Structure of PDB 6lqs Chain RJ

Receptor sequence

>6lqsRJ (length=731) Species: 559292 (Saccharomyces cerevisiae S288C)

TMQRSSDVNERKLHVPMVDRTPEDDPPPFIVAVVGPPGTGKTTLIRSLVR
RMTKSTLNDIQGPITVVSGKHRRLTFLECPADDLNAMIDIAKIADLVLLL
IDGNFGFEMETMEFLNIAQHHGMPRVLGVATHLDLFKSQSTLRASKKRLK
HRFWTEVYQGAKLFYLSGVINGRYPDREILNLSRFISVMKFRPLKWRNEH
PYMLADRFTDLTHPELIETQGLQIDRKVAIYGYLHGTPLPSAPGTRVHIA
GVGDFSVAQIEKLPDPCPTPFLIYAPMSDNIGKLIYMDNISPEECIRRWR
DLEKFVPYFDTFEKLAKKWKSVDAIKERFLTWYELQKAKISKQLEINNIE
YQEMTPEQRQRIEGFKAGSYVRIVFEKVPMEFVKNFNPKFPIVMGGLLPT
EIKFGIVKARLRRHRWHKKILKTNDPLVLSLGWRRFQTLPIYTTTDSRTR
TRMLKYTPEHTYCNAAFYGPLCSPNTPFCGVQIVANSDTGNGFRIAATGI
VEEIDVNIEIVKKLKLVGFPYKIFKNTAFIKDMFSSAMEVARFEGAQIKT
VSGIRGEIKRALSKPEGHYRAAFEDKILMSDIVILRSWYPVRVKKFYNPV
TSLLLKEKTEWKGLRLTGQIRAAMNLETPSNPDSAYHKIERVERHFNGLK
VPKAVQKELPFKSQIHVVLGGDEKKARSFIQKVLTISKAKDSKRKEQKAS
QRKERLKKLAKMEEEKSQRDKEKKKEYFAQN

3D structure

• PDB: 6lqs Cryo-EM structure of 90 S small ribosomal subunit precursors in transition states.
• Chain: RJ
• Resolution: 3.8 Å

Interaction with ligand

Site #	Ligand	Ligand chain	Binding residues on receptor (original residue number in PDB)	Binding residues on receptor (residue number reindexed from 1)	Binding affinity
BS01	rna	RJ	K1157 K1158 Y1160 F1161	K724 K725 Y727 F728
BS02	rna	RJ	Q44 R45 R52 K53 H55 V56 M58 R166 F177 K178 T182 K188 W195 Y199 G201 R218 R225 F226 F232 R233 P234 Y751 K755 K837 I838 K840 T862 R870 K873 Y874 T879 K931 K933 F942 K943 N944 T945 K967 V969 R973 K977 R978 S981 R988 E992 D993 K994 R1004 P1047 S1052 Y1054 R1062 H1063 N1065 K1068 I1119 A1122 K1123 K1126 R1127 K1128 K1131 R1135 R1138 R1152 K1156 K1158 F1161 A1162 N1164	Q3 R4 R11 K12 H14 V15 M17 R125 F136 K137 T141 K147 W154 Y158 G160 R177 R184 F185 F191 R192 P193 Y333 K337 K419 I420 K422 T444 R452 K455 Y456 T461 K513 K515 F524 K525 N526 T527 K549 V551 R555 K559 R560 S563 R570 E574 D575 K576 R586 P629 S634 Y636 R644 H645 N647 K650 I686 A689 K690 K693 R694 K695 K698 R702 R705 R719 K723 K725 F728 A729 N731
BS03	GTP	RJ	G79 T80 G81 K82 T83 T84 E119 H173 G209 V210 Y215	G38 T39 G40 K41 T42 T43 E78 H132 G168 V169 Y174
BS04	MG	RJ	T83 E119	T42 E78

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:6lqs, PDBe:6lqs, PDBj:6lqs
• PDBsum: 6lqs
• PubMed: 32943522
• UniProt: Q08965|BMS1_YEAST Ribosome biogenesis protein BMS1 (Gene Name=BMS1)