Structure of PDB 7v08 Chain Y Binding Site BS01

Receptor Information

>7v08 Chain Y (length=126) Species: 1247190 (Saccharomyces cerevisiae BY4741)

AKQSLDVSSDRRKARKAYFTAPSSQRRVLLSAPLSKELRAQYGIKALPIR
RDDEVLVVRGSKKGQEGKISSVYRLKFAVQVDKVTKEKVNGASVPINLHP
SKLVITKLHLDKDRKALIQRKGGKLE

Ligand information

>7v08 Chain 1 (length=2986)

guuugaccucaaaucagguaggaguacccgcugaacuuaagcauaucaau
aagcggaggaaaagaaaccaaccgggauugccuuaguaacggcgagugaa
gcggcaaaagcucaaauuugaaaucugguaccuucggugcccgaguugua
auuuggagagggcaacuuuggggccguuccuugucuauguuccuuggaac
aggacgucauagagggugagaaucccguguggcgaggagugcgguucuuu
guaaagugccuucgaagagucgaguuguuugggaaugcagcucuaagugg
gugguaaauuccaucuaaagcuaaauauuggcgagagaccgauagcgaac
aaguacagugauggaaagaugaaaagaacuuugaaaagagagugaaaaag
uacgugaaauuguugaaagggaagggcauuugaucagacaggccagcauc
aguuuugguggcaggauaaauccauaggaauguagcuugccucgguaagu
auuauagccugugggaauacugccagcugggacugaggacugcgacguaa
gucaaggaugcuggcauaaugguuauaugccgcccgucuugaaacacgga
ccaaggagucuaacgucuaugcgaguguuuggguguaaaacccauacgcg
uaaugaaagugaacguagguuggggccucgcaagaggugcacaaucgacc
gauccugaugucuucggauggauuugaguaagagcauagcuguugggacc
cgaaagauggugaacuaugccugaauagggugaagccagaggaaacucug
guggaggcucguagcgguucugacgugcaaaucgaucgucgaauuugggu
auaggggcgaaagacuaaucgaaccaucuaguagcugguuccugccgaag
uuucccucaggauagcagaagcucguaucaguuuuaugaguguaagaagu
ccuuguuugaacguggacauuugaaugaagagcuuuuagugggccauuuu
ugguaagcagaacuggcgaugcgggaugaaccgaacguagaguuaaggug
ccggaauacacgcucaucagacaccacaaaagguguuaguucaucuagac
agccggacgguggccauggaagucggaauccgcuaaggaguguguaacaa
cucaccggccgaaugaacuagcccugaaaauggauggcgcucaagcgugu
uaccuauacucuaccgucaggguugaugcccugacgaguaggcaggcgug
gaggucagugacgaagccuagaccguaaggucgggucgaacggccucuag
ugcagaucuuggugguaguagcaaauauucaaaugagaacuuugaagacu
gaaguggggaaagguuccacgucaacagcaguuggacguggguuagucga
uccuaagagauggggaagcuccguuucaaaggccugauuuuaugcaggcc
accaucgaaagggaauccgguuaagauuccggaaccuggauauggauucu
ucacgguaacguaacugaauguggagacgucggcgcgagcccugggagga
guuaucuuuucuucuuaacagcuuaucaccccggaauugguuuauccgga
gauggggucuuauggcuggaagaggccagcaccuuugcuggcuccggugc
gcuugugacggcccgugaaaauccacaggaaggaauaguuuucaugccag
gucguacugauaaccgcagcaggucuccaaggugaacagccucuaguuga
uagaauaauguagauaagggaagucggcaaaauagauccguaacuucggg
auaaggauuggcucuaagggucggacgaucaacuuagaacugguacggac
aaggggaaucugacugucuaauuaaaacauagcauugcgauggucagaaa
gugauguugacgcaaugugauuucugcccagugcucugaaugucaaagug
aagaaauucaaccaagcgcggguaaacggcgggaguacucucuuaaggua
gccaauggauuaacgagauucccacugucccuaucuacuaucuagcgaaa
ccacagccaagggaacgggcuuggcagaaucagcggggaaagaagacccu
guugagcuugacucuaguuugacauugugaagagacauaguuucuuuacu
uauucaaugaagcggagcuggauccacguucuagcauucaaggucccauu
cggggcugauccggguugaagacauugucagguggggaguuuggcugggg
cggcacauguccuaaggggggcucauggagaacagaaaucuccaguagaa
caaaaggguaaaagcccccuugauuuugauuuucagugugaauacaaacc
augaaaguguggccuaucgauccuuuagucccucggaauuugaggcuaga
ggugccagaaaaguuaccacagggauaacuggcuuguggcagucaagcgu
uauagcgacauugcuuuuugauucgaugucggcucuuccuaucauaccga
agcagaauucgguaagcguuggauacccacuaauagggaacggcuggguu
uagaccgucgugagacagguuaguuuuacccuacugaugaauguuaccgc
aauaguaauugaacuuaguacgagaggaacaguucauucggauaauuggu
uuuugcggcugucugaucaggcauugccgcgaagcuaccauccgcuggau
uauggcugaacgccucuaagucagaauccaugcuagaacgcggugauuuc
uuugcuccacacaauauagauggauacgaauaaggcguccuuguggcguc
gcugaaccauagcaggcuagcaacggugcacuuggcggaaaggccuuggg
ugcuugcuggcgaauugcaaugucauuuugcguggggauaaaucauuugu
auacgacuuagauguacaacgggguauuguaagcaguagaguagcguuac
gaucugcugagauuaagccuuuguugucugauuugu

