7C08

Crystal structure of S34Y mutant of yeast U2AF1 complex bound to 3' splice site RNA, 5'-UAGGU.

External Resource: Annotation

Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	RRM_1_6	e7c08A2	A: a+b two layers	X: Alpha-beta plaits	H: RNA-binding domain, RBD (From Topology)	T: RNA-binding domain, RBD	F: RRM_1_6	ECOD (1.6)
A	zf-CCCH	e7c08A3	A: few secondary structure elements	X: CCCH zinc finger	H: CCCH zinc finger (From Topology)	T: CCCH zinc finger	F: zf-CCCH	ECOD (1.6)
A	zf-CCCH_6	e7c08A1	A: few secondary structure elements	X: CCCH zinc finger	H: CCCH zinc finger (From Topology)	T: CCCH zinc finger	F: zf-CCCH_6	ECOD (1.6)
D	RRM_1_6	e7c08D3	A: a+b two layers	X: Alpha-beta plaits	H: RNA-binding domain, RBD (From Topology)	T: RNA-binding domain, RBD	F: RRM_1_6	ECOD (1.6)
D	zf-CCCH	e7c08D1	A: few secondary structure elements	X: CCCH zinc finger	H: CCCH zinc finger (From Topology)	T: CCCH zinc finger	F: zf-CCCH	ECOD (1.6)
D	zf-CCCH_6	e7c08D2	A: few secondary structure elements	X: CCCH zinc finger	H: CCCH zinc finger (From Topology)	T: CCCH zinc finger	F: zf-CCCH_6	ECOD (1.6)
G	RRM_1_6	e7c08G1	A: a+b two layers	X: Alpha-beta plaits	H: RNA-binding domain, RBD (From Topology)	T: RNA-binding domain, RBD	F: RRM_1_6	ECOD (1.6)
G	zf-CCCH	e7c08G3	A: few secondary structure elements	X: CCCH zinc finger	H: CCCH zinc finger (From Topology)	T: CCCH zinc finger	F: zf-CCCH	ECOD (1.6)
G	zf-CCCH_6	e7c08G2	A: few secondary structure elements	X: CCCH zinc finger	H: CCCH zinc finger (From Topology)	T: CCCH zinc finger	F: zf-CCCH_6	ECOD (1.6)
J	RRM_1_6	e7c08J1	A: a+b two layers	X: Alpha-beta plaits	H: RNA-binding domain, RBD (From Topology)	T: RNA-binding domain, RBD	F: RRM_1_6	ECOD (1.6)
J	zf-CCCH	e7c08J3	A: few secondary structure elements	X: CCCH zinc finger	H: CCCH zinc finger (From Topology)	T: CCCH zinc finger	F: zf-CCCH	ECOD (1.6)
J	zf-CCCH_6	e7c08J2	A: few secondary structure elements	X: CCCH zinc finger	H: CCCH zinc finger (From Topology)	T: CCCH zinc finger	F: zf-CCCH_6	ECOD (1.6)
M	RRM_1_6	e7c08M3	A: a+b two layers	X: Alpha-beta plaits	H: RNA-binding domain, RBD (From Topology)	T: RNA-binding domain, RBD	F: RRM_1_6	ECOD (1.6)
M	zf-CCCH	e7c08M1	A: few secondary structure elements	X: CCCH zinc finger	H: CCCH zinc finger (From Topology)	T: CCCH zinc finger	F: zf-CCCH	ECOD (1.6)
M	zf-CCCH_6	e7c08M2	A: few secondary structure elements	X: CCCH zinc finger	H: CCCH zinc finger (From Topology)	T: CCCH zinc finger	F: zf-CCCH_6	ECOD (1.6)
P	RRM_1_6	e7c08P1	A: a+b two layers	X: Alpha-beta plaits	H: RNA-binding domain, RBD (From Topology)	T: RNA-binding domain, RBD	F: RRM_1_6	ECOD (1.6)
P	zf-CCCH	e7c08P2	A: few secondary structure elements	X: CCCH zinc finger	H: CCCH zinc finger (From Topology)	T: CCCH zinc finger	F: zf-CCCH	ECOD (1.6)
P	zf-CCCH_6	e7c08P3	A: few secondary structure elements	X: CCCH zinc finger	H: CCCH zinc finger (From Topology)	T: CCCH zinc finger	F: zf-CCCH_6	ECOD (1.6)
S	RRM_1_6	e7c08S2	A: a+b two layers	X: Alpha-beta plaits	H: RNA-binding domain, RBD (From Topology)	T: RNA-binding domain, RBD	F: RRM_1_6	ECOD (1.6)
S	zf-CCCH	e7c08S3	A: few secondary structure elements	X: CCCH zinc finger	H: CCCH zinc finger (From Topology)	T: CCCH zinc finger	F: zf-CCCH	ECOD (1.6)
S	zf-CCCH_6	e7c08S1	A: few secondary structure elements	X: CCCH zinc finger	H: CCCH zinc finger (From Topology)	T: CCCH zinc finger	F: zf-CCCH_6	ECOD (1.6)
