Structure of PDB 7ajt Chain CL

Receptor sequence

>7ajtCL (length=781) Species: 559292 (Saccharomyces cerevisiae S288C)

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

3D structure

• PDB: 7ajt Structure of the Maturing 90S Pre-ribosome in Association with the RNA Exosome.
• Chain: CL
• Resolution: 4.6 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	CL	L1067 S1081 Q1082 I1083 Q1085 M1086 P1088 Q1089 K1091 T1093 Y1094 K1107 R1110 S1111 Q1114 L1117 T1118	L684 S698 Q699 I700 Q702 M703 P705 Q706 K708 T710 Y711 K724 R727 S728 Q731 L734 T735
BS02	rna	CL	K38 R45 D48 R52 K53 H55 V56 M58 R166 K178 R184 K191 Y199 Q200 G201 R218 N222 R225 K231 F232 R233 Y751 K755 K837 I838 K840 T862 D864 S865 T867 R868 R870 K873 Y874 E877 H878 T879 K930 K931 K933 K940 F942 K943 N944 T945 F947 K967 V969 K977 R978 L980 S981 R988 E992 D993 K994 L996 M997 I1002 R1039 T1046 N1049 S1052 Y1054 R1062 H1063 N1065 K1123 K1126 R1127 R1135 R1138 K1140 L1142 K1156 F1161	K3 R10 D13 R17 K18 H20 V21 M23 R131 K143 R149 K156 Y164 Q165 G166 R183 N187 R190 K196 F197 R198 Y368 K372 K454 I455 K457 T479 D481 S482 T484 R485 R487 K490 Y491 E494 H495 T496 K547 K548 K550 K557 F559 K560 N561 T562 F564 K584 V586 K594 R595 L597 S598 R605 E609 D610 K611 L613 M614 I619 R656 T663 N666 S669 Y671 R679 H680 N682 K740 K743 R744 R752 R755 K757 L759 K773 F778
BS03	rna	CL	K1154 K1157 Y1160 F1161	K771 K774 Y777 F778
BS04	GTP	CL	P78 T80 G81 K82 T83 T84 T172 H173 G209 V210 Y215	P43 T45 G46 K47 T48 T49 T137 H138 G174 V175 Y180
BS05	MG	CL	K82 T83 E119	K47 T48 E84

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:7ajt, PDBe:7ajt, PDBj:7ajt
• PDBsum: 7ajt
• PubMed: 33326748
• UniProt: Q08965|BMS1_YEAST Ribosome biogenesis protein BMS1 (Gene Name=BMS1)