Structure of PDB 8bn3 Chain L7 Binding Site BS02

Receptor Information

>8bn3 Chain L7 (length=219) Species: 4932 (Saccharomyces cerevisiae)

VAAERAARKAANKEKRAIILERNAAYQKEYETAERNIIQAKRDAKAAGSY
YVEAQHKLVFVVRIKGINKIPPKPRKVLQLLRLTRINSGTFVKVTKATLE
LLKLIEPYVAYGYPSYSTIRQLVYKRGFGKINKQRVPLSDNAIIEANLGK
YGILSIDDLIHEIITVGPHFKQANNFLWPFKLSNPSGGWGVPRKFKHFIQ
GGSFGNREEFINKLVKSMN

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): R33 N37 R41 R60 R67 K70 K90 G91 I92 N93 K94 P97 K98 K101 L105 R107 R110 I111 N112 A122 E125 L126 Y141 S142 R145 K150 R151 K155 K158 Q159 R160 D165 K196 N200 K206 L207 S208 N209 P210 S211 G212 W214 P217 R218 K219 K241
• Binding residue (residue number reindexed from 1): R8 N12 R16 R35 R42 K45 K65 G66 I67 N68 K69 P72 K73 K76 L80 R82 R85 I86 N87 A97 E100 L101 Y116 S117 R120 K125 R126 K130 K133 Q134 R135 D140 K171 N175 K181 L182 S183 N184 P185 S186 G187 W189 P192 R193 K194 K216

Gene Ontology

Molecular Function

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

Biological Process

• GO:0000463 maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
• GO:0000470 maturation of LSU-rRNA
• GO:0002181 cytoplasmic translation
• GO:0042273 ribosomal large subunit biogenesis

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:8bn3, PDBe:8bn3, PDBj:8bn3
• PDBsum: 8bn3
• PubMed: 38324474
• UniProt: P05737|RL7A_YEAST Large ribosomal subunit protein uL30A (Gene Name=RPL7A)