..........................<<<<<<.....<<....>>.....
.>>>>>.>.........<<....>>..<<<<<......<<.....>>...
..>>>>>..[[[..<<.......<<.<<<<<<...>>>>>>.>>......
.>>....<<<<<<.<<<<<<<<<<<<<<<<<<<<<<....<<<<......
>>>>.(.......<<<......)>>>..>.>>>>>>>>>..>>>>>>>..
..>>>>>>>>>>>........<<<<<<<.<....>.>>>>>>>.....((
(((..<<<<<<)))))..]]].............................
.....<<....>>...............<<<<....>>>>..........
........................<<<<<.<<<<<......<<<<<<<.<
<<<<<<<<<<<<<<.....<<<<<<<<<......<<<<<......>>>>>
.......>>>>>>>.>.>.>>>>>.>>>>>>>>>>........<<<....
>>>.....>>>>>>>.....>>>>>.>>>>>..<<<<........>>>><
<<<<<...<<<<<<<.<<<<<<..<<<...<<<<.....>>>>...>>>.
..<<....>>.......<<<<<..<<<<<....>>>>>...>>>>>.<<<
<<<<<..............>>>>.>>.>>....>>>>>>.>>>>>>>.<<
.<...<<<<<<.....<<<<<<<<<..<<<....<<<<<<<....>>>>>
>>.....>>>...<<<<.<<.<<........>>>>>>>>....>>>>>>>
>>...<<.......>>......>>>>>>......>.>>..<<<<<<....
..<<<....>>>..<<<<<<<<<<...<<<.<<<<<<<..>>>>>...<<
<<.<<<....>>>.>>>>.....>>>>>.>>>>>>>>.>>..<<<<.<<<
<<.....>>>>>.>>>>....<<<......>>>...<<<<<<<..<<<<(
((.....<<<<<<......<..........<<<.<<<<<<<<<<......
.<<<<<.<<<...<<.........>>...>>>.........<<......>
>...>>>>>...>>>>>>>>>>>>>..........))).>....>>>>>>
.>>>>..>>>>>>><<<<<<<<<....>>>>>>>>>....>>>>>><.<<
<<<<<<.<<......<<<<.<<<<....>>>>>>>>...>>>>>>>>>>.
.>.....>>>>>><<.....<<.....<<<<<<.......>>>>>><<<<
.....<<<<<.<<...<<<<<<...<<.....>>.>>>>>>....((<<<
<<<...<<....<<<....>>>........<<<<<<........>>>>>>
....>>....>>...<<<<<........>>>>>))<<<<.<<<<<<<...
..<<<....>>>...<...<<<<<<...<<<<.<<<<<<<.<<<<<<<<<
<..{{{..>>>>>><...<<<<<....<<<<<<....<<<.....>>>..
..>>>>>>.....>>>>>....><<<<<<<......>>>>>>>>>>>...
>>>>>>>.>>>>.........>>>>>>...>......>>>..>>>>>>>>
>>>>..>>.....<<......>>>>>>>.<<<<.....>>>>..>>>>..
<<<<.....<<<<<<<.<<...............<<<<<.....<..>..
....>>>>><<.<<<<<<<<<<<..>>>>>..>>>>>>.>>.........
