Structure of PDB 7n8b Chain AY Binding Site BS01

Receptor Information

>7n8b Chain AY (length=126) Species: 4932 (Saccharomyces cerevisiae)

AKQSLDVSSDRRKARKAYFTAPSSQRRVLLSAPLSKELRAQYGIKALPIR
RDDEVLVVRGSKKGQEGKISSVYRLKFAVQVDKVTKEKVNGASVPINLHP
SKLVITKLHLDKDRKALIQRKGGKLE

Ligand information

>7n8b Chain A1 (length=3156)

uugaccucaaaucagguaggaguacccgcugaacuuaagcauaucaauaa
gcggaggaaaagaaaccaaccgggauugccuuaguaacggcgagugaagc
ggcaaaagcucaaauuugaaaucugguaccuucggugcccgaguuguaau
uuggagagggcaacuuuggggccguuccuugucuauguuccuuggaacag
gacgucauagagggugagaaucccguguggcgaggagugcgguucuuugu
aaagugccuucgaagagucgaguuguuugggaaugcagcucuaagugggu
gguaaauuccaucuaaagcuaaauauuggcgagagaccgauagcgaacaa
guacagugauggaaagaugaaaagaacuuugaaaagagagugaaaaagua
cgugaaauuguugaaagggaagggcauuugaucagacaugguguuuugua
uuucacuggccagcaucaguuuugguggcaggauaaauccauaggaaugu
agcuugccucgguaaguauuauagccugugggaauacugccagcugggac
ugaggacugcgacguaagucaaggaugcuggcauaaugguuauaugccgc
ccgucuugaaacacggaccaaggagucuaacgucuaugcgaguguuuggg
uguaaaacccauacgcguaaugaaagugaacguagguuggggccucgcaa
gaggugcacaaucgaccgauccugaugucuucggauggauuugaguaaga
gcauagcuguugggacccgaaagauggugaacuaugccugaauaggguga
agccagaggaaacucugguggaggcucguagcgguucugacgugcaaauc
gaucgucgaauuuggguauaggggcgaaagacuaaucgaaccaucuagua
gcugguuccugccgaaguuucccucaggauagcagaagcucguaucaguu
uuaugagguaaagcgaaugauuagagguuccggggucaccuugaccuauu
cucaaacuuuaaauauguaagaaguccuuguuacuuaauugaacguggac
auuugaaugaagagcuuuuagugggccauuuuugguaagcagaacuggcg
augcgggaugaaccgaacguagaguuaaggugccggaauacacgcucauc
agacaccacaaaagguguuaguucaucuagacagccggacgguggccaug
gaagucggaauaggaguguguaacaacucaccggccgaaugaacuagccc
ugaaaauggauggcgcucaagcguguuaccuauacucuaccgucaggguu
gauaugaugcccugacgaguaggcaggcguggaggucagugacgaagccu
agaccguaaggucgggucgaacggccucuagugcagaucuuggugguagu
agcaaauauucaaaugagaacuuugaagacugaaguggggaaagguucca
cgucaacagcaguuggacguggguuagucgauccuaagagauggggaagc
uccguuucaaaggccugauuuuaugcaggccaccaucgaaagggaauccg
guuaagauuccggaaccuggauauggauucuucacgguaacguaacugaa
uguggagacgucggcgcgagcccugggaggaguuaucuuuucuucuuaac
agcuuaucaccccggaauugguuuauccggagauggggucuuauggcugg
aagaggccagcaccuuugcuggcuccggugcgcuugugacggcccgugaa
aauccacaggaaggaauaguuuucaugccaggucguacugauaaccgcag
caggucuccaaggugaacagccucuaguugauagaauaauguagauaagg
gaagucggcaaaauagauccguaacuucgggauaaggauuggcucuaagg
gucggguacgaucaacuuagaacugguacggacaaggggaaucugacugu
cuaauuaaaacauagcauugcgauggucagaaagugauguugacgcaaug
ugauuucugcccagugcucugaaugucaaagugaagaaauucaaccaagc
gcggguaaacggcgggaguaacuaugacucucuuaagguagccaaaugcc
ucgucaucuaauuagugacgcgcaugaauggauuaacgagauucccacug
ucccuaucuacuaucuagcgaaaccacagccaagggaacgggcuuggcag
aaucagcggggaaagaagacccuguugagcuugacucuaguuugacauug
ugaagagacauaguuucuuuacuuauucaaugaagcggagcuggaauuca
uuuuccacguucuagcauucaaggucccauucggggcugauccggguuga
agacauugucagguggggaguuuggcuggggcggcacaucuguuaaacga
uaacgcagauguccuaaggggggcucauggagaacagaaaucuccaguag
aacaaaaggguaaaagcccccuugauuuugauuuucagugugaauacaaa
ccaugaaaguguggccuaucgauccuuuagucccucggaauuugaggcua
gaggugccagaaaaguuaccacagggauaacuggcuuguggcagucaagc
guucauagcgacauugcuuuuugauucuucgaugucggcucuuccuauca
uaccgaagcagaauucgguaagcguuggauuguucacccacuaauaggga
acgugagcuggguuuagaccgucgugagacagguuaguuuuacccuacug
augaauguuaccgcaauaguaauugaacuuaguacgagaggaacaguuca
uucggauaauugguuuuugcggcugucugaucaggcauugccgcgaagcu
accauccgcuggauuauggcugaacgccucuaagucagaauccaugcuag
aacgcggugauuucuuugcuccacacaauauagauggauacgaauaaggc
guccuuguggcgucgcugaaccauagcaggcuagcaacggugcacuuggc
ggaaaggccuugggugcuugcuggcgaauugcaaugucauuuugcguggg
gauaaaucauuuguauacgacuuagauguacaacgggguauuguaagcag
uagaguagccuuguuguuacgaucugcugagauuaagccuuuguugucug
auuugu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7n8b CryoEM structures of pseudouridine-free ribosome suggest impacts of chemical modifications on ribosome conformations.
• Resolution: 3.05 Å
• Binding residue (original residue number in PDB): A2 Q4 S5 L6 S9 S10 R12 K14 A15 R16 Y19 V29 L30 S32 P34 K37 K46 R60 G61 S62 K87 K89 V90 N91 H100 S102 K103 R121 K122
• Binding residue (residue number reindexed from 1): A1 Q3 S4 L5 S8 S9 R11 K13 A14 R15 Y18 V28 L29 S31 P33 K36 K45 R59 G60 S61 K86 K88 V89 N90 H99 S101 K102 R120 K121

Gene Ontology

Molecular Function

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

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006412 translation
• GO:0042273 ribosomal large subunit biogenesis

Cellular Component

• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0015934 large ribosomal subunit
• GO:0022625 cytosolic large ribosomal subunit
• GO:0032991 protein-containing complex
• GO:0043232 intracellular non-membrane-bounded organelle
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:7n8b, PDBe:7n8b, PDBj:7n8b
• PDBsum: 7n8b
• PubMed: 35489333
• UniProt: P05743|RL26A_YEAST Large ribosomal subunit protein uL24A (Gene Name=RPL26A)