Structure of PDB 7ug6 Chain m Binding Site BS01

Receptor Information

>7ug6 Chain m (length=469) Species: 559292 (Saccharomyces cerevisiae S288C)

GTGKKEKSRRIREGDTKDGNLRVKGENFYRDSKRVKFLNMYTSGKEIRNK
KGNLIRAASFQDSTIPDARVQPDRRWFGNTRVISQDALQHFRSALGETQK
DTYQVLLRRNKLPMSLLEEKDADESPKARILDTESYADAFGPKAQRKRPR
LAASNLEDLVKATNEDITKYEEKQVLDATLGGNQEDKENGWTSAAKEAIF
SKGQSKRIWNELYKVIDSSDVVIHVLDARDPLGTRCKSVEEYMKKETPHK
HLIYVLNKCDLVPTWVAAAWVKHLSKERPTLAFHASITNSFGKGSLIQLL
RQFSQLHTDRKQISVGFIGYPNTGKSSIINTLRKKKVCQVAPIPGETKVW
QYITLMKRIFLIDCPGIVPPSSKDSEEDILFRGVVRVEHVTHPEQYIPGV
LKRCQVKHLERTYEISGWKDATEFIEILARKQGRLLKGGEPDESGVSKQI
LNDFNRGKIPWFVLPPEKE

Ligand information

>7ug6 Chain 1 (length=3058)

