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


Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
ASCOP2B SuperfamilyRNA-binding domain, RBD 8039196 3000110 SCOP2B (2022-06-29)
BSCOP2B SuperfamilyRNA-binding domain, RBD 8039196 3000110 SCOP2B (2022-06-29)
CSCOP2B SuperfamilyRNA-binding domain, RBD 8039196 3000110 SCOP2B (2022-06-29)
DSCOP2B SuperfamilyRNA-binding domain, RBD 8039196 3000110 SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
A2OG-FeII_Oxy_2e3thtA1 A: beta sandwichesX: jelly-rollH: Double-stranded beta-helix (From Topology)T: Double-stranded beta-helixF: 2OG-FeII_Oxy_2ECOD (1.6)
ARRM_1_1e3thtA2 A: a+b two layersX: Alpha-beta plaitsH: RNA-binding domain, RBD (From Topology)T: RNA-binding domain, RBDF: RRM_1_1ECOD (1.6)
B2OG-FeII_Oxy_2e3thtB1 A: beta sandwichesX: jelly-rollH: Double-stranded beta-helix (From Topology)T: Double-stranded beta-helixF: 2OG-FeII_Oxy_2ECOD (1.6)
BRRM_1_1e3thtB2 A: a+b two layersX: Alpha-beta plaitsH: RNA-binding domain, RBD (From Topology)T: RNA-binding domain, RBDF: RRM_1_1ECOD (1.6)
C2OG-FeII_Oxy_2e3thtC1 A: beta sandwichesX: jelly-rollH: Double-stranded beta-helix (From Topology)T: Double-stranded beta-helixF: 2OG-FeII_Oxy_2ECOD (1.6)
CRRM_1_1e3thtC2 A: a+b two layersX: Alpha-beta plaitsH: RNA-binding domain, RBD (From Topology)T: RNA-binding domain, RBDF: RRM_1_1ECOD (1.6)
D2OG-FeII_Oxy_2e3thtD1 A: beta sandwichesX: jelly-rollH: Double-stranded beta-helix (From Topology)T: Double-stranded beta-helixF: 2OG-FeII_Oxy_2ECOD (1.6)
DRRM_1_1e3thtD2 A: a+b two layersX: Alpha-beta plaitsH: RNA-binding domain, RBD (From Topology)T: RNA-binding domain, RBDF: RRM_1_1ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

ChainDomainClassArchitectureTopologyHomologyProvenance Source (Version)
A3.30.70.330 Alpha Beta 2-Layer Sandwich Alpha-Beta Plaits RRM (RNA recognition motif) domainCATH (4.3.0)
A2.60.120.1520 Mainly Beta Sandwich Jelly Rolls CATH (4.3.0)
B3.30.70.330 Alpha Beta 2-Layer Sandwich Alpha-Beta Plaits RRM (RNA recognition motif) domainCATH (4.3.0)
B2.60.120.1520 Mainly Beta Sandwich Jelly Rolls CATH (4.3.0)
C3.30.70.330 Alpha Beta 2-Layer Sandwich Alpha-Beta Plaits RRM (RNA recognition motif) domainCATH (4.3.0)
C2.60.120.1520 Mainly Beta Sandwich Jelly Rolls CATH (4.3.0)
D3.30.70.330 Alpha Beta 2-Layer Sandwich Alpha-Beta Plaits RRM (RNA recognition motif) domainCATH (4.3.0)
D2.60.120.1520 Mainly Beta Sandwich Jelly Rolls CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
A, B, C, D
PF00076RNA recognition motif (RRM_1)RNA recognition motifThe 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
PF135322OG-Fe(II) oxygenase superfamily (2OG-FeII_Oxy_2)2OG-Fe(II) oxygenase superfamily- Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
A, B, C, D
Alkylated DNA repair protein alkB homolog 8