Structure of PDB 7z34 Chain b Binding Site BS01

Receptor Information

>7z34 Chain b (length=630) Species: 559292 (Saccharomyces cerevisiae S288C)

MQLSWKDIPTVAPANDLLDIVLNRTQRKTPTVIRPGFKITRIRAFYMRKV
KYTGEGFVEKFEDILKGFPNINDVHPFHRDLMDTLYEKNHYKISLAAISR
AKSLVEQVARDYVRLLKFGQSLFQCKQLKRAALGRMATIVKKLRDPLAYL
EQVRQHIGRLPSIDPNTRTLLICGYPNVGKSSFLRCITKSDVDVQPYAFT
TKSLYVGHFDYKYLRFQAIDTPGILDRPTEEMNNIEMQSIYAIAHLRSCV
LYFMDLSEQCGFTIEAQVKLFHSIKPLFANKSVMVVINKTDIIRPEDLDE
ERAQLLESVKEVPGVEIMTSSCQLEENVMEVRNKACEKLLASRIENAQPQ
ARDDVKRTPFIPESVKNLKKYDPEDPNRRKLARDIEAENGGAGVFNVNLK
DKYLLEDDEWKNDIMPEILDGKNVYDFLDPEIAAKLQALEEEEEKLENEG
FYNSDDEEEIYDGFEASEVDDIKEKAAWIRNRQKTMIAEARNRKSLKNKA
IMPRSKLTKSFGKMEEHMSTLGHDMSALQDKQNRAARKNRYVERGSDVVF
GDQDALTASTENGVKLRQTDRLLDGVADGSMRSKADRMAKMERRERNRHA
KQGESDRHNAVSLSKHLFSGKRGVGKTDFR

Ligand information

>7z34 Chain 1 (length=3347)

