Structure of PDB 6zqd Chain CL Binding Site BS01

Receptor Information

>6zqd Chain CL (length=808) Species: 559292 (Saccharomyces cerevisiae S288C)

EQSNKQHRKAKEKNTAKKKLHTQGHNAKAFAVAAPGKMARTMQRSSDVNE
RKLHVPMVDRTPEDDPPPFIVAVVGPPGTGKTTLIRSLVRRMTKSTLNDI
QGPITVVSGKHRRLTFLECPADDLNAMIDIAKIADLVLLLIDGNFGFEME
TMEFLNIAQHHGMPRVLGVATHLDLFKSQSTLRASKKRLKHRFWTEVYQG
AKLFYLSGVINGRYPDREILNLSRFISVMKFRPLKWRNEHPYMLADRFTD
LTHPELIETQGLQIDRKVAIYGYLHGTPLPSAPGTRVHIAGVGDFSVAQI
EKLPDPCPTPFYQQKLDDFERDKDKLIYAPMSDVNIGKLIYMDNISPEEC
IRRWRGVDLEKFVPYFDTFEKLAKKWKSVDAIKERFLREMNAAKKEKLRA
QFEIEEGENFKEDDENNEYDTWYELQKAKISKQLEINNIEYQEMTPEQRQ
RIEGFKAGSYVRIVFEKVPMEFVKNFNPKFPIVMGGLLPTEIKFGIVKAR
LRRHRWHKKILKTNDPLVLSLGWRRFQTLPIYTTTDSRTRTRMLKYTPEH
TYCNAAFYGPLCSPNTPFCGVQIVANSDTGNGFRIAATGIVEEIDVNIEI
VKKLKLVGFPYKIFKNTAFIKDMFSSAMEVARFEGAQIKTVSGIRGEIKR
ALSKPEGHYRAAFEDKILMSDIVILRSWYPVRVKKFYNPVTSLLLKEKTE
WKGLRLTGQIRAAMNLETPSNPDSAYHKIERVERHFNGLKVPKAVQKELP
FKSQIHAKRAVVLGGDEKKARSFIQKVLTISKAKDSKRKEQKASQRKERL
KKLAKMEE

Ligand information

>6zqd Chain D3 (length=1409)

ucugguugauccugccaguagucauaugcuugucucaaagauuaagccau
gcaugucuaaguauaagcaauuuauacagugaaacugcgaauggcucauu
aaaucaguuaucguuuauuugauaguuccuuacaugguauaacuguggua
auucuagagcuaauacaugcuaucucgacccuuuggaagagauguauuua
uuagauaucuucggacugaugauucauaauaacuuuucgaaucgcauggc
cuugugcuggcgaugguucauucaaauuucugcccuaucaacuuucgaug
guaggauaguggccuaccaugguuucaacggguaacggggaauaaggguu
cgauuccggagagggagccugagaaacggcuaccacauccaaggaaggca
gcaggcgcgcaaauuacccaauccuaauucagggagguagugacaauaaa
uaacgauacagggcccauucgggucuuguaauuggaaugaguacaaugua
aauaccuuaacgaggaacaauuggagggcaagucuggugccagcagccgc
gguaauuccagcuccaauagcguauauuguuguugcaguuaaaaagcucg
uaguugaacuggcccgguuggccggucggauuuccaacggggccuuuccu
ucuggcuaaccuugaguccuuguggcucuuggcgaaccaguuacuuugaa
aaaauuagaguguucaaagcaggcguauugcucgauauauuagcauggaa
uaauaguaggagguucuauucuaggaccaucguauuaauagggacggucg
ggggcaucaguauucaauugucagaggugaaauucuuggauuuauugaag
acuaacuacugcgaaagcauuugccaaggacguuuucauuaaucaagaac
gaaaguuaggggaucgaagaugaucagauaccgucguagucuuaaccaua
aacuaugccgacuagggaucgggugguguuuuuuuaaugacccacucggc
accuuacgagaaaucaaagucuuuggguucugggggaguauggucgcaag
gcuaaaaaaggaauugacggaagggcaccaccaggaguggagccugcggc
gcgcuacacugacggagccagcgagaccuuggccgagaggucuugggaaa
cuccgucgugcuggggauagagcauuguaauuauugcucuucaacgagga
auuccuaguaagcgcaagucaucagcuugcguugauuacgucccugcccu
uuguacacaccgcccgucgcuaguaccgauugaauggcuuagugaggccu
caggaucugcuuagagaagggggcaacuccaucucagagcggagauuugg
acaaacuuggucauuugaggaacuaauuccguaggugaaccugcggaagg
aucauuaaa

