
agaaagugauguugacgcaaugugauuucugcccagugcucugaauguca
aagugaagaaauucaaccaagcgcggguaaacggcggaagguagccaaau
gccucgucaucuaauuagugacgcgcaugaauggauuaacgagauuccca
cugucccuaucuacuaucuagcgaaaccacagccaagggaacgggcuugg
cagaaucagcggggaaagaagacccuguugagcuugacucuaguuugaca
uugugaaguacuuauucaaugaagcggagcuggaauucauuuuccacguu
cuagcauucaaggucccauucggggcugauccggguugaagacauuguca
gguggggaguuuggcuggggcggcacaucuguuaaacgauaacgcagaug
uccuaaggggggcucauggagaacagaaaucuccaguagaacaaaagggu
aaaagcccccuugauuuugauuuucagugugaauacaaaccaugaaagug
uggccuaucgauccuuuagucccucggaauuugaggcuagaggugccaga
aaaguuaccacagggauaacuggcuuguggcagucaagcguucauagcga
cauugcuuuuugauucuucgaugucggcucuuccuaucauaccgaagcag
aauucgguaagcguuggauuguucacccacuaauagggaacgugagcugg
guuuagaccgucgugagacagguuaguuuuacccuacugaugaauguuac
cgcaauaguaauugaacuuaguacgagaggaacaguucauucggauaauu
gguuuuugcggcugucugaucaggcauugccgcgaagcuaccauccgcug
gauuauggcugaacgccucuaagucagaauccaugcuagaacgcggugau
uucuuugcuccacacaauauagauggauacgaauaaggcguccuuguggc
gucgcugaaccauagcaggcuagcaacggugcacuuggcggaaaggccuu
gggugcuugcuggcgaauugcaaugucauuuugcguggggauaaaucauu
uguauacgacuuagauguacaacgggguauuguaagcaguagaguagccu
uguuguuacgaucugcugagauuaagccuuuguugucugauuugu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8p8u Real-space refinement in PHENIX for cryo-EM and crystallography.
• Resolution: 2.23 Å
• Binding residue (original residue number in PDB): P2 S3 R4 T6 K7 T8 R9 K10 R12 G13 V15 G18 K19 G20 R21 I22 G23 H25 R26 K27 H28 P29 G30 G31 R32 G33 M34 G36 H39 H40 H41 R42 I43 N44 Y52 F53 G54 K55 V56 M58 R59 Y60 F61 H62 K63 H67 V72 N74 K111 L113 G114 K115 R117 S131 K132 L133
• Binding residue (residue number reindexed from 1): P1 S2 R3 T5 K6 T7 R8 K9 R11 G12 V14 G17 K18 G19 R20 I21 G22 H24 R25 K26 H27 P28 G29 G30 R31 G32 M33 G35 H38 H39 H40 R41 I42 N43 Y51 F52 G53 K54 V55 M57 R58 Y59 F60 H61 K62 H66 V71 N73 K110 L112 G113 K114 R116 S130 K131 L132

Gene Ontology

Molecular Function

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

Biological Process

• GO:0002181 cytoplasmic translation

Cellular Component

• GO:0005634 nucleus
• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0022625 cytosolic large ribosomal subunit
• GO:0043232 intracellular non-membrane-bounded organelle
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8p8u, PDBe:8p8u, PDBj:8p8u
• PDBsum: 8p8u
• UniProt: P02406|RL28_YEAST Large ribosomal subunit protein uL15 (Gene Name=RPL28)