Structure of PDB 7r7a Chain L Binding Site BS01

Receptor Information

>7r7a Chain L (length=121) Species: 1247190 (Saccharomyces cerevisiae BY4741)

ILKNHFRKHWQERVKVHFDQAGKKVSRRNARATRAAKIAPRPLDLLRPVV
RAPTVKYNRKVRAGRGFTLAEVKAAGLTAAYARTIGIAVDHRRQNRNQEI
FDANVQRLKEYQSKIIVFPRN

Ligand information

>7r7a Chain 1 (length=2571)

guuugaccucaaaucagguaggaguacccgcugaacuuaagcauaucaau
aagcggaggaaaagaaaccaaccgggauugccuuaguaacggcgagugaa
gcggcaaaagcucaaauuugaaaucugguaccuucggugcccgaguugua
auuuggagagggcaacuuuggggccguuccuugucuauguuccuuggaac
aggacgucauagagggugagaaucccguguggcgaggagugcgguucuuu
guaaagugccuucgaagagucgaguuguuugggaaugcagcucuaagugg
gugguuccaucuaaagcuaaauauuggcgagagaccgauagcgaacaagu
acagugauggaaagaugaaaagaacuuugaaaagagagugaaaaaguacg
ugaaauuguugaaagggaagggcauuugaucagacaugguguuuugugcc
cucugcuccuuguggguaggggaaucucgcauuucacugggccagcauca
guuuugguggcaggauaaauccauaggaauguagcuugccucgguaagua
uuauagccugugggaauacugccagcugggacugaggacugcgacguaag
ucaaggaugcuggcauaaugguuauaugccgcccgucuugaaacacggac
caaggagucuaacgucuaugcgaguguuuggguguaaaacccauacgcgu
aaugaaagugaacguagguuggggccucgcaagaggugcacaaucgaccg
auccugaggauggauuugaguaagagcauagcuguugggacccgaaagau
ggugaacuaugccugaauagggugaagccagaggaaacucugguggaggc
ucggcggucgaucgucgaauuuggguauaggggcgaaagacaaccaucua
guagcugguuccugccgaaguuucccucaggauagcagaagcucguauca
guuuuaugaauguaagaaugaagagcuuuuagugggccauuuuugguaag
cagaacuggcgaugcgggaugaaccgaacguagaguuaaggugccggaau
acacgcucaucagacaccacaaaagguguuaguucaucuagacagccgga
cgguggccauggaagucggaauccgcuaaggaguguguaacaacucaccg
gccgaaugaacuagcccugaaaauggauggcgcucaagcguguuaccuau
acucuaccgucaggguugauaugaugcccugacgaguaggcaggcgugga
ggucagugacgaagccuagaccguaaggucgggucgaacggccucuagug
cagaucuuggugguaguagcaaauauucaaaugagaacuuugaagacuga
aguggggaaagguuccacgucaacagcaguuggacguggguuagucgauc
cuaagagauggggaagcuccguuucaaaggccugauuuuaugcaggccac
caucgaaagggaauccgguuaagauuccggaaccuggauauggauucuuc
acgguaacguaacugaauguggagacgucggcgcgagcccugggaggagu
uaucuuuucuucuuaacagcuuaucaccccggaauugguuuauccggaga
uggggucuuauggcuggaagaggccagcaccuuugcuggcuccggugcgc
uugugacggcccgugaaaauccacaggaaggaauaguuuucaugccaggu
cguacuucuccaaggugaacagccucuaguugauagaauuccguaacuuc
gggauaaggauuggcucuaagggucggguagugagggccuuggucacggc
cuuggcuugcuacaauuaacgaucaacuuagaacugguacggacaauauc
uagcgaaaccacagccaagggaacgggcuuggcagaaucagcggggaacc
cuguugagcuugacucuaguuugacauugugaagagacauagagggugua
gaauaagugggagcuucggcgccagugaaauaccacuaccuuuauaguuu
cuuuacuauugucagguggggaguaaaguuaccacagggauaacuggcuu
guggcagucaagcguucauagcgacauugcuuuccuaucauaccgaagca
gaauucgguaagcguuggacccacuaauagggaacggaccgucgugagac
agguuaguuuuacccuacugaugaauguuaccgcaauaguaauugaacuu
aguacgagaggaacaguucauucggauaauugguuuuugcggcugucuga
ucaggcauugccgcgaagcuaccauccgcuggauuauggcugaacgccuc
uaagucagaauccaugcuagaacgcggugauuucuuugcuccacacaaua
uagauggauacgaauaaggcguccuuguggcgucgcugaaccauagcagg
cuagcaacggugcacuuggcggaaaggccuugggugcuugcuggcgaauu
gcaaugucauuuugcguggggauaaaucauuuguauacgacuuagaugua
caacgggguauuguaagcaguagaguagccguuacgaucugcugagauua
agccuuuguugucugauuugu

