4QOZ

Crystal structure of the histone mRNA stem-loop, stem-loop binding protein (phosphorylated), and 3'hExo ternary complex

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations
Protein Modification Annotation

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
C	SCOP2 Family	Histone RNA hairpin-binding protein RBD-like	8051011	4007154	SCOP2 (2022-06-29)
C	SCOP2 Superfamily	Histone RNA hairpin-binding protein RBD-like	8052385	3002113	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	Ribonuclease H-like	8043204	3000143	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Ribonuclease H-like	8043204	3000143	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
C	SLBP_RNA_bind	e4qozC1	A: alpha arrays	X: Histone RNA hairpin-binding protein RNA-binding domain (From Topology)	H: Histone RNA hairpin-binding protein RNA-binding domain (From Topology)	T: Histone RNA hairpin-binding protein RNA-binding domain	F: SLBP_RNA_bind	ECOD (1.6)
B	SAP	e4qozB1	A: alpha arrays	X: LEM/SAP HeH motif-like	H: LEM/SAP HeH motif	T: LEM/SAP HeH motif	F: SAP	ECOD (1.6)
B	RNase_T	e4qozB2	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: RNase_T	ECOD (1.6)
E	SAP	e4qozE1	A: alpha arrays	X: LEM/SAP HeH motif-like	H: LEM/SAP HeH motif	T: LEM/SAP HeH motif	F: SAP	ECOD (1.6)
E	RNase_T	e4qozE2	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: RNase_T	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C	1.10.8.1120	Mainly Alpha	Orthogonal Bundle	Helicase, Ruva Protein	domain 3	CATH (4.3.0)
B	3.30.420.10	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (4.3.0)
B	1.10.720.30	Mainly Alpha	Orthogonal Bundle	Transcription Termination Factor Rho, Rna-binding Domain	Chain A, Domain 1	CATH (4.3.0)
E	3.30.420.10	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (4.3.0)
E	1.10.720.30	Mainly Alpha	Orthogonal Bundle	Transcription Termination Factor Rho, Rna-binding Domain	Chain A, Domain 1	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C	PF15247	Histone RNA hairpin-binding protein RNA-binding domain (SLBP_RNA_bind)	Histone RNA hairpin-binding protein RNA-binding domain	-	Family
B, E	PF00929	Exonuclease (RNase_T)	Exonuclease	-	Family
B, E	PF02037	SAP domain (SAP)	SAP domain	The SAP (after SAF-A/B, Acinus and PIAS) motif is a putative DNA/RNA binding domain found in diverse nuclear and cytoplasmic proteins.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C	Histone RNA hairpin-binding protein	RNA binding binding organic cyclic compound binding nucleic acid binding mRNA binding pre-mRNA binding histone pre-mRNA stem-loop binding identical protein binding protein binding histone pre-mRNA DCP binding	cellular biosynthetic process RNA metabolic process mRNA processing nucleobase-containing compound metabolic process organic substance metabolic process organic substance biosynthetic process RNA 3'-end processing RNA processing histone mRNA metabolic process mRNA 3'-end processing cellular metabolic process mRNA 3'-end processing by stem-loop binding and cleavage primary metabolic process gene expression cellular biosynthetic process RNA metabolic process mRNA processing nucleobase-containing compound metabolic process organic substance metabolic process organic substance biosynthetic process RNA 3'-end processing RNA processing histone mRNA metabolic process mRNA 3'-end processing cellular metabolic process mRNA 3'-end processing by stem-loop binding and cleavage primary metabolic process gene expression macromolecule biosynthetic process mRNA metabolic process nucleic acid metabolic process organic cyclic compound metabolic process biosynthetic process nucleic acid catabolic process metabolic process cellular process macromolecule metabolic process RNA transport nitrogen compound transport transport organic substance transport nucleic acid transport mRNA transport establishment of localization localization establishment of RNA localization macromolecule localization RNA localization nucleobase-containing compound transport organonitrogen compound metabolic process cap-dependent translational initiation organonitrogen compound biosynthetic process translation cytoplasmic translation cytoplasmic translational initiation translational initiation protein metabolic process	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle cellular anatomical entity nucleolus intracellular organelle lumen intracellular organelle organelle lumen organelle intracellular non-membrane-bounded organelle nuclear lumen non-membrane-bounded organelle membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle cellular anatomical entity nucleolus intracellular organelle lumen intracellular organelle organelle lumen organelle intracellular non-membrane-bounded organelle nuclear lumen non-membrane-bounded organelle histone pre-mRNA 3'end processing complex protein-containing complex nuclear protein-containing complex ribonucleoprotein complex cytoplasm cytosol nucleoplasm histone mRNA stem-loop binding complex
A, D	histone mRNA stem-loop	-	-	-
