Structure of PDB 6ylh Chain m Binding Site BS01

Receptor Information

>6ylh Chain m (length=439) Species: 4932 (Saccharomyces cerevisiae)

TGKKEKSRRIREGRVKGENFYRDSKRVKFLNMYTSGKEIRNKKGNLIRAA
SFQDSTIPDARVQPDRRWFGNTRVISQDALQHFRSALGETQKDTYQVLLR
RNKLPMSLLARILDTESYADAFGPKAQRKRPRLAASNLEDLVKATNEDIT
KYEEKQVLDAENGWTSAAKEAIFSKGQSKRIWNELYKVIDSSDVVIHVLD
ARDPLGTRCKSVEEYMKKETPHKHLIYVLNKCDLVPTWVAAAWVKHLSKE
RPTLAFHASITNSFGKGSLIQLLRQFSQLHTDRKQISVGFIGYPNTGKSS
IINTLRKKKVCQVAPIPGETKVWQYITLMKRIFLIDCPGIVPPSSKDSEE
DILFRGVVRVEHVTHPEQYIPGVLKRCQVKHLERTYEISGWKDATEFIEI
LARKQGRLLKGGEPDESGVSKQILNDFNRGKIPWFVLPP

Ligand information

>6ylh Chain 1 (length=3039)

