Structure of PDB 6zqc Chain CL Binding Site BS02

Receptor Information

>6zqc Chain CL (length=781) Species: 559292 (Saccharomyces cerevisiae S288C)

PGKMARTMQRSSDVNERKLHVPMVDRTPEDDPPPFIVAVVGPPGTGKTTL
IRSLVRRMTKSTLNDIQGPITVVSGKHRRLTFLECPADDLNAMIDIAKIA
DLVLLLIDGNFGFEMETMEFLNIAQHHGMPRVLGVATHLDLFKSQSTLRA
SKKRLKHRFWTEVYQGAKLFYLSGVINGRYPDREILNLSRFISVMKFRPL
KWRNEHPYMLADRFTDLTHPELIETQGLQIDRKVAIYGYLHGTPLPSAPG
TRVHIAGVGDFSVAQIEKLPDPCPTPFYQQKLDDFERLIYAPMSDVGGVL
MDKDAVYIDIGNIGKLIYMDNISPEECIRRWRGVDLEKFVPYFDTFEKLA
KKWKSVDAIKERFLDTWYELQKAKISKQLEINNIEYQEMTPEQRQRIEGF
KAGSYVRIVFEKVPMEFVKNFNPKFPIVMGGLLPTEIKFGIVKARLRRHR
WHKKILKTNDPLVLSLGWRRFQTLPIYTTTDSRTRTRMLKYTPEHTYCNA
AFYGPLCSPNTPFCGVQIVANSDTGNGFRIAATGIVEEIDVNIEIVKKLK
LVGFPYKIFKNTAFIKDMFSSAMEVARFEGAQIKTVSGIRGEIKRALSKP
EGHYRAAFEDKILMSDIVILRSWYPVRVKKFYNPVTSLLLKEKTEWKGLR
LTGQIRAAMNLETPSNPDSAYHKIERVERHFNGLKVPKAVQKELPFKSQI
HQMKPQKKKTYMAKRAVVLGGDEKKARSFIQKVLTISKAKDSKRKEQKAS
QRKERLKKLAKMEEEKSQRDKEKKKEYFAQN

Ligand information

>6zqc Chain D3 (length=1327)

aagauaguuaucugguugauccugccagucauaugcuugucucaaagauu
aagccaugcaugucuaaguauaagcaauuuauacagugaaacugcgaaug
gcucauuaaaucaguuaucguuuauuugauagcaugguauaacuguggua
auucuagagcuaauacaugcuaucucgacccuuuggaagagauuauuuau
uagauucuucggacucuugaugauucauaauaacuuuucgaaucgcaugg
ccuugugcuggcgaugguucauucaaauuucugcccuaucaacuuucgau
gguaggauaguggccuaccaugguuucaacggguaacggggaauaagggu
ucgauuccggagagggagccugagaaacggcuaccacauccaaggaaggc
agcaggcgcgcaaauuacccaauccuaauucagggagguagugacaauaa
auaacgauacagggcccauucgggucuuguaauuggaaugaguacaaugu
aaauaccuuaacgaggaacaauuggagggcaagucuggugccagcagccg
cgguaauuccagcuccaauagcguauauugcucguaguugaacuuugggc
ccgguuggccggucggauuuccaacggggccuuuuuacuuugaaaaaauu
agaguguucaaagcaggcguauugcucgauauauuagcauggaauaauag
gacguuugguucuauuuuguugguuucuaggaccaucguaauuaauaggg
acggucgggggcaucaguauucaauugucagaggugaaauucuuggauuu
auugaagacuaacuacugcgaaagcauuugccaaggacguuuucauuaau
caagaacgaaacuaugccgacuagggaucgggugguguuuuuuuaaugac
ccacucggcaccuuacgaggaguauggucgcaaggcugaaacuuaaagga
auugacggaagggcaccaccaggaguggagccugcggaaacucaccaggu
ccagacacaauauuugugggugguggugcaugugaugcccuuguucuggc
gcgcgcuacacugacggagccagcgagucuaaccuuggccgagaggucuu
gguaaaaacuccgucggggaacgaggaauuccuaguaagcgcaagucauc
agcuugcguugauuacgucccugcccuuuguacacaccgcccgucgcuag
uaccgauugaauggcuuagugaggccucaggaucugcuuagagaaggggg
caacuccaucucagagcggaaauuuggacaaacuuggucauuuagaggaa
cuaaguuuccguaggugaaccugcgga

