Structure of PDB 7v08 Chain A Binding Site BS01

Receptor Information

>7v08 Chain A (length=213) Species: 1247190 (Saccharomyces cerevisiae BY4741)

GRVIRNQRKGAGSIFTSHTRLRQGAAKLRTLDYAERHGYIRGIVKQIVHD
SGRGAPLAKVVFRDPYKYRLREEIFIANEGVHTGQFIYAGKKASLNVGNV
LPLGSVPEGTIVSNVEEKPGDRGALARASGNYVIIIGHNPDENKTRVRLP
SGAKKVISSDARGVIGVIAGGGRVDKPLLKAGRAFHKYRLKRNSWPKTRG
VAMNPVDHPHGGG

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): G2 R3 V4 N7 Q8 R9 K10 G11 S14 I15 S18 H19 T20 R21 R23 G25 A26 Y34 R37 H38 G39 Y40 I44 H50 S52 R54 R64 D65 Y67 K68 Y69 R70 L71 G85 F87 Y89 K93 A94 S95 E118 K119 A125 L126 A127 R128 A129 S130 N132 L150 P151 S152 K156 R174 V175 K177 L179 L180 K181 A182 G183 F186 H187 K188 L191 R193 N194 W196 P197 K198 T199 R200 G201 V202 A203 M204 N205 V207 D208 H211
• Binding residue (residue number reindexed from 1): G1 R2 V3 N6 Q7 R8 K9 G10 S13 I14 S17 H18 T19 R20 R22 G24 A25 Y33 R36 H37 G38 Y39 I43 H49 S51 R53 R63 D64 Y66 K67 Y68 R69 L70 G84 F86 Y88 K92 A93 S94 E117 K118 A124 L125 A126 R127 A128 S129 N131 L149 P150 S151 K155 R173 V174 K176 L178 L179 K180 A181 G182 F185 H186 K187 L190 R192 N193 W195 P196 K197 T198 R199 G200 V201 A202 M203 N204 V206 D207 H210

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0019843 rRNA binding

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006412 translation
• GO:0042273 ribosomal large subunit biogenesis
• GO:1990145 maintenance of translational fidelity

Cellular Component

• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0022625 cytosolic large ribosomal subunit
• GO:0022626 cytosolic ribosome
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:7v08, PDBe:7v08, PDBj:7v08
• PDBsum: 7v08
• PubMed: 36864048
• UniProt: P0CX45|RL2A_YEAST Large ribosomal subunit protein uL2A (Gene Name=RPL2A)