...<<<<<<<<<..<<<.........>>>..<<<<<<<....<<<<....
.>>>>......>>>>>>>.......<<<..<<<<<<.....<<....<<<
<<....>>>>.>...>>..>>>>..>>>>><<<<<..>>>>>........
..<<.>>......>>.>>>>>>>.....>>.>>>>>>>..>>>>>>....
>>....<<<<<........>>>>>....[[[[[..[[[........((((
(([[[.[[..<<<<<.<<<<<<<<..<<<<<<<<<.....>>>>>>>>>.
..<<<<<.....<<<<...<<..>>................<<<<<<...
.>>>>>>..>>>>..>>>>>.....>>>>>>>>..>>>>>.......<<<
<<<..<..>..>>..<<<<<<<...<<<<<<.......>>>>>>.....<
<......>>....>>>>>>>....<<<<.<.<<<.....>>>.>>>>><<
<<....>>>.>>>>>.[[...[[.((((..((((.>>>>>>)))))))).
]].....]]..]]]]]..)))))).............<<<<<<...<<..
....>>...>>>>>>.............<<<<<..<<<<<..<.<<<<<<
<......>>>>>>>...>.<<<....>>>.....>>>>>...>>>>>...
..<<<<<<<....>>>.>>>>........]]].]]]]]....<<<<<<<<
..<<<<.<.<<<<<<...............>>>>>>.><<<<<...<<<<
....<<<<<<<<<<}}}.>>>>>..>>>>>...>>>>..>>>>>.<<<<.
..<<<<<...........>>>>>...>>>>.>>>>....>>>>>>>>...
.....<<<<<.<.<.......<<..........<<<<<<.....>>>>>>
......>>.......<<<<<<...<<<<<.<..<<<......>>>..>.>
>>>>.>>>>>>...............>..>.>>>.>>..<<<<<<<....
.........>.....<<<<<<<<<.<<<....<<<<.<..<<<<..>>>>
..>>>>>...>>>....>>>>.>>>>>.>>>>>>..

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7v08 rRNA methylation by Spb1 regulates the GTPase activity of Nog2 during 60S ribosomal subunit assembly.
• Resolution: 2.36 Å
• Binding residue (original residue number in PDB): A2 K3 Q4 S5 L6 S9 S10 K14 A15 R16 Y19 L30 S32 P34 R40 K46 R60 G61 S62 K87 K89 N91 H100 S102 K103
• Binding residue (residue number reindexed from 1): A1 K2 Q3 S4 L5 S8 S9 K13 A14 R15 Y18 L29 S31 P33 R39 K45 R59 G60 S61 K86 K88 N90 H99 S101 K102

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:7v08, PDBe:7v08, PDBj:7v08
• PDBsum: 7v08
• PubMed: 36864048
• UniProt: P05743|RL26A_YEAST Large ribosomal subunit protein uL24A (Gene Name=RPL26A)