guuugaccucaaaucagguaggaguacccgcugaacuuaagcauaucaau
aagcggaggaaaagaaaccaaccgggauugccuuaguaacggcgagugaa
gcggcaaaagcucaaauuugaaaucugguaccuucggugcccgaguugua
auuuggagagggcaacuuuggggccguuccuugucuauguuccuuggaac
aggacgucauagagggugagaaucccguguggcgaggagugcgguucuuu
guaaagugccuucgaagagucgaguuguuugggaaugcagcucuaagugg
gugguaaauuccaucuaaagcuaaauauuggcgagagaccgauagcgaac
aaguacagugauggaaagaugaaaagaacuuugaaaagagagugaaaaag
uacgugaaauuguugaaagggaagggcauuugaucagagccagcaucagu
uuugguggcaggauaaauccauaggaauguagcuugccucgguaaguauu
auagccugugggaauacugccagcugggacugaggacugcgacguaaguc
aaggaugcuggcauaaugguuauaugccgcccgucuugaaacacggacca
aggagucuaacgucuaugcgaguguuuggguguaaaacccauacgcguaa
ugaaagugaacguagguuggggccucgcaagaggugcacaaucgaccgau
ccugaugucuucggauggauuugaguaagagcauagcuguugggacccga
aagauggugaacuaugccugaauagggugaagccagaggaaacucuggug
gaggcucguagcgguucugacgugcaaaucgaucgucgaauuuggguaua
ggggcgaaagacuaaucgaaccaucuaguagcugguuccugccgaaguuu
cccucaggauagcagaagcucguaucaguuuuaugagauuagagguuccg
gggucgaaaugaccuugaccuauucuguaagaaguccuuguuugaacgug
gacgaaugaagcuuuuagugggccauuuuugguaagcagaacuggcgaug
cgggaugaaccgaacguagaguuaaggugccggaauacacgcucaucaga
caccacaaaagguguuaguucaucuagacagccggacgguggccauggaa
gucggaauccgcuaaggaguguguaacaacucaccggccgaaugaacuag
cccugaaaauggauggcgcucaagcguguuaccuauacucuaccgucagg
guuaugcccugacgaguaggcaggcguggaggucagugacgaagccuaga
ccguaaggucgggucgaacggccucuagugcagaucuuggugguaguagc
aaauauucaaaugagaacuuugaagacugaaguggggaaagguuccacgu
caacagcaguuggacguggguuagucgauccuaagagauggggaagcucc
guuucaaaggccuggcaggccaccaucgaaagggaauccgguuaagauuc
cggaaccuggauauggauucuucacgguaacguaacugaauguggagacg
ucggcgcgagcccugggaggaguuaucuuuucuucuuaacagcuuaucac
cccggaauugguuuauccggagauggggucuuauggcuggaagaggccag
caccuuugcuggcuccggugcgcuugugacggcccgugaaaauccacagg
aaggaauaguuuucaugccaggucguacugauaaccgcagcaggucucca
aggugaacagccucuaguugauagaauaauguagauaagggaagucggca
aaauagauccguaacuucgggauaaggauuggcucuaagggucggcgauc
aacuuagaacugguacggacaaggggaaucugacugucuaauuaaaacau
agcauugcgauggucagaaagugauguugacgcaaugugauuucugccca
gugcucugaaugucaaagugaagaaauucaaccaagcgcggguaaacggc
gggaguacucucuuaagguagggauuaacgagauucccacugucccuauc
uacuaucuagcgaaaccacagccaagggaacgggcuuggcagaaucagcg
gggaaagacccuguugagcuugacucuaguuugacauugugaagagacau
agaggguguagaauaagugggagcuucggcgccagugaaauaccacuacc
uuuauaguuucuuuacuuauucaaugaagcggagcuggaauucauuuucc
acguucuagcauucaaggucccauucggggcugauccggguugaagacau
ugucagguggggaguuucacaucuguugcagaugucuaaggggggcucau
ggagaacagaaaucuccaguagaacaaaggguaaaagcccccuugauuuu
gauuuuugugaauacaaaccaugaaaguguggccccuuuagucccucgga
auuugaggcuagaggaaaguuaccacaggguggcuuguggcagucaagcg
uucauagcgacauugcuuuuugauucuucgaucggcucuuccuaucauac
cgaagcagaauucgguaagcguuggauuguucacccacuaauagggaacg
ugagcugguagaccgucgugagacagguuaguuuuacccuacugaugaau
guuaccgcaauaguaauugaacuuaguacgagaggaacaguucauucgga
uaauugguuuuugcggcugucugaucaggcauugccgcgaagcuaccauc
cgcuggauuauggcugaacgccucuaagucagaauccaugcuagaacgcg
gugauuugcuccacacaaauagauggauacgaauaaggcguccuuguggc
gucgcugaaccauagcaggcuagcaacggugcacuuggcggaaaggccuu
gggugcuugcuggcgaauugcaaugucauuugcguggggauaaaucauuu
guauacgacuuagauguacaacgggguauuguaagcaguagaguagccgu
uacgaucugcugagauuaagccuuuguugucugauuugu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6ylh Construction of the Central Protuberance and L1 Stalk during 60S Subunit Biogenesis.
• Resolution: 3.1 Å
• Binding residue (original residue number in PDB): T3 G4 K5 K6 E7 R13 K25 F29 Y30 R31 R35 N50 K51 R130 L132 K144 Q146 K148 R149 I202 K205 S208 R210 I211 W212 N213 Y216 S241 C262 D263 H287 T291 N292 S293 F294 K296 G297 Q301 R304 K338 K339 V340 P345 Y355 T357 M359 K360 R361 P373 S374 V387 R389 E391 H392 Q435 R437 K440 G441 Q452 R459 G460 K461
• Binding residue (residue number reindexed from 1): T1 G2 K3 K4 E5 R11 K16 F20 Y21 R22 R26 N41 K42 R111 L113 K125 Q127 K129 R130 I172 K175 S178 R180 I181 W182 N183 Y186 S211 C232 D233 H257 T261 N262 S263 F264 K266 G267 Q271 R274 K308 K309 V310 P315 Y325 T327 M329 K330 R331 P343 S344 V357 R359 E361 H362 Q405 R407 K410 G411 Q422 R429 G430 K431

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:6ylh, PDBe:6ylh, PDBj:6ylh
• PDBsum: 6ylh
• PubMed: 32668200
• UniProt: P53742|NOG2_YEAST Nucleolar GTP-binding protein 2 (Gene Name=NOG2)