uugaccucaaaucagguaggaguacccgcugaacuuaagcauaucaauaa
gcggaggaaaagaaaccaaccgggauugccuuaguaacggcgagugaagc
ggcaaaagcucaaauuugaaaucugguaccuucggugcccgaguuguaau
uuggagagggcaacuuuggggccguuccuugucuauguuccuuggaacag
gacgucauagagggugagaaucccguguggcgaggagugcgguucuuugu
aaagugccuucgaagagucgaguuguuugggaaugcagcucuaagugggu
gguaaauuccaucuaaagcuaaauauuggcgagagaccgauagcgaacaa
guacagugauggaaagaugaaaagaacuuugaaaagagagugaaaaagua
cgugaaauuguugaaagggaagggcauuugaucagacaugguguuuugug
cucgcauuucacugggccagcaucaguuuugguggcaggauaaauccaua
ggaauguagcuugccucgguaaguauuauagccugugggaauacugccag
cugggacugaggacugcgacguaagucaaggaugcuggcauaaugguuau
augccgcccgucuugaaacacggaccaaggagucuaacgucuaugcgagu
guuuggguguaaaacccauacgcguaaugaaagugaacguagguuggggc
cucgcaagaggugcacaaucgaccgauccugaugucuucggauggauuug
aguaagagcauagcuguugggacccgaaagauggugaacuaugccugaau
agggugaagccagaggaaacucugguggaggcucguagcgguucugacgu
gcaaaucgaucgucgaauuuggguauaggggcgaaagacuaaucgaacca
ucuaguagcugguuccugccgaaguuucccucaggauagcagaagcucgu
aucaguuuuaugagguaaagcgaaugauuagagguuccggggucgaaaug
accuugaccuauucucaaacuuuaaauauguaagaaguccuuguuacuua
auugaacguggacauuugaaugaagagcuuuuagugggccauuuuuggua
agcagaacuggcgaugcgggaugaaccgaacguagaguuaaggugccgga
auacacgcucaucagacaccacaaaagguguuaguucaucuagacagccg
gacgguggccauggaagucggaauccgcuaaggaguguguaacaacucac
cggccgaaugaacuagcccugaaaauggauggcgcucaagcguguuaccu
auacucuaccgucaggguugauaugaugcccugacgaguaggcaggcgug
gaggucagugacgaagccuagaccguaaggucgggucgaacggccucuag
ugcagaucuuggugguaguagcaaauauucaaaugagaacuuugaagacu
gaaguggggaaagguuccacgucaacagcaguuggacguggguuagucga
uccuaagagauggggaagcuccguuucaaaggccugauuuuaugcaggcc
accaucgaaagggaauccgguuaagauuccggaaccuggauauggauucu
ucacgguaacguaacugaauguggagacgucggcgcgagcccugggagga
guuaucuuuucuucuuaacagcuuaucaccccggaauugguuuauccgga
gauggggucuuauggcuggaagaggccagcaccuuugcuggcuccggugc
gcuugugacggcccgugaaaauccacaggaaggaauaguuuucaugccag
gucguacugauaaccgcagcaggucuccaaggugaacagccucuaguuga
uagaauaauguagauaagggaagucggcaaaauagauccguaacuucggg
auaaggauuggcucuaaggguagugagggccuuggucagacgcagcgggc
gugcuuguggacugcuugguggggcuugcucugcuaggcggacuacuugc
gugccuuguuguagacggccuugguaggucucuuguagaccgucgcuugc
uacaaacuuagaacugguacggacaaggggaaucugacugucuaauuaaa
acauagcauugcgauggucagaaagugauguugacgcaaugugauuucug
cccagugcucugaaugucaaagugaagaaauucaaccaagcgcggguaaa
cggcgggaguuaugacucucuuaagguagccaaaugccucgucaucuaau
uagugacgcgcaugaauggauuaacgagauucccacugucccuaucuacu
aucuagcgaaaccacagccaagggaacgggcuuggcagaaucagcgggga
aagaagacccuguugagcuugacucuaguuugacauugugaagagacaua
gaggguguagaauaagugggagcuucggcgccagugaaauaccacuaccu
uuauaguuucuuuacuuauucaaugaagcggagcuggaauucauuuucca
cguucuagcauucaaggucccauucggggcugauccggguugaagacauu
gucagguggggaguuuggcuggggcggcacaucuguuaaacgauaacgca
gauguccuaaggggggcucauggagaacagaaaucuccaguagaacaaaa
ggguaaaagcccccuugauuuugauuuucagugugaauacaaaccaugaa
aguguggccuaucgauccuuuagucccucggaauuugaggcuagaggugc
cagaaaaguuaccacagggauaacuggcuuguggcagucaagcguucaua
gcgacauugcuuuuugauucuucgaucggcucuuccuaucauaccgaagc
agaauucgguaagcguuggauuguucacccacuaauagggaacgugagcu
ggguuuagaccgucgugagacagguuaguuuuacccuacugaugaauguu
accgcaauaguaauugaacuuaguacgagaggaacaguucauucggauaa
uugguuuuugcggcugucugaucaggcauugccgcgaagcuaccauccgc
uggauuauggcugaacgccucuaagucagaauccaugcuagaacgcggug
auuucuuugcuccacacaauauagauggauacgaauaaggcguccuugug
gcgucgcugaaccauagcaggcuagcaacggugcacuuggcggaaaggcc
uugggugcuugcuggcgaauugcaaugucauuuugcguggggauaaauca
uuuguauacgacuuagauguacaacgggguauuguaagcaguagaguagc
cuuguuguuacgaucugcugagauuaagccuuuguugucugauuugu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7z34 Visualizing maturation factor extraction from the nascent ribosome by the AAA-ATPase Drg1.
• Resolution: 3.8 Å
• Binding residue (original residue number in PDB): K6 D19 L22 N23 Q26 R27 T31 V32 I33 R34 P35 K38 R41 M47 K49 P69 N70 I71 K92 I93 L95 R100 R110 K117 F123 K126 K129 A131 L133 G134 R135 R144 Q152 Q155 R159 Y197 F199 H208 I504 R508 K511 L513 K514 N515 I518 P520 R521 S522 T586 D587 R588 L589 K601 M605 M608 R610 R611 N614 K618 Q619 R624 H625 H633 K638 V641 G642 T644 F646 R647
• Binding residue (residue number reindexed from 1): K6 D19 L22 N23 Q26 R27 T31 V32 I33 R34 P35 K38 R41 M47 K49 P69 N70 I71 K92 I93 L95 R100 R110 K117 F123 K126 K129 A131 L133 G134 R135 R144 Q152 Q155 R159 Y197 F199 H208 I487 R491 K494 L496 K497 N498 I501 P503 R504 S505 T569 D570 R571 L572 K584 M588 M591 R593 R594 N597 K601 Q602 R607 H608 H616 K621 V624 G625 T627 F629 R630

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003924 GTPase activity
• GO:0005515 protein binding
• GO:0005525 GTP binding

Biological Process

• GO:0000054 ribosomal subunit export from nucleus
• GO:0006364 rRNA processing
• GO:0042254 ribosome biogenesis
• GO:0042273 ribosomal large subunit biogenesis
• GO:1902626 assembly of large subunit precursor of preribosome

Cellular Component

• GO:0005634 nucleus
• GO:0005730 nucleolus
• GO:0005737 cytoplasm
• GO:0030687 preribosome, large subunit precursor

External links

• PDB: RCSB:7z34, PDBe:7z34, PDBj:7z34
• PDBsum: 7z34
• PubMed: 36097293
• UniProt: Q02892|NOG1_YEAST Nucleolar GTP-binding protein 1 (Gene Name=NOG1)