V	RRM_1_6	e7c08V1	A: a+b two layers	X: Alpha-beta plaits	H: RNA-binding domain, RBD (From Topology)	T: RNA-binding domain, RBD	F: RRM_1_6	ECOD (1.6)
V	zf-CCCH	e7c08V3	A: few secondary structure elements	X: CCCH zinc finger	H: CCCH zinc finger (From Topology)	T: CCCH zinc finger	F: zf-CCCH	ECOD (1.6)
V	zf-CCCH_6	e7c08V2	A: few secondary structure elements	X: CCCH zinc finger	H: CCCH zinc finger (From Topology)	T: CCCH zinc finger	F: zf-CCCH_6	ECOD (1.6)
Y	RRM_1_6	e7c08Y1	A: a+b two layers	X: Alpha-beta plaits	H: RNA-binding domain, RBD (From Topology)	T: RNA-binding domain, RBD	F: RRM_1_6	ECOD (1.6)
Y	zf-CCCH	e7c08Y2	A: few secondary structure elements	X: CCCH zinc finger	H: CCCH zinc finger (From Topology)	T: CCCH zinc finger	F: zf-CCCH	ECOD (1.6)
Y	zf-CCCH_6	e7c08Y3	A: few secondary structure elements	X: CCCH zinc finger	H: CCCH zinc finger (From Topology)	T: CCCH zinc finger	F: zf-CCCH_6	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, D, G, J, M A, D, G, J, M, P, S, V, Y	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, D, G, J, M A, D, G, J, M, P, S, V, Y	PF00642	Zinc finger C-x8-C-x5-C-x3-H type (and similar) (zf-CCCH)	Zinc finger C-x8-C-x5-C-x3-H type (and similar)	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, D, G, J, M A, D, G, J, M, P, S, V, Y	Splicing factor U2AF 23 kDa subunit	pre-mRNA binding RNA binding pre-mRNA 3'-splice site binding binding organic cyclic compound binding nucleic acid binding cation binding ion binding metal ion binding small molecule binding	cellular biosynthetic process RNA metabolic process mRNA processing nucleobase-containing compound metabolic process organic substance metabolic process heterocycle metabolic process organic substance biosynthetic process nitrogen compound metabolic process RNA processing RNA splicing cellular metabolic process cellular nitrogen compound metabolic process primary metabolic process gene expression cellular biosynthetic process RNA metabolic process mRNA processing nucleobase-containing compound metabolic process organic substance metabolic process heterocycle metabolic process organic substance biosynthetic process nitrogen compound metabolic process RNA processing RNA splicing cellular metabolic process cellular nitrogen compound 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 cis splicing, via spliceosome mRNA splicing, via spliceosome metabolic process cellular process RNA splicing, via transesterification reactions with bulged adenosine as nucleophile macromolecule metabolic process cellular aromatic compound metabolic process ribonucleoprotein complex biogenesis protein-RNA complex assembly cellular component organization cellular component biogenesis spliceosomal complex assembly protein-RNA complex organization cellular component assembly protein-containing complex assembly cellular component organization or biogenesis mRNA splice site recognition mRNA 3'-splice site recognition protein-containing complex organization	membrane-bounded organelle protein-containing complex intracellular anatomical structure nucleus nuclear protein-containing complex intracellular membrane-bounded organelle cellular anatomical entity intracellular organelle spliceosomal complex organelle ribonucleoprotein complex cytoplasm cytosol U2AF complex membrane-bounded organelle protein-containing complex intracellular anatomical structure nucleus nuclear protein-containing complex intracellular membrane-bounded organelle cellular anatomical entity intracellular organelle spliceosomal complex organelle ribonucleoprotein complex cytoplasm cytosol U2AF complex U2-type spliceosomal complex commitment complex prespliceosome U2-type prespliceosome
