4QOZ | pdb_00004qoz

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)
E	SCOP2B Superfamily	Ribonuclease H-like	8043204	3000143	SCOP2B (2022-06-29)
B	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)
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)
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)

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)
E	3.30.420.10	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (utative)
E	1.10.720.30	Mainly Alpha	Orthogonal Bundle	Transcription Termination Factor Rho, Rna-binding Domain	Chain A, Domain 1	CATH (utative)
B	3.30.420.10	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (utative)
B	1.10.720.30	Mainly Alpha	Orthogonal Bundle	Transcription Termination Factor Rho, Rna-binding Domain	Chain A, Domain 1	CATH (utative)

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	This family includes a variety of exonuclease proteins, such as ribonuclease T and the epsilon subunit of DNA polymerase III.;	Domain
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 nucleic acid binding mRNA binding pre-mRNA binding histone pre-mRNA stem-loop binding identical protein binding protein binding histone pre-mRNA DCP binding	histone mRNA metabolic process mRNA 3'-end processing mRNA 3'-end processing by stem-loop binding and cleavage RNA metabolic process primary metabolic process gene expression nucleobase-containing compound biosynthetic process mRNA metabolic process macromolecule biosynthetic process mRNA processing nucleic acid metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process biosynthetic process histone mRNA metabolic process mRNA 3'-end processing mRNA 3'-end processing by stem-loop binding and cleavage RNA metabolic process primary metabolic process gene expression nucleobase-containing compound biosynthetic process mRNA metabolic process macromolecule biosynthetic process mRNA processing nucleic acid metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process biosynthetic process metabolic process cellular process RNA 3'-end processing macromolecule metabolic process RNA processing RNA transport nitrogen compound transport transport nucleic acid transport mRNA transport establishment of localization localization establishment of RNA localization macromolecule localization RNA localization nucleobase-containing compound transport cap-dependent translational initiation translation protein biosynthetic process cytoplasmic translation cytoplasmic translational initiation translational initiation protein metabolic process	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen 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
B, E	3'-5' exoribonuclease 1	hydrolase activity, acting on ester bonds nuclease activity catalytic activity, acting on a nucleic acid 3'-5' exonuclease activity hydrolase activity exonuclease activity catalytic activity pre-mRNA binding RNA binding binding nucleic acid binding histone pre-mRNA stem-loop binding rRNA binding ribonucleoprotein complex binding hydrolase activity, acting on ester bonds nuclease activity catalytic activity, acting on a nucleic acid 3'-5' exonuclease activity hydrolase activity exonuclease activity catalytic activity pre-mRNA binding RNA binding 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 RNA exonuclease activity RNA nuclease activity cation binding ion binding metal ion binding small molecule binding	regulation of biosynthetic process regulation of biological process regulation of cellular process negative regulation of metabolic process biological regulation negative regulation of biological process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulatory ncRNA-mediated gene silencing regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process regulation of biosynthetic process regulation of biological process regulation of cellular process negative regulation of metabolic process biological regulation negative regulation of biological process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulatory ncRNA-mediated gene silencing regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of cellular process regulation of macromolecule biosynthetic process metabolic process cellular process macromolecule metabolic process regulation of metabolic process negative regulation of macromolecule metabolic process ribonucleoprotein complex biogenesis RNA metabolic process primary metabolic process rRNA processing nucleobase-containing compound biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process cellular component biogenesis nucleic acid biosynthetic process ribosome biogenesis rRNA 3'-end processing RNA 3'-end processing RNA processing cellular component organization or biogenesis rRNA metabolic process 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 membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen histone pre-mRNA 3'end processing complex protein-containing complex nuclear protein-containing complex ribonucleoprotein complex cytoplasm
A, D	histone mRNA stem-loop	-	-	-

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	IPR013520	Ribonuclease H-like domain	Domain
B, E	IPR003034	SAP domain	Domain
B, E	IPR036361	SAP domain superfamily	Homologous Superfamily
B, E	IPR051274	3'-5' Exoribonuclease	Family
B, E	IPR012337	Ribonuclease H-like superfamily	Homologous Superfamily

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 U.S. National Science Foundation (DBI-2321666), 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 R01GM157729.