Structure of PDB 7n8b Chain Ab Binding Site BS01

Receptor Information

>7n8b Chain Ab (length=58) Species: 4932 (Saccharomyces cerevisiae)

AKSKNHTAHNQTRKAHRNGIKKPKTYKYPSLKGVDPKFRRNHKHALHGTA
KALAAAKK

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): K3 S4 K5 N6 H7 T8 A9 H10 N11 Q12 T13 R14 K15 H17 R18 N19 T26 Y27 K28 Y29 P30 S31 K33 D36 P37 K38 F39 R40 R41 N42 H43 K44 H45 A46 L47 G49 T50
• Binding residue (residue number reindexed from 1): K2 S3 K4 N5 H6 T7 A8 H9 N10 Q11 T12 R13 K14 H16 R17 N18 T25 Y26 K27 Y28 P29 S30 K32 D35 P36 K37 F38 R39 R40 N41 H42 K43 H44 A45 L46 G48 T49

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006412 translation

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:7n8b, PDBe:7n8b, PDBj:7n8b
• PDBsum: 7n8b
• PubMed: 35489333
• UniProt: P05747|RL29_YEAST Large ribosomal subunit protein eL29 (Gene Name=RPL29)