Structure of PDB 6zqf Chain JD Binding Site BS01

Receptor Information

>6zqf Chain JD (length=807) Species: 559292 (Saccharomyces cerevisiae S288C)

GTYRKRFNEKARSGHMAKLKELKRIRNKQFTRSKVSRLKKKRLDKFIEHQ
LKREERKTIIGKLQDYKAYVPINENSTRKAFYVEVSRSDEIQKARIQLPV
FGEEHKIMEAIHHNDVVIICGETGSGKTTQVPQFLYEAGFGAEDSPDYPG
MVGITQPRRVAAVSMAERVANELGDHGHKVGYQIRFDSTAKEDTKVKFMT
DGVLLREMMHDFKLTKYSSIIIDEAHERNINTDILIGMLSRCVRLRAKLH
KENPIEHKKLKLIIMSATLRVSDFSENKTLFPIAPPVLQVDQFPVSIHFN
RRTAFNYTDEAFRKTCKIHQKLPPGAILVFLTGQQEITHMVKRLRKEEGQ
TANDPLYVLPLYSLLPTKEQMRVFQKPPQGSRLCIVATNVAETSLTIPGV
RYVVDSGRSKERKYNESNGVQSFEVGWVSKASANQRSGRAGRTGPGHCYR
LYSSAVFEHDFEQEILRMPVESIVLQMKSMAIHNIINFPFPTPPDRVALS
KAIQLLQYLGALDNKEMITEDGKKMSLFPLSPRFSKMLLVSDEKACLPYI
VAIVSALSVKFYKSRSQFSKLDKFSDVFRLLSVVSAMDYVPKEQKEIFMK
KNFLRGKLMEEIVKLRKQLMYIIKSNTSKENIAVVIRNEVIQIKLLKQMI
CAGFVDHVAVRADVLFPDDAKITNRTSIINIPYIPVLATRTPNIEDCFVY
IHPTSILNNLGEMPPKYMLYYSLHLGGNNKTRMNTLCDIASTPLANIARK
GLLLTYSKPLGLKTVNLSPTERYCYVVPRFGKIGWDLNPIAVHQKKQKGQ
WTVIKFI

Ligand information

>6zqf Chain D3 (length=1392)

uaucugguugauccugccaguucauaugcuugucucaaagauuaagccau
gcaugucuaaguauaagcaauuuauacagugaaacugcgaauggcucauu
aaaucaguuaucguuuauuugauaguuccuuuacuacaugguauaacugu
gguaauucuagagcuaauacaugcuuaaaaucucgacccuuuggaagaga
uguauuuauuagauaaaaaaucaaugucuucggacucuuugaugauucau
aauaacuuuucgaaucgcauggccuugugcuggcgaugguucauucaaau
uucugcccuaucaacuuucgaugguaggauaguggccuaccaugguuuca
acggguaacggggaauaaggguucgauuccggagagggagccugagaaac
ggcuaccacauccaaggaaggcagcaggcgcgcaaauuacccaauccuaa
uucagggagguagugacaauaaauaacgauacagggcccauucgggucuu
guaauuggaaugaguacaauguaaauaccuuaacgaggaacaauuggagg
gcaagucuggugccagcagccgcgguaauuccagcuccaauagcguauau
uauguugcaguuaaaaagcucguaguugaacuuugggcccgguuggccgg
ucggauuuccaacggggccuuuccuucuggcuaaccuugaguccuugugg
cucuuggcgaaccaggacuuuuacuuugaaaaaauuagaguguucaaagc
aggcguauugcucgaauauauuagcauggaauaauagaauaggacguuug
guucuauuuuguugguuucuaggaccaucguaaugauuaauagggacggu
cgggggcaucaguauucaauugucagaggugaaauucuuggauuuauuga
agacuaacuacugcgaaagcauuugccaaggacguuuucauuaaucaaga
acgaaaguuaggggaucgaagaugaucagauaccgucguagucuuaacca
uaaacuaugccgacuagggaucgggugguguuuuuuuaaugacccacucg
gcaccuuacgagaaaucaaagucuuuggguucuggggggaguauggucgc
aaggcuaaauuaaaggaauugacggaagggcaccaccaggaguggagccu
gcggcacgcgcgcuacacugacggagccagcgagucuaaccuuggccgag
aggucuugguaaucuugugaaacuccgucgugcuggggauagagcauugu
aauuauugcucuucaacgaggaauuccuaguaagcgcaagucaucagcuu
gcguugauuacgucccugcccuuuguacacaccgcccgucgcuaguaccg
gaacuaauuccguaggugaaccugcggaaggaucauuaaaga