.<<<<<.......>>>>>.....<<<<<<...<.<..........<<<.<
<<..<<....<<....<<..........>>...>>.>>......<<....
....<<<..<<..<<....<<<..............<<....<<.<<...
....>>.>>.....>>.....<<<<<..<<....>>..>>>>><...<<<
<<<....<<....>>.<<......>>>>>>>>.....>...<<<<..<<<
.....>>>.>>>>....>>>...>>>>..>>>.<<<....<<<....<<<
<<<<<.......>>>>>>>>>>>......>>>...<<<.<<<<....>>>
>....>>>.>>.<<.<<<..........>>>.>>.<.<<<..>>>.>...
>>>>>>.........<<<....<<<.....>>>..>>>.......>.>..
...<<<<<<<.<<<<<....>>>>>.>>>.>>>>......<<..<.....
......>..>>.........<<<<<<.......<<<....>>>.......
...........>>>>>>..>>>>>>..........<<<((.....<.<<.
..<<<.<<..<<<<<.<<<<<.....<>.....>>>>>.>>>>>..<<<<
.<<<<.<..<<..<<<<<.....>>>>>..>>..>.>>>><<<<<.<<..
.....<<..<<.......>>.<<<.....>>>...>>......>>.>>..
>>>....>>>>.<<.<<<...>>>.>>.......>>....<<<<<<.<<.
..<<<<..<<..<<<<<<.<...<<<..(...>>>......>.>>>>>>.
.>>.......<<....>>...>>>>...>>>>>.>>>...>>>...>>.>
....<<<<<<....<...<<<<..)......>>>>...>.>>>>>>....
......<<<.<<.<<<..<<<<<<<<.<<<........>>>>>>>>>>>.
.>>>...<<..))>>...>>.....>>>.>>>..................
...............<<<<<<<<<<<<..<<.<<<<<<..<<<.<<<.>>
>.>>>.....<<<<<<<.........<<..<<<<....>>>>..>>....
>>>>>>>...........<<<<<<.<<....>>.>>>>>>..........
>>>>>>....<<<<<<<.........>>>>>>>......>>...>>>>>>
>............>>>>>..<<<<.<<....<<<<<<<<.<<<..<.<<.
.<...<<<<<<<.<<<<.<<<......>>>.>>>>.>>>>>>>..>..>>
.>..>>>.>>>>>>>>..>>.>>>>.<<<<<<<<<....>>>>>>>>>..
.........

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6zqd 90 S pre-ribosome transformation into the primordial 40 S subunit.
• Resolution: 3.8 Å
• Binding residue (original residue number in PDB): Q3 S4 N5 Q7 H8 R9 K10 K12 T16 K18 H22 N27 K29 A30 A32 V33 A34 A35 P36 G37 K38 M43 R45 R52 K53 H55 V56 P57 M58 R166 R184 K188 K191 W195 Y199 R225 R233 K755 K837 I838 K840 R868 R870 K873 Y874 H878 T879 K930 K931 K933 F942 K943 T945 V969 R973 K977 R988 E992 D993 K994 R1004 P1047 S1052 Y1054 K1068 K1071 K1126 R1127 R1135 R1138 L1142 K1144
• Binding residue (residue number reindexed from 1): Q2 S3 N4 Q6 H7 R8 K9 K11 T15 K17 H21 N26 K28 A29 A31 V32 A33 A34 P35 G36 K37 M42 R44 R51 K52 H54 V55 P56 M57 R165 R183 K187 K190 W194 Y198 R224 R232 K427 K509 I510 K512 R540 R542 K545 Y546 H550 T551 K602 K603 K605 F614 K615 T617 V641 R645 K649 R660 E664 D665 K666 R676 P719 S724 Y726 K740 K743 K787 R788 R796 R799 L803 K805

Gene Ontology

Molecular Function

• GO:0003729 mRNA binding
• GO:0003924 GTPase activity
• GO:0005515 protein binding
• GO:0005524 ATP binding
• GO:0005525 GTP binding
• GO:0016887 ATP hydrolysis activity
• GO:0034511 U3 snoRNA binding

Biological Process

• GO:0000462 maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
• GO:0000472 endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
• GO:0000479 endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
• GO:0000480 endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
• GO:0030490 maturation of SSU-rRNA
• GO:0042254 ribosome biogenesis
• GO:0042274 ribosomal small subunit biogenesis
• GO:2000232 regulation of rRNA processing

Cellular Component

• GO:0005634 nucleus
• GO:0005654 nucleoplasm
• GO:0005730 nucleolus
• GO:0005737 cytoplasm
• GO:0005739 mitochondrion
• GO:0030686 90S preribosome
• GO:0032040 small-subunit processome

External links

• PDB: RCSB:6zqd, PDBe:6zqd, PDBj:6zqd
• PDBsum: 6zqd
• PubMed: 32943521
• UniProt: Q08965|BMS1_YEAST Ribosome biogenesis protein BMS1 (Gene Name=BMS1)