..........................<<<<<<.....<......>.....
.>>>>>.>.........<<....>>..<<<<<......<<.....>>...
..>>>>>..<<<..<........<<.<<<<<<...>>>>>>.>>......
..>....<<<<<<<.<<<<<<<<<<<<<<<<<<<<<....<<<<......
>>>>.(.......<<<......)>>>..>.>>>>>>>>..>>>>>>>>..
..>>>>>>>>>>>........<<<<<<<........>>>>>>>.....<<
<<<<..>>>>>>..>>>.................................
.<<....>>...............<<<<....>>>>..............
....................<<<<<.<<<<<.....<<<<<....<<..<
<<<<<<<.......>>>>>>>>......>>....>>>>>.<<<<<<<.<<
<<<<<<<<<<<<<.....<<<<<<<<<......<<<<<......>>>>>.
......>>>>>>>.>.>.>>>>>.>>>>>>>>>>........<<<....>
>>.....>>>>>>>.....>>>>>.>>>>>..<<<<........>>>><<
<<<<....<<<<<<.<<<<<<..<<<...<<<<.....>>>>...>>>..
.<<....>>.......<<<<<..<<<<<....>>>>>...>>>>>.<<<<
<<<<.......>>>.>>>.>>....>>>>>>.>>>>>>..<<.<...<<<
<<<...<<<<<<<<<<...<<<....<<<<<<<....>>>>>>>.....>
>>.<<<<....>>>>.....>>>>>>>>>>...<....>...>>>>>>..
....>.>>..<<<<<<....<.<<<....>>>.><<<<<<<<<<...<<<
.<<<<<<....>>>>.>>>>>.>>>>>>>>.>>..<<<<.<<<<<.....
>>>>>.>>>>....<<<......>>>...<<<<<<<..<<<<(((.....
<<<<<<.....<<..........<<<.<<<<<<<<<<.......<<<<<.
<<<...<<.........>>...>>>.........<<......>>...>>>
>>...>>>>>>>>>>>>>..........))).>>...>>>>>>.>>>>..
>>>>>>><<<<<<<<<.........>>>>>>>>>....>>>>>>..<<<<
<<<<.<<......<<<<.<<<<....>>>>>>>>...>>>>>>>>>>...
.....>>>>>><<.....<<.....<<<<<<.......>>>>>><<<<..
...<<<<<.<<...<<<<<<...<<.....>>.>>>>>>....((<<<<<
<...<<....<<<....>>>........<<<<<<........>>>>>>..
..>>....>>...<<<<<........>>>>>))<<<<.<<<<<<......
<<<....>>>.......<<<<<<...<<<<.<<<<<<<.<<<<<<<<<<.
.(((..>>>>>><...<<<<<....<<<<<<....<<<.....>>>....
>>>>>>.....>>>>>....><<<<<<<......>>>>>>>>>>>...>>
>>>>>.>>>>.........>>>>>>............>>.>>>>>>>>>>
>>..>>>>>>>.<<<<.....>>>>..>>>>..<<<<..<<<<<<.<<<<
.....................<<<<<.<<<<<<<<..<<..<<<<..>>>
>..>>>>>>>>>>......>>>>>......>>>...>>>>>>>.....>>
>>>>....>>....<<<<<........>>>>>....<<<<<..<<<..<<
<<<<.<<<<<<..<<<<.<<<<.<<...<<<<<<<<<<..<<<<<.....
.....<<<<<..<<....>>............>>>>>.>>>>>...>>>>
>>>>>>....>>.>>>>..>>>>..>>>>>.>.>>>>>>...........
..<<<<<<...<<.......>>...>>>>>>.<<<<..<.<<<<<<<...
...>>>>>>>...>.<<<..>>>.....>>>>....<<<<<<<....>>>
.>>>>........>>>.>>>>>....<<<<<<<<..<<<<.<.<<<<<<.
..............>>>>>>.><<<<<...<<<<....<<<<<<<<<<))
).>>>>>..>>>>>...>>>>..>>>>>.<<<<...<<<<<.........
..>>>>>...>>>>.>>>>....>>>>>>>>.......<<<<<<.<<<.<
.....<<..........<<<<<<.....>>>>>>......>>.......<
<<<<<...<<<<<.<..<<<......>>>..>.>>>>>.>>>>>>.....
.........>.>>>.>>>>>>..<<<<<.<.............>.....<
<<<<<<<<.<<<....<<<<....<<<.....>>>...>>>>...>>>..
..>>>>.>>>>>..>>>>>..

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7r7a Sequence-specific remodeling of a topologically complex RNP substrate by Spb4.
• Resolution: 3.04 Å
• Binding residue (original residue number in PDB): L10 K11 N12 H13 F14 R15 K16 H17 W18 Q19 Q28 A29 K31 K32 R35 R36 R39 R42 R55 V58 R59 A60 P61 T62 Y65 N66 K68 R70 G72 R73 R91 D98 H99 R100 R101 Q102 R104
• Binding residue (residue number reindexed from 1): L2 K3 N4 H5 F6 R7 K8 H9 W10 Q11 Q20 A21 K23 K24 R27 R28 R31 R34 R47 V50 R51 A52 P53 T54 Y57 N58 K60 R62 G64 R65 R83 D90 H91 R92 R93 Q94 R96

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:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0022625 cytosolic large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:7r7a, PDBe:7r7a, PDBj:7r7a
• PDBsum: 7r7a
• PubMed: 36482249
• UniProt: Q12690|RL13A_YEAST Large ribosomal subunit protein eL13A (Gene Name=RPL13A)