5TF6

Structure and conformational plasticity of the U6 small nuclear ribonucleoprotein core

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

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	8093095	3000110	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	RNA-binding domain RBD	8093096	3000110	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	RNA-binding domain RBD	8093094	3000110	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	RNA-binding domain RBD	8093090	3000110	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	RNA-binding domain RBD	8093096	3000110	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	RNA-binding domain RBD	8093094	3000110	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	RNA-binding domain RBD	8093095	3000110	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	RNA-binding domain RBD	8093090	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	RRM_1_1	e5tf6A3	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)
A	RRM_occluded	e5tf6A4	A: a+b two layers	X: Alpha-beta plaits	H: RNA-binding domain, RBD (From Topology)	T: RNA-binding domain, RBD	F: RRM_occluded	ECOD (1.6)
C	RRM_1_1	e5tf6C3	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	RRM_occluded	e5tf6C1	A: a+b two layers	X: Alpha-beta plaits	H: RNA-binding domain, RBD (From Topology)	T: RNA-binding domain, RBD	F: RRM_occluded	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)
C	3.30.70.330	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	RRM (RNA recognition motif) domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C	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, C	PF16842	Occluded RNA-recognition motif (RRM_occluded)	Occluded RNA-recognition motif	This family is an unusual, usually C-terminal, RNA-recognition motif found in fungi. In yeast it is the fourth RRM domain on the essential splicing factor Prp24. Structurally, it has a non-canonical RRM fold with the expected beta-aloha-beta-beta-alp ...	This family is an unusual, usually C-terminal, RNA-recognition motif found in fungi. In yeast it is the fourth RRM domain on the essential splicing factor Prp24. Structurally, it has a non-canonical RRM fold with the expected beta-aloha-beta-beta-alpha-beta RRM-fold is flanked by N- and C-terminal alpha-helices. These two additional flanking alpha-helices occlude the beta-sheet face. The electropositive surface thereby presented is an alternative RNA-binding surface that allows both binding and unwinding of the U6 small nuclear RNA's internal stem loop, at least in vitro [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, C	U4/U6 snRNA-associated-splicing factor PRP24	RNA binding snRNA binding binding organic cyclic compound binding nucleic acid binding U6 snRNA binding	ribonucleoprotein complex biogenesis cellular biosynthetic process RNA metabolic process mRNA processing protein-RNA complex assembly cellular component organization cellular component biogenesis nucleobase-containing compound metabolic process spliceosomal complex assembly protein-RNA complex organization cellular component assembly organic substance metabolic process protein-containing complex assembly organic substance biosynthetic process ribonucleoprotein complex biogenesis cellular biosynthetic process RNA metabolic process mRNA processing protein-RNA complex assembly cellular component organization cellular component biogenesis nucleobase-containing compound metabolic process spliceosomal complex assembly protein-RNA complex organization cellular component assembly organic substance metabolic process protein-containing complex assembly organic substance biosynthetic process cellular component organization or biogenesis RNA processing RNA splicing protein-containing complex organization cellular metabolic process primary metabolic process gene expression mRNA metabolic process macromolecule biosynthetic process nucleic acid metabolic process organic cyclic compound metabolic process biosynthetic process RNA splicing, via transesterification reactions mRNA splicing, via spliceosome cellular process metabolic process RNA splicing, via transesterification reactions with bulged adenosine as nucleophile macromolecule metabolic process spliceosomal tri-snRNP complex assembly spliceosomal snRNP assembly	membrane-bounded organelle spliceosomal snRNP complex protein-containing complex U6 snRNP intracellular anatomical structure nucleus nuclear protein-containing complex Sm-like protein family complex intracellular membrane-bounded organelle cellular anatomical entity intracellular organelle small nuclear ribonucleoprotein complex organelle ribonucleoprotein complex membrane-bounded organelle spliceosomal snRNP complex protein-containing complex U6 snRNP intracellular anatomical structure nucleus nuclear protein-containing complex Sm-like protein family complex intracellular membrane-bounded organelle cellular anatomical entity intracellular organelle small nuclear ribonucleoprotein complex organelle ribonucleoprotein complex spliceosomal complex
B, D	U6 snRNA	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C	IPR034397	Prp24, RNA recognition motif1	Domain
A, C	IPR000504	RNA recognition motif domain	Domain
A, C	IPR034398	Prp24, RNA recognition motif2	Domain
A, C	IPR008669	LSM-interacting domain	Domain
A, C	IPR012677	Nucleotide-binding alpha-beta plait domain superfamily	Homologous Superfamily
A, C	IPR031766	Occluded RNA-recognition motif	Domain
A, C	IPR034540	Prp24, RNA recognition motif 3	Domain
A, C	IPR035979	RNA-binding domain superfamily	Homologous Superfamily

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.