B, E, H, K, N B, E, H, K, N, Q, T, W, Z	Splicing factor U2AF 59 kDa subunit	RNA binding binding organic cyclic compound binding nucleic acid binding mRNA binding poly-pyrimidine tract binding single-stranded RNA binding pre-mRNA binding pre-mRNA 3'-splice site 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 heterocycle 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 heterocycle metabolic process protein-containing complex assembly organic substance biosynthetic process nitrogen compound metabolic process cellular component organization or biogenesis RNA processing RNA splicing protein-containing complex organization cellular metabolic process cellular nitrogen compound 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 cellular aromatic compound metabolic process mRNA cis splicing, via spliceosome mRNA branch site recognition	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen cellular anatomical entity intracellular membrane-bounded organelle intracellular organelle lumen nuclear speck nuclear body intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen cellular anatomical entity intracellular membrane-bounded organelle intracellular organelle lumen nuclear speck nuclear body intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen protein-containing complex U2AF complex nuclear protein-containing complex U2-type spliceosomal complex spliceosomal complex ribonucleoprotein complex commitment complex prespliceosome U2-type prespliceosome
AA [auth 1], C, F, I, L, AA [auth 1], C, F, I, L, O, R, U, X	RNA (5'-R(UUPAPGPGPU)-3')	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, D, G, J, M A, D, G, J, M, P, S, V, Y	IPR003954	RNA recognition motif domain, eukaryote	Domain
A, D, G, J, M A, D, G, J, M, P, S, V, Y	IPR000504	RNA recognition motif domain	Domain
A, D, G, J, M A, D, G, J, M, P, S, V, Y	IPR000571	Zinc finger, CCCH-type	Domain
A, D, G, J, M A, D, G, J, M, P, S, V, Y	IPR009145	U2 auxiliary factor small subunit	Family
A, D, G, J, M A, D, G, J, M, P, S, V, Y	IPR012677	Nucleotide-binding alpha-beta plait domain superfamily	Homologous Superfamily
A, D, G, J, M A, D, G, J, M, P, S, V, Y	IPR035979	RNA-binding domain superfamily	Homologous Superfamily
B, E, H, K, N B, E, H, K, N, Q, T, W, Z	IPR006529	U2 snRNP auxilliary factor, large subunit, splicing factor	Family
B, E, H, K, N B, E, H, K, N, Q, T, W, Z	IPR000504	RNA recognition motif domain	Domain
B, E, H, K, N B, E, H, K, N, Q, T, W, Z	IPR012677	Nucleotide-binding alpha-beta plait domain superfamily	Homologous Superfamily
B, E, H, K, N B, E, H, K, N, Q, T, W, Z	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.

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7C08

Crystal structure of S34Y mutant of yeast U2AF1 complex bound to 3' splice site RNA, 5'-UAGGU.

External Resource: Annotation

Domain Annotation: ECOD Classification ECOD Database Homepage

Protein Family Annotation Pfam Database Homepage

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

InterPro: Protein Family Classification InterPro Database Homepage