Structure of PDB 3jct Chain m Binding Site BS01

Receptor Information

>3jct Chain m (length=469) Species: 559292 (Saccharomyces cerevisiae S288C)

GTGKKEKSRRIREGDTKDGNLRVKGENFYRDSKRVKFLNMYTSGKEIRNK
KGNLIRAASFQDSTIPDARVQPDRRWFGNTRVISQDALQHFRSALGETQK
DTYQVLLRRNKLPMSLLEEKDADESPKARILDTESYADAFGPKAQRKRPR
LAASNLEDLVKATNEDITKYEEKQVLDATLGGNQEDKENGWTSAAKEAIF
SKGQSKRIWNELYKVIDSSDVVIHVLDARDPLGTRCKSVEEYMKKETPHK
HLIYVLNKCDLVPTWVAAAWVKHLSKERPTLAFHASITNSFGKGSLIQLL
RQFSQLHTDRKQISVGFIGYPNTGKSSIINTLRKKKVCQVAPIPGETKVW
QYITLMKRIFLIDCPGIVPPSSKDSEEDILFRGVVRVEHVTHPEQYIPGV
LKRCQVKHLERTYEISGWKDATEFIEILARKQGRLLKGGEPDESGVSKQI
LNDFNRGKIPWFVLPPEKE

Ligand information

>3jct 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

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3jct Diverse roles of assembly factors revealed by structures of late nuclear pre-60S ribosomes
• Resolution: 3.08 Å
• Binding residue (original residue number in PDB): G2 T3 K5 K6 E7 R10 G20 N21 K25 F29 Y30 R31 R35 F38 R49 K51 K52 R57 R75 R76 T81 R82 Y104 R109 R110 K112 R130 I131 L132 K144 Q146 K148 K205 R210 W212 S241 Y245 L264 V265 P266 T267 W268 A271 K275 H276 S278 T291 N292 R304 Q305 D312 R313 K314 K339 V340 A344 P345 G348 K351 Q354 Y355 T357 K360 P373 S374 V387 R389 Q408 K410 H411 Q435 R437 K451 Q452 R459 K461 F465 P469 K471
• Binding residue (residue number reindexed from 1): G1 T2 K4 K5 E6 R9 G19 N20 K24 F28 Y29 R30 R34 F37 R48 K50 K51 R56 R74 R75 T80 R81 Y103 R108 R109 K111 R129 I130 L131 K143 Q145 K147 K202 R207 W209 S238 Y242 L261 V262 P263 T264 W265 A268 K272 H273 S275 T288 N289 R301 Q302 D309 R310 K311 K336 V337 A341 P342 G345 K348 Q351 Y352 T354 K357 P370 S371 V384 R386 Q405 K407 H408 Q432 R434 K448 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:3jct, PDBe:3jct, PDBj:3jct
• PDBsum: 3jct
• PubMed: 27251291
• UniProt: P53742|NOG2_YEAST Nucleolar GTP-binding protein 2 (Gene Name=NOG2)