guuugaccucaaaucagguaggaguacccgcugaacuuaagcauaucaau
aagcggaggaaaagaaaccaaccgggauugccuuaguaacggcgagugaa
gcggcaaaagcucaaauuugaaaucugguaccuucggugcccgaguugua
auuuggagagggcaacuuuggggccguuccuugucuauguuccuuggaac
aggacgucauagagggugagaaucccguguggcgaggagugcgguucuuu
guaaagugccuucgaagagucgaguuguuugggaaugcagcucuaagugg
gugguaaauuccaucuaaagcuaaauauuggcgagagaccgauagcgaac
aaguacagugauggaaagaugaaaagaacuuugaaaagagagugaaaaag
uacgugaaauuguugaaagggaagggcauuugaucagacaggccagcauc
aguuuugguggcaggauaaauccauaggaauguagcuugccucgguaagu
auuauagccugugggaauacugccagcugggacugaggacugcgacguaa
gucaaggaugcuggcauaaugguuauaugccgcccgucuugaaacacgga
ccaaggagucuaacgucuaugcgaguguuuggguguaaaacccauacgcg
uaaugaaagugaacguagguuggggccucgcaagaggugcacaaucgacc
gauccugaugucuucggauggauuugaguaagagcauagcuguugggacc
cgaaagauggugaacuaugccugaauagggugaagccagaggaaacucug
guggaggcucguagcgguucugacgugcaaaucgaucgucgaauuugggu
auaggggcgaaagacuaaucgaaccaucuaguagcugguuccugccgaag
uuucccucaggauagcagaagcucguaucaguuuuaugagguaaagcgaa
aacuuuaaauauguaagaaguccuuguuugaacguggacauuugaaugaa
gagcuuuuagugggccauuuuugguaagcagaacuggcgaugcgggauga
accgaacguagaguuaaggugccggaauacacgcucaucagacaccacaa
aagguguuaguucaucuagacagccggacgguggccauggaagucggaau
ccgcuaaggaguguguaacaacucaccggccgaaugaacuagcccugaaa
auggauggcgcucaagcguguuaccuauacucuaccgucaggguugauau
gaugcccugacgaguaggcaggcguggaggucagugacgaagccuagacc
guaaggucgggucgaacggccucuagugcagaucuuggugguaguagcaa
auauucaaaugagaacuuugaagacugaaguggggaaagguuccacguca
acagcaguuggacguggguuagucgauccuaagagauggggaagcuccgu
uucaaaggccugauuuuaugcaggccaccaucgaaagggaauccgguuaa
gauuccggaaccuggauauggauucuucacgguaacguaacugaaugugg
agacgucggcgcgagcccugggaggaguuaucuuuucuucuuaacagcuu
aucaccccggaauugguuuauccggagauggggucuuauggcuggaagag
gccagcaccuuugcuggcuccggugcgcuugugacggcccgugaaaaucc
acaggaaggaauaguuuucaugccaggucguacugauaaccgcagcaggu
cuccaaggugaacagccucuaguugauagaauaauguagauaagggaagu
cggcaaaauagauccguaacuucgggauaaggauuggcucuaagggucgg
acgaucaacuuagaacugguacggacaaggggaaucugacugucuaauua
aaacauagcauugcgauggucagaaagugauguugacgcaaugugauuuc
ugcccagugcucugaaugucaaagugaagaaauucaaccaagcgcgggua
aacggcgggaguaacuaugacucucuuaagguagccaaauggauuaacga
gauucccacugucccuaucuacuaucuagcgaaaccacagccaagggggc
uuggcagaaucagcggggaaagaagacccuguugagcuugacucuaguuu
gacauugugaagagacauaguuucuuuacuuauucaaugaagcggagcug
gaauucauuuuccacguucuagcauucaaggucccauucggggcugaucc
ggguugaagacauugucagguggggaguuugggggcggcacaucuguuaa
acgauaacgcagauguccuaaggggggcucauggagaacagaaaucucca
guagaacaaaaggguaaaagcccccuugauuuugauuuucagugugaaua
caaaccaugaaaguguggccuaucgauccuuuagucccucggaauuugag
gcuagaggugccagaaaaguuaccacagggauaacuggcuuguggcaguc
aagcguucauagcgacauugcuuuuugauucuucgaugucggcucuuccu
aucauaccgaagcagaauucgguaagcguuggauuguucacccacuaaua
gggagugagcuggguuuagaccgucgugagacagguuaguuuuacccuac
ugaugaauguuaccgcaauaguaauugaacuuaguacgagaggaacaguu
cauucggauaauugguuuuugcggcugucugaucaggcauugccgcgaag
cuaccauccgcuggauuauggcugaacgccucuaagucagaauccaugcu
agaacgcggugauuucuuugcuccacacaauauagauggauacgaauaag
gcguccuuguggcgucgcugaaccauagcaggcuagcaacggugcacuug
gcggaaaggccuugggugcuugcuggcgaauugcaaugucauuuugcgug
gggauaaaucauuuguauacgacuuagauguacaacgggguauuguaagc
aguagaguagccuuguuguuacgaucugcugagauuaagccuuuguuguc
ugauuugu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7ug6 A single 2'-O-methylation of ribosomal RNA gates assembly of a functional ribosome.
• Resolution: 2.9 Å
• Binding residue (original residue number in PDB): G2 T3 G4 K5 K6 E7 R10 R13 G20 N21 R23 K25 N28 F29 Y30 R31 R35 K37 F38 L39 M41 K46 K51 K52 I56 R75 R76 T81 R82 Y104 R109 K112 K128 R130 I131 L132 K144 Q146 K148 K209 W212 N213 Y216 Y245 L264 V265 P266 W268 A271 A272 K275 H276 T291 N292 K296 I300 R304 Q305 Q308 R313 K314 Q315 K337 K338 V340 P345 V352 W353 Q354 Y355 I356 T357 S374 K376 E391 H392 Q408 K410 H411 Q435 R437 Q452 R459 K461 F465 P469 K471
• Binding residue (residue number reindexed from 1): G1 T2 G3 K4 K5 E6 R9 R12 G19 N20 R22 K24 N27 F28 Y29 R30 R34 K36 F37 L38 M40 K45 K50 K51 I55 R74 R75 T80 R81 Y103 R108 K111 K127 R129 I130 L131 K143 Q145 K147 K206 W209 N210 Y213 Y242 L261 V262 P263 W265 A268 A269 K272 H273 T288 N289 K293 I297 R301 Q302 Q305 R310 K311 Q312 K334 K335 V337 P342 V349 W350 Q351 Y352 I353 T354 S371 K373 E388 H389 Q405 K407 H408 Q432 R434 Q449 R456 K458 F462 P466 K468

Gene Ontology

Molecular Function

• GO:0003924 GTPase activity
• GO:0005515 protein binding
• GO:0005525 GTP binding
• GO:0070180 large ribosomal subunit rRNA binding

Biological Process

• GO:0000055 ribosomal large subunit export from nucleus
• GO:0042254 ribosome biogenesis
• GO:2000200 regulation of ribosomal subunit export from nucleus

Cellular Component

• GO:0005634 nucleus
• GO:0005654 nucleoplasm
• GO:0005730 nucleolus
• GO:0030687 preribosome, large subunit precursor

External links

• PDB: RCSB:7ug6, PDBe:7ug6, PDBj:7ug6
• PDBsum: 7ug6
• PubMed: 36536102
• UniProt: P53742|NOG2_YEAST Nucleolar GTP-binding protein 2 (Gene Name=NOG2)