...<<<<<.......>>>>>...<<<<<<...<.<..........<<<.<
<<..<<....<<....<<..........>>...>>.>>......<<....
....<<<..<<..<<....<<<..................<.....<<.<
<.......>>.>>......>.........<<<<<..<<....>>..>>>>
><...<<<<<<.........(((..<<<....>>>..............>
>>>>>.....>...<<<<..<<<.....>>>.>>>>....>>>...>>>>
..>>>.<<<....<<<....<<<<<<<<.......>>>>>>>>>>>....
..>>>...<<<.<<<<....>>>>....>>>.>>.<<.<<<.........
.>>>.>>.<.<<....>>.>...>>>>>>.........<<<....<<<..
...>>>..>>>.......>.>.....<<<<<..<.<..........>.>.
.>>.>>>......<<..<...........>..>>.........<<<<<<.
......<<<....>>>..................>>>>>>..>>>>>>..
.......<<<.[.....<.<<...<<<.<<....<<<<<<.<<<<<....
<..>....>>>>>.>>>>>>....<<<<<<....................
...........>>>>>>...<<<<<.<<.......<<...<.......>.
.<<<.....>>>....>>......>>.>>..>>>.........<<...<<
<<<<<<......)))....>>>>>>>>..>>.....>>....<<<<<<.<
<...<<<<..<<..<<<<<<.<...<<<......>>>......>.>>>>>
.>.>>......<<<....>>>..>>>>...>>>>>.>>>...>>>...>>
.>....<<<<<<<...<...<<<<.........>>>>...>>>>>>>>..
........<<<.<<.<<<..<<<<<<<<.<<<........>>>>>>>>>>
>..>>>...<<..].>>...>>.....>>>.>>>................
....................<<<<<<<<<<<<..<<..<<<<<..<<<.<
<<.....>>>.>>>.....<<<<<<<......<<.....<<..<<<<...
.>>>>..>>....>>.......>>>>>>>...........<<<<<<....
......>>>>>>..........>>>>>.....<<<<<<<.........>>
>>>>>......>>...>>>>>>>............>>>>>..<<<<.<<>
>.>>>>.<<<<<<<<<....>>>>>>>>>.............

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6zqf 90 S pre-ribosome transformation into the primordial 40 S subunit.
• Resolution: 4.9 Å
• Binding residue (original residue number in PDB): G2 R27 K88
• Binding residue (residue number reindexed from 1): G1 R26 K34

Enzymatic activity

• Enzyme Commision number: 3.6.4.13: RNA helicase.

Gene Ontology

Molecular Function

• GO:0003676 nucleic acid binding
• GO:0003723 RNA binding
• GO:0003724 RNA helicase activity
• GO:0004386 helicase activity
• GO:0005515 protein binding
• GO:0005524 ATP binding
• GO:0008186 ATP-dependent activity, acting on RNA
• GO:0016787 hydrolase activity
• GO:0016887 ATP hydrolysis activity

Biological Process

• GO:0000462 maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
• GO:0006364 rRNA processing
• GO:0006396 RNA processing
• GO:0022613 ribonucleoprotein complex biogenesis
• GO:0030490 maturation of SSU-rRNA
• GO:0042254 ribosome biogenesis

Cellular Component

• GO:0005634 nucleus
• GO:0005654 nucleoplasm
• GO:0005730 nucleolus
• GO:0005739 mitochondrion
• GO:0030686 90S preribosome
• GO:0032040 small-subunit processome
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:6zqf, PDBe:6zqf, PDBj:6zqf
• PDBsum: 6zqf
• PubMed: 32943521
• UniProt: Q04217|DHR1_YEAST Probable ATP-dependent RNA helicase DHR1 (Gene Name=ECM16)