Structure of PDB 7d63 Chain RJ

Receptor sequence

>7d63RJ (length=796) Species: 559292 (Saccharomyces cerevisiae S288C)

TMQRSSDVNERKLHVPMVDRTPEDDPPPFIVAVVGPPGTGKTTLIRSLVR
RMTKSTLNDIQGPITVVSGKHRRLTFLECPADDLNAMIDIAKIADLVLLL
IDGNFGFEMETMEFLNIAQHHGMPRVLGVATHLDLFKSQSTLRASKKRLK
HRFWTEVYQGAKLFYLSGVINGRYPDREILNLSRFISVMKFRPLKWRNEH
PYMLADRFTDLTHPELIETQGLQIDRKVAIYGYLHGTPLPSAPGTRVHIA
GVGDFSVAQIEKLPDPCPTPFRKRLDDKDKLIYAPMSDVGGVLMDKDAVY
IDIERGEGEKLMTGLQSVEQSIAEKFDGVNIGKLIYMDNISPEECIRRWR
DLEKFVPYFDTFEKLAKKWKSVDAIKERFLTWYELQKAKISKQLEINNIE
YQEMTPEQRQRIEGFKAGSYVRIVFEKVPMEFVKNFNPKFPIVMGGLLPT
EIKFGIVKARLRRHRWHKKILKTNDPLVLSLGWRRFQTLPIYTTTDSRTR
TRMLKYTPEHTYCNAAFYGPLCSPNTPFCGVQIVANSDTGNGFRIAATGI
VEEIDVNIEIVKKLKLVGFPYKIFKNTAFIKDMFSSAMEVARFEGAQIKT
VSGIRGEIKRALSKPEGHYRAAFEDKILMSDIVILRSWYPVRVKKFYNPV
TSLLLKEKTEWKGLRLTGQIRAAMNLETPSNPDSAYHKIERVERHFNGLK
VPKAVQKELPFKSQIHQMKPQKKKTYMAKRAVVLGGDEKKARSFIQKVLT
ISKAKDSKRKEQKASQRKERLKKLAKMEEEKSQRDKEKKKEYFAQN

3D structure

• PDB: 7d63 Cryo-EM structure of 90S preribosome with inactive Utp24 (state C)
• Chain: RJ
• Resolution: 12.3 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	K1154 K1157 K1158 Y1160 F1161	K786 K789 K790 Y792 F793
BS02	rna	RJ	R45 R52 R92 R166 F177 T182 R184 H192 Y199 G201 K203 L204 F205 Y206 N222 R225 F226 S228 V229 R346 K837 I838 T862 D864 S865 R868 R870 L872 K873 Y874 T879 K931 K933 F942 K943 T945 F947 K967 R973 K977 R978 S981 R988 E992 D993 K994 M997 R1004 R1039 T1046 P1047 S1052 Y1054 K1123 K1126 R1127 R1135 R1138 L1142 D1153 K1156 K1158 F1161 A1162	R4 R11 R51 R125 F136 T141 R143 H151 Y158 G160 K162 L163 F164 Y165 N181 R184 F185 S187 V188 R274 K469 I470 T494 D496 S497 R500 R502 L504 K505 Y506 T511 K563 K565 F574 K575 T577 F579 K599 R605 K609 R610 S613 R620 E624 D625 K626 M629 R636 R671 T678 P679 S684 Y686 K755 K758 R759 R767 R770 L774 D785 K788 K790 F793 A794
BS03	GTP	RJ	P78 T80 G81 K82 T83 T84 H173 V210 Y215	P37 T39 G40 K41 T42 T43 H132 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:7d63, PDBe:7d63, PDBj:7d63
• PDBsum: 7d63
• UniProt: Q08965|BMS1_YEAST Ribosome biogenesis protein BMS1 (Gene Name=BMS1)