B, E	3'-5' exoribonuclease 1	nuclease activity hydrolase activity, acting on ester bonds 3'-5' exonuclease activity hydrolase activity exonuclease activity catalytic activity pre-mRNA binding RNA binding binding organic cyclic compound binding nucleic acid binding histone pre-mRNA stem-loop binding rRNA binding ribonucleoprotein complex binding nuclease activity hydrolase activity, acting on ester bonds 3'-5' exonuclease activity hydrolase activity exonuclease activity catalytic activity pre-mRNA binding RNA binding binding organic cyclic compound binding nucleic acid binding histone pre-mRNA stem-loop binding rRNA binding ribonucleoprotein complex binding protein-containing complex binding ribosome binding 3'-5'-RNA exonuclease activity catalytic activity, acting on RNA RNA exonuclease activity, producing 5'-phosphomonoesters catalytic activity, acting on a nucleic acid RNA exonuclease activity RNA nuclease activity exonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters cation binding ion binding metal ion binding small molecule binding	regulation of cellular process cellular biosynthetic process negative regulation of biological process negative regulation of cellular metabolic process organic substance metabolic process organic substance biosynthetic process negative regulation of cellular process negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of biological process cellular metabolic process negative regulation of metabolic process biological regulation regulation of cellular metabolic process regulation of cellular process cellular biosynthetic process negative regulation of biological process negative regulation of cellular metabolic process organic substance metabolic process organic substance biosynthetic process negative regulation of cellular process negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of biological process cellular metabolic process negative regulation of metabolic process biological regulation regulation of cellular metabolic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process negative regulation of cellular biosynthetic process regulatory ncRNA-mediated gene silencing regulation of cellular biosynthetic process regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process regulation of macromolecule biosynthetic process metabolic process cellular process macromolecule metabolic process regulation of metabolic process ribonucleoprotein complex biogenesis RNA metabolic process rRNA processing nucleobase-containing compound metabolic process cellular component biogenesis ribosome biogenesis RNA 3'-end processing RNA processing cellular component organization or biogenesis rRNA metabolic process primary metabolic process nucleic acid metabolic process organic cyclic compound metabolic process ncRNA metabolic process nucleic acid catabolic process rRNA 3'-end processing exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) maturation of 5.8S rRNA maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle cellular anatomical entity nucleolus intracellular organelle lumen intracellular organelle organelle lumen organelle intracellular non-membrane-bounded organelle nuclear lumen non-membrane-bounded organelle membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle cellular anatomical entity nucleolus intracellular organelle lumen intracellular organelle organelle lumen organelle intracellular non-membrane-bounded organelle nuclear lumen non-membrane-bounded organelle histone pre-mRNA 3'end processing complex protein-containing complex nuclear protein-containing complex ribonucleoprotein complex cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C	IPR038294	SLBP, RNA-binding domain superfamily	Homologous Superfamily
C	IPR029344	Histone RNA hairpin-binding protein, RNA-binding domain	Domain
C	IPR026502	Histone RNA stem-loop-binding protein SLBP1/SLBP2	Family
B, E	IPR036397	Ribonuclease H superfamily	Homologous Superfamily
B, E	IPR047201	ERI-1-like, DEDDh 3'-5' exonuclease domain	Domain
B, E	IPR003034	SAP domain	Domain
B, E	IPR036361	SAP domain superfamily	Homologous Superfamily
B, E	IPR012337	Ribonuclease H-like superfamily	Homologous Superfamily
B, E	IPR013520	Exonuclease, RNase T/DNA polymerase III	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
C	Pharos: Q14493	IgA glomerulonephritis lymphoplasmacytic lymphoma ovarian cancer juvenile dermatomyositis malignant colon neoplasm psoriasis lung cancer osteoarthritis
B, E	Pharos: Q8IV48	atypical teratoid rhabdoid tumor glioblastoma malignant glioma pilocytic astrocytoma subependymal giant cell astrocytoma breast cancer large cell medulloblastoma medulloblastoma primitive neuroectodermal tumor ulcerative colitis chronic obstructive pulmonary disease malignant ependymoma ovarian cancer Sjogren syndrome

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
C	TPO	Parent Component: THR RESID: AA0038 PSI-MOD : O-phospho-L-threonine MOD:00047

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.