3THT

Crystal structure and RNA binding properties of the RRM/AlkB domains in human ABH8, an enzyme catalyzing tRNA hypermodification, Northeast Structural Genomics Consortium Target HR5601B

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

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	RNA-binding domain, RBD	8039196	3000110	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	RNA-binding domain, RBD	8039196	3000110	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	RNA-binding domain, RBD	8039196	3000110	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	RNA-binding domain, RBD	8039196	3000110	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)
A	2OG-FeII_Oxy_2	e3thtA1	A: beta sandwiches	X: jelly-roll	H: Double-stranded beta-helix (From Topology)	T: Double-stranded beta-helix	F: 2OG-FeII_Oxy_2	ECOD (1.6)
A	RRM_1_1	e3thtA2	A: a+b two layers	X: Alpha-beta plaits	H: RNA-binding domain, RBD (From Topology)	T: RNA-binding domain, RBD	F: RRM_1_1	ECOD (1.6)
B	2OG-FeII_Oxy_2	e3thtB1	A: beta sandwiches	X: jelly-roll	H: Double-stranded beta-helix (From Topology)	T: Double-stranded beta-helix	F: 2OG-FeII_Oxy_2	ECOD (1.6)
B	RRM_1_1	e3thtB2	A: a+b two layers	X: Alpha-beta plaits	H: RNA-binding domain, RBD (From Topology)	T: RNA-binding domain, RBD	F: RRM_1_1	ECOD (1.6)
C	2OG-FeII_Oxy_2	e3thtC1	A: beta sandwiches	X: jelly-roll	H: Double-stranded beta-helix (From Topology)	T: Double-stranded beta-helix	F: 2OG-FeII_Oxy_2	ECOD (1.6)
C	RRM_1_1	e3thtC2	A: a+b two layers	X: Alpha-beta plaits	H: RNA-binding domain, RBD (From Topology)	T: RNA-binding domain, RBD	F: RRM_1_1	ECOD (1.6)
D	2OG-FeII_Oxy_2	e3thtD1	A: beta sandwiches	X: jelly-roll	H: Double-stranded beta-helix (From Topology)	T: Double-stranded beta-helix	F: 2OG-FeII_Oxy_2	ECOD (1.6)
D	RRM_1_1	e3thtD2	A: a+b two layers	X: Alpha-beta plaits	H: RNA-binding domain, RBD (From Topology)	T: RNA-binding domain, RBD	F: RRM_1_1	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.30.70.330	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	RRM (RNA recognition motif) domain	CATH (4.3.0)
A	2.60.120.1520	Mainly Beta	Sandwich	Jelly Rolls		CATH (4.3.0)
B	3.30.70.330	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	RRM (RNA recognition motif) domain	CATH (4.3.0)
B	2.60.120.1520	Mainly Beta	Sandwich	Jelly Rolls		CATH (4.3.0)
C	3.30.70.330	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	RRM (RNA recognition motif) domain	CATH (4.3.0)
C	2.60.120.1520	Mainly Beta	Sandwich	Jelly Rolls		CATH (4.3.0)
D	3.30.70.330	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	RRM (RNA recognition motif) domain	CATH (4.3.0)
D	2.60.120.1520	Mainly Beta	Sandwich	Jelly Rolls		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF00076	RNA recognition motif (RRM_1)	RNA recognition motif	The RRM motif (a.k.a. RRM, RBD, or RNP domain) is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and pro ...	The RRM motif (a.k.a. RRM, RBD, or RNP domain) is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and protein components of snRNPs. The motif also appears in a few single stranded DNA binding proteins. The RRM structure consists of four strands and two helices arranged in an alpha/beta sandwich, with a third helix present during RNA binding in some cases The C-terminal beta strand (4th strand) and final helix are hard to align and have been omitted in the SEED alignment The LA proteins (Swiss:P05455) have an N terminal rrm which is included in the seed. There is a second region towards the C terminus that has some features characteristic of a rrm but does not appear to have the important structural core of a rrm. The LA proteins (Swiss:P05455) are one of the main autoantigens in Systemic lupus erythematosus (SLE), an autoimmune disease.	Domain
A, B, C, D	PF13532	2OG-Fe(II) oxygenase superfamily (2OG-FeII_Oxy_2)	2OG-Fe(II) oxygenase superfamily	-	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Alkylated DNA repair protein alkB homolog 8	transferase activity, transferring one-carbon groups transferase activity methyltransferase activity S-adenosylmethionine-dependent methyltransferase activity catalytic activity tRNA (5-carboxymethyluridine(34)-5-O)-methyltransferase activity tRNA methyltransferase activity RNA methyltransferase activity catalytic activity, acting on RNA tRNA (uridine) methyltransferase activity catalytic activity, acting on a nucleic acid catalytic activity, acting on a tRNA cation binding transition metal ion binding transferase activity, transferring one-carbon groups transferase activity methyltransferase activity S-adenosylmethionine-dependent methyltransferase activity catalytic activity tRNA (5-carboxymethyluridine(34)-5-O)-methyltransferase activity tRNA methyltransferase activity RNA methyltransferase activity catalytic activity, acting on RNA tRNA (uridine) methyltransferase activity catalytic activity, acting on a nucleic acid catalytic activity, acting on a tRNA cation binding transition metal ion binding iron ion binding ion binding binding metal ion binding small molecule binding zinc ion binding oxidoreductase activity oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen 2-oxoglutarate-dependent dioxygenase activity dioxygenase activity RNA binding organic cyclic compound binding tRNA binding nucleic acid binding	cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process RNA metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process tRNA processing RNA processing tRNA modification primary metabolic process cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process RNA metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process tRNA processing RNA processing tRNA modification primary metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process macromolecule methylation tRNA metabolic process RNA modification biosynthetic process methylation macromolecule modification metabolic process macromolecule metabolic process RNA methylation tRNA methylation tRNA wobble uridine modification tRNA wobble base modification	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR051422	AlkB Family tRNA Methyltransferase/Dioxygenase	Family
A, B, C, D	IPR005123	Oxoglutarate/iron-dependent dioxygenase domain	Domain
A, B, C, D	IPR000504	RNA recognition motif domain	Domain
A, B, C, D	IPR029063	S-adenosyl-L-methionine-dependent methyltransferase superfamily	Homologous Superfamily
A, B, C, D	IPR012677	Nucleotide-binding alpha-beta plait domain superfamily	Homologous Superfamily
A, B, C, D	IPR027450	Alpha-ketoglutarate-dependent dioxygenase AlkB-like	Domain
A, B, C, D	IPR015095	Alkylated DNA repair protein AlkB, homologue 8, N-terminal	Domain
A, B, C, D	IPR034256	ALKBH8, RNA recognition motif	Domain
A, B, C, D	IPR013216	Methyltransferase type 11	Domain
A, B, C, D	IPR035979	RNA-binding domain superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C, D	Pharos: Q96BT7	Neoplasm Invasiveness breast carcinoma breast cancer pilocytic astrocytoma osteosarcoma large cell medulloblastoma ovarian cancer

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.