Structure of PDB 6zqg Chain CL

Receptor sequence

>6zqgCL (length=710) Species: 559292 (Saccharomyces cerevisiae S288C)

EQSNKQHRKAKEKNTAKKKLHTQGHNAKAFAVAAPGKMARTMQRSSDVNE
RKLHVPMVDRTPEDDPPPFIVAVVGPPGTGKTTLIRSLVRRMTKSTLNDI
QGPITVVSGKHRRLTFLECPADDLNAMIDIAKIADLVLLLIDGNFGFEME
TMEFLNIAQHHGMPRVLGVATHLDLFKSQSTLRASKKRLKHRFWTEVYQG
AKLFYLSGVINGRYPDREILNLSRFISVMKFRPLKWRNEHPYMLADRFTD
LTHPELIETQGLQIDRKVAIYGYLHGTPLPSAPGTRVHIAGVGDFSVAQI
EKLPDPCPTPFYQQKLDDFERDKDKLIYAPMSDVNIGKLIYMDNISPEEC
IRRWRGVDLEKFVPYFDTFEKLAKKWKSVDAIKERFLREMNAAKKEKLRA
QFEIEEGENFKYDTWYELQKAKISKQLEINNIEYQEMTPEQRQRIEGFKA
GSYVRIVFEKVPMEFVKNFNPKFPIVMGGLLPTEIKFGIVKARLRRHRWH
KKILKTNDPLVLSLGWRRFQTLPIYTTTDSRTRTRMLKYTPEHTYCNAAF
YGPLCSPNTPFCGVQIVANSDTGNGFRIAATGIVEEIDVNIEIVKKLKLV
GFPYKIFKNTAFIKDMFSSAMEVARFEGAQIKTVSGIRGEIKRALSKPEG
HYRAAFEDKILMSDIVILRSWYPVRVKKFYNPVTSLLLKEKTEWKGLRLT
GQIRAAMNLE

3D structure

• PDB: 6zqg 90 S pre-ribosome transformation into the primordial 40 S subunit.
• Chain: CL
• Resolution: 3.5 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	Q3 N5 K6 H8 R9 K10 H22 N27 A30 F31 A34 A35 G37 K38 R41 M43 Q44 R45 H55 V56 M58 R166 K191 Y199 R225 K231 R233 P234 E733 D748 K755 K837 I838 K840 R870 K873 Y874 T879 K931 K933 F942 K943 V969 R973 K977 R978 K982 P983 E984 R988 E992 D993	Q2 N4 K5 H7 R8 K9 H21 N26 A29 F30 A33 A34 G36 K37 R40 M42 Q43 R44 H54 V55 M57 R165 K190 Y198 R224 K230 R232 P233 E405 D413 K420 K502 I503 K505 R535 K538 Y539 T544 K596 K598 F607 K608 V634 R638 K642 R643 K647 P648 E649 R653 E657 D658
BS02	GTP	CL	P78 G81 K82 T83 T84 H173 D175	P77 G80 K81 T82 T83 H172 D174
BS03	MG	CL	T83 E119	T82 E118

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