...........................<<.<<<<<<...<.<........
..<<<.<<<..<<....<<....<<..........>>...>>.>>.....
.<<..<.....<<<..<<..<<....<<<.......<<....<<.<<<..
...>>>.>>.....>>.....<<<<<..<<....>>..>>>>>...<<<<
<<...<<....>>....<<......>>>>>>>>.........<<<<.<<<
<.....>>>>>>>>....>>>...>>>>..>>>.<<<....<<......<
<<<<<<.......>>>>>>>..>>......>>>...<<<<<<<<....>>
>>...>>>>>>>.<<.<<<<........>>>>.>>.<.<<<..>>>.>..
.>>>>>>.........<<<....<<<.....>>>..>>>.......>.>.
....<<<<<<<.<<<<<....>>>>>.>>>.>>>>......<<..<....
.......>..>>.........<<<<<<.......<<<....>>>......
............>>>>>>..>>>>>>>>.<.<<...<<<.<<....<<<<
<<.<<<<<............>>>>>.>>>>>>..<<<<<.<<......<.
...<<.......>>..<<.....>>.....>......>>.>>..>>>...
.<<<...<<<<<<...............>>>>>>..>>>..>>....<<<
<<<.<<...<<<<..<<..<<<<<<.<...<<<......>>>......>.
>>>>>>..>>.......<<....>>...>>>>..>.>>>>.>>>...>>>
...>>.>..........<<...<<<..<<<<<<<<.<<<........>>>
>>>>>>>>..>>>..>>..................<<.........>>..
...<<<<<<<<<<<<..<<.<<<<<<..<<<.<<<<........<<<<<.
<....<<<<<...>>>>>......<<<.<<..>>..>>>...>.>>>>>>
>>>.>>>.....<<<<<<<............<<<..<<<<....>>>>..
>>>.....>>>>>>>............>>>>>>....<<<<<<<<.....
..>>>>>>>>......>>...>>>>>>>............>>>>>..<<<
<.<<....<<<<<<<<.<<<..<.<<..<...<<<<<<<...<<.<.<..
....>.>.>>...>>>>>>>..>..>>.>..>>>.>>>>>>>>...>>.>
>>>....<<<<<<<<....>>>>>>>>

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6zqc 90 S pre-ribosome transformation into the primordial 40 S subunit.
• Resolution: 3.8 Å
• Binding residue (original residue number in PDB): K38 R41 R45 D48 R52 K53 H55 V56 R166 K178 S179 R184 K191 Y199 R218 N222 R225 V229 K231 F232 R233 Y751 K837 I838 K840 T862 S865 R868 R870 K873 Y874 H878 T879 K930 K931 K933 K940 I941 F942 K943 T945 V969 K977 R978 S981 R988 E992 D993 K994 M997 R1004 R1039 T1046 P1050 S1052 Y1054 R1062 H1063 N1065 K1123 K1126 R1127 R1135 R1138 K1140 L1142 K1158 F1161
• Binding residue (residue number reindexed from 1): K3 R6 R10 D13 R17 K18 H20 V21 R131 K143 S144 R149 K156 Y164 R183 N187 R190 V194 K196 F197 R198 Y368 K454 I455 K457 T479 S482 R485 R487 K490 Y491 H495 T496 K547 K548 K550 K557 I558 F559 K560 T562 V586 K594 R595 S598 R605 E609 D610 K611 M614 R621 R656 T663 P667 S669 Y671 R679 H680 N682 K740 K743 R744 R752 R755 K757 L759 K775 F778

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