Structure of PDB 8bn3 Chain N8 Binding Site BS01

Receptor Information

>8bn3 Chain N8 (length=148) Species: 4932 (Saccharomyces cerevisiae)

PSRFTKTRKHRGHVSAGKGRIGKHRKHPGGRGMAGGQHHHRINMDKYHPG
YFGKVGMRYFHKQQAHFWKPVLNLDKLWTLIPEDKRDQYLKSASKETAPV
IDTLAAGYGKILGKGRIPNVPVIVKARFVSKLAEEKIRAAGGVVELIA

Ligand information

>8bn3 Chain 1 (length=3143)

uugaccucaaaucagguaggaguacccgcugaacuuaagcauaucaauaa
gcggaggaaaagaaaccaaccgggauugccuuaguaacggcgagugaagc
ggcaaaagcucaaauuugaaaucugguaccuucggugcccgaguuguaau
uuggagagggcaacuuuggggccguuccuugucuauguuccuuggaacag
gacgucauagagggugagaaucccguguggcgaggagugcgguucuuugu
aaagugccuucgaagagucgaguuguuugggaaugcagcucuaagugggu
gguaaauuccaucuaaagcuaaauauuggcgagagaccgauagcgaacaa
guacagugauggaaagaugaaaagaacuuugaaaagagagugaaaaagua
cgugaaauuguugaaagggaagggcauuugaucaggccagcaucaguuuu
gguggcaggauaaauccauaggaauguagcuugccucgguaaguauuaua
gccugugggaauacugccagcugggacugaggacugcgacguaagucaag
gaugcuggcauaaugguuauaugccgcccgucuugaaacacggaccaagg
agucuaacgucuaugcgaguguuuggguguaaaacccauacgcguaauga
aagugaacguagguuggggccucgcaagaggugcacaaucgaccgauccu
gaugucuucggauggauuugaguaagagcauagcuguugggacccgaaag
auggugaacuaugccugaauagggugaagccagaggaaacucugguggag
gcucguagcgguucugacgugcaaaucgaucgucgaauuuggguauaggg
gcgaaagacuaaucgaaccaucuaguagcugguuccugccgaaguuuccc
ucaggauagcagaagcucguaucaguuuuaugagguaaagcgaaugauua
gagguuccggggucgaaaugaccuugaccuauucucaaacuuuaaauaug
uaagaaguccuuguuacuuaauugaacguggacauuugaaugaagagcuu
uuagugggccauuuuugguaagcagaacuggcgaugcgggaugaaccgaa
cguagaguuaaggugccggaauacacgcucaucagacaccacaaaaggug
uuaguucaucuagacagccggacgguggccauggaagucggaauccgcua
aggaguguguaacaacucaccggccgaaugaacuagcccugaaaauggau
ggcgcucaagcguguuaccuauacucuaccgucaggguugauaugaugcc
cugacgaguaggcaggcguggaggucagugacgaagccuagaccguaagg
ucgggucgaacggccucuagugcagaucuuggugguaguagcaaauauuc
aaaugagaacuuugaagacugaaguggggaaagguuccacgucaacagca
guuggacguggguuagucgauccuaagagauggggaagcuccguuucaaa
ggccugauuuuaugcaggccaccaucgaaagggaauccgguuaagauucc
ggaaccuggauauggauucuucacgguaacguaacugaauguggagacgu
cggcgcgagcccugggaggaguuaucuuuucuucuuaacagcuuaucacc
ccggaauugguuuauccggagauggggucuuauggcuggaagaggccagc
accuuugcuggcuccggugcgcuugugacggcccgugaaaauccacagga
aggaauaguuuucaugccaggucguacugauaaccgcagcaggucuccaa
ggugaacagccucuaguugauagaauaauguagauaagggaagucggcaa
aauagauccguaacuucgggauaaggauuggcucuaagggucgaucaacu
uagaacugguacggacaaggggaaucugacugucuaauuaaaacauagca
uugcgauggucagaaagugauguugacgcaaugugauuucugcccagugc
ucugaaugucaaagugaagaaauucaaccaagcgcggguaaacggcggga
guaacuaugacucucuuaagguagccaaaugccucgucaucuaauuagug
acgcgcaugaauggauuaacgagauucccacugucccuaucuacuaucua
gcgaaaccacagccaagggaacgggcuuggcagaaucagcggggaaagaa
gacccuguugagcuugacucuaguuugacauugugaagagacauuuauag
uuucuuuacuuauucaaugaagcggagcuggaauucauuuuccacguucu
agcauucaaggucccauucggggcugauccggguugaagacauugucagg
uggggaguuuggcuggggcggcacaucuguuaaacgauaacgcagauguc
cuaaggggggcucauggagaacagaaaucuccaguagaacaaaaggguaa
aagcccccuugauuuugauuuucagugugaauacaaaccaugaaagugug
gccuaucgauccuuuagucccucggaauuugaggcuagaggugccagaaa
aguuaccacagggauaacuggcuuguggcagucaagcguucauagcgaca
uugcuuuuugauucuucgaugucggcucuuccuaucauaccgaagcagaa
uucgguaagcguuggauuguucacccacuaauagggaacgugagcugggu
uuagaccgucgugagacagguuaguuuuacccuacugaugaauguuaccg
caauaguaauugaacuuaguacgagaggaacaguucauucggauaauugg
uuuuugcggcugucugaucaggcauugccgcgaagcuaccauccgcugga
uuauggcugaacgccucuaagucagaauccaugcuagaacgcggugauuu
cuuugcuccacacaauauagauggauacgaauaaggcguccuuguggcgu
cgcugaaccauagcaggcuagcaacggugcacuuggcggaaaggccuugg
gugcuugcuggcgaauugcaaugucauuuugcguggggauaaaucauuug
uauacgacuuagauguacaacgggguauuguaagcaguagaguagccuug
uuguuacgaucugcugagauuaagccuuuguugucugauuugu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8bn3 Evolving precision: rRNA Expansion Segment 7S enhances translation accuracy in eukaryal ribosomes
• Resolution: 2.4 Å
• Binding residue (original residue number in PDB): P2 S3 R4 T6 K7 T8 R9 K10 R12 G13 V15 A17 G18 K19 G20 R21 I22 G23 H25 R26 K27 H28 P29 G30 G31 R32 G33 M34 G36 H39 H40 H41 R42 I43 N44 K47 Y52 F53 G54 K55 G57 M58 R59 Y60 F61 H62 K63 Q64 H67 V72 N74 K77 K111 L113 G114 K115 G116 R117 S131 K132 L133
• Binding residue (residue number reindexed from 1): P1 S2 R3 T5 K6 T7 R8 K9 R11 G12 V14 A16 G17 K18 G19 R20 I21 G22 H24 R25 K26 H27 P28 G29 G30 R31 G32 M33 G35 H38 H39 H40 R41 I42 N43 K46 Y51 F52 G53 K54 G56 M57 R58 Y59 F60 H61 K62 Q63 H66 V71 N73 K76 K110 L112 G113 K114 G115 R116 S130 K131 L132

Gene Ontology

Molecular Function

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

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006412 translation

Cellular Component

• GO:0005634 nucleus
• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0015934 large ribosomal subunit
• GO:0022625 cytosolic large ribosomal subunit
• GO:0043232 intracellular non-membrane-bounded organelle
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8bn3, PDBe:8bn3, PDBj:8bn3
• PDBsum: 8bn3
• PubMed: 38324474
• UniProt: P02406|RL28_YEAST Large ribosomal subunit protein uL15 (Gene Name=RPL28)