Structure of PDB 7d4i Chain RJ

Receptor sequence

>7d4iRJ (length=738) Species: 559292 (Saccharomyces cerevisiae S288C)

TMQRSSDVNERKLHVPMVDRTPEDDPPPFIVAVVGPPGTGKTTLIRSLVR
RMTKSTLNDIQGPITVVSGKHRRLTFLECPADDLNAMIDIAKIADLVLLL
IDGNFGFEMETMEFLNIAQHHGMPRVLGVATHLDLFKSQSTLRASKKRLK
HRFWTEVYQGAKLFYLSGVINGRYPDREILNLSRFISVMKFRPLKWRNEH
PYMLADRFTDLTHPELIETQGLQIDRKVAIYGYLHGTPLPSAPGTRVHIA
GVGDFSVAQIEKLPDPCPTPFYQQKLLIYAPMSNIGKLIYMDNISPEECI
RRWRDLEKFVPYFDTFEKLAKKWKSVDAIKERFLTWYELQKAKISKQLEI
NNIEYQEMTPEQRQRIEGFKAGSYVRIVFEKVPMEFVKNFNPKFPIVMGG
LLPTEIKFGIVKARLRRHRWHKKILKTNDPLVLSLGWRRFQTLPIYTTTD
SRTRTRMLKYTPEHTYCNAAFYGPLCSPNTPFCGVQIVANSDTGNGFRIA
ATGIVEEIDVNIEIVKKLKLVGFPYKIFKNTAFIKDMFSSAMEVARFEGA
QIKTVSGIRGEIKRALSKPEGHYRAAFEDKILMSDIVILRSWYPVRVKKF
YNPVTSLLLKEKTEWKGLRLTGQIRAAMNLETPSNPDSAYHKIERVERHF
NGLKVPKAVQKELPFKSQIAKRAVVLGGDEKKARSFIQKVLTISKAKDSK
RKEQKASQRKERLKKLAKMEEEKSQRDKEKKKEYFAQN

3D structure

• PDB: 7d4i Cryo-EM structure of 90S small ribosomal precursors complex with Dhr1
• Chain: RJ
• Resolution: 4.0 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 Y1160 F1161	K728 K731 Y734 F735
BS02	rna	RJ	T42 R45 D48 R52 K53 H55 V56 M58 R166 F177 S179 T182 R184 Y199 Q200 G201 R225 V229 K231 F232 R233 P234 Y751 K837 I838 K840 D864 S865 R868 R870 L872 K873 Y874 E877 H878 T879 K930 K931 K933 F942 K943 N944 T945 K967 V969 R973 K977 R978 S981 K982 R988 E992 D993 K994 R1004 S1052 Y1054 R1062 K1068 I1119 A1122 K1123 K1126 R1127 R1135 R1138 K1156 F1161 N1164	T1 R4 D7 R11 K12 H14 V15 M17 R125 F136 S138 T141 R143 Y158 Q159 G160 R184 V188 K190 F191 R192 P193 Y337 K423 I424 K426 D450 S451 R454 R456 L458 K459 Y460 E463 H464 T465 K516 K517 K519 F528 K529 N530 T531 K553 V555 R559 K563 R564 S567 K568 R574 E578 D579 K580 R590 S638 Y640 R648 K654 I693 A696 K697 K700 R701 R709 R712 K730 F735 N738
BS03	GTP	RJ	P78 G79 T80 G81 K82 T83 T84 H173 G209	P37 G38 T39 G40 K41 T42 T43 H132 G168

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:7d4i, PDBe:7d4i, PDBj:7d4i
• PDBsum: 7d4i
• UniProt: Q08965|BMS1_YEAST Ribosome biogenesis protein BMS1 (Gene Name=BMS1)