3DXB

Structure of the UHM domain of Puf60 fused to thioredoxin

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	8065225	3000110	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	RNA-binding domain, RBD	8065225	3000110	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	RNA-binding domain, RBD	8065225	3000110	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	RNA-binding domain, RBD	8065225	3000110	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	RNA-binding domain, RBD	8065225	3000110	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	RNA-binding domain, RBD	8065225	3000110	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	RNA-binding domain, RBD	8065225	3000110	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	RNA-binding domain, RBD	8065225	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_9	e3dxbA2	A: a+b two layers	X: Alpha-beta plaits	H: RNA-binding domain, RBD (From Topology)	T: RNA-binding domain, RBD	F: RRM_1_9	ECOD (1.6)
A	Thioredoxin	e3dxbA1	A: a+b three layers	X: Thioredoxin-like	H: Thioredoxin-like (From Topology)	T: Thioredoxin-like	F: Thioredoxin	ECOD (1.6)
B	RRM_1_9	e3dxbB4	A: a+b two layers	X: Alpha-beta plaits	H: RNA-binding domain, RBD (From Topology)	T: RNA-binding domain, RBD	F: RRM_1_9	ECOD (1.6)
B	Thioredoxin	e3dxbB3	A: a+b three layers	X: Thioredoxin-like	H: Thioredoxin-like (From Topology)	T: Thioredoxin-like	F: Thioredoxin	ECOD (1.6)
C	RRM_1_9	e3dxbC1	A: a+b two layers	X: Alpha-beta plaits	H: RNA-binding domain, RBD (From Topology)	T: RNA-binding domain, RBD	F: RRM_1_9	ECOD (1.6)
C	Thioredoxin	e3dxbC2	A: a+b three layers	X: Thioredoxin-like	H: Thioredoxin-like (From Topology)	T: Thioredoxin-like	F: Thioredoxin	ECOD (1.6)
D	RRM_1_9	e3dxbD1	A: a+b two layers	X: Alpha-beta plaits	H: RNA-binding domain, RBD (From Topology)	T: RNA-binding domain, RBD	F: RRM_1_9	ECOD (1.6)
D	Thioredoxin	e3dxbD2	A: a+b three layers	X: Thioredoxin-like	H: Thioredoxin-like (From Topology)	T: Thioredoxin-like	F: Thioredoxin	ECOD (1.6)
E	RRM_1_9	e3dxbE1	A: a+b two layers	X: Alpha-beta plaits	H: RNA-binding domain, RBD (From Topology)	T: RNA-binding domain, RBD	F: RRM_1_9	ECOD (1.6)
E	Thioredoxin	e3dxbE2	A: a+b three layers	X: Thioredoxin-like	H: Thioredoxin-like (From Topology)	T: Thioredoxin-like	F: Thioredoxin	ECOD (1.6)
F	RRM_1_9	e3dxbF4	A: a+b two layers	X: Alpha-beta plaits	H: RNA-binding domain, RBD (From Topology)	T: RNA-binding domain, RBD	F: RRM_1_9	ECOD (1.6)
F	Thioredoxin	e3dxbF3	A: a+b three layers	X: Thioredoxin-like	H: Thioredoxin-like (From Topology)	T: Thioredoxin-like	F: Thioredoxin	ECOD (1.6)
G	RRM_1_9	e3dxbG4	A: a+b two layers	X: Alpha-beta plaits	H: RNA-binding domain, RBD (From Topology)	T: RNA-binding domain, RBD	F: RRM_1_9	ECOD (1.6)
G	Thioredoxin	e3dxbG3	A: a+b three layers	X: Thioredoxin-like	H: Thioredoxin-like (From Topology)	T: Thioredoxin-like	F: Thioredoxin	ECOD (1.6)
H	RRM_1_9	e3dxbH4	A: a+b two layers	X: Alpha-beta plaits	H: RNA-binding domain, RBD (From Topology)	T: RNA-binding domain, RBD	F: RRM_1_9	ECOD (1.6)
H	Thioredoxin	e3dxbH3	A: a+b three layers	X: Thioredoxin-like	H: Thioredoxin-like (From Topology)	T: Thioredoxin-like	F: Thioredoxin	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.30.10	Alpha Beta	3-Layer(aba) Sandwich	Glutaredoxin	Glutaredoxin	CATH (4.3.0)
A	3.30.70.330	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	RRM (RNA recognition motif) domain	CATH (4.3.0)
B	3.40.30.10	Alpha Beta	3-Layer(aba) Sandwich	Glutaredoxin	Glutaredoxin	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)
C	3.40.30.10	Alpha Beta	3-Layer(aba) Sandwich	Glutaredoxin	Glutaredoxin	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)
D	3.40.30.10	Alpha Beta	3-Layer(aba) Sandwich	Glutaredoxin	Glutaredoxin	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)
E	3.40.30.10	Alpha Beta	3-Layer(aba) Sandwich	Glutaredoxin	Glutaredoxin	CATH (4.3.0)
E	3.30.70.330	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	RRM (RNA recognition motif) domain	CATH (4.3.0)
F	3.40.30.10	Alpha Beta	3-Layer(aba) Sandwich	Glutaredoxin	Glutaredoxin	CATH (4.3.0)
F	3.30.70.330	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	RRM (RNA recognition motif) domain	CATH (4.3.0)
G	3.40.30.10	Alpha Beta	3-Layer(aba) Sandwich	Glutaredoxin	Glutaredoxin	CATH (4.3.0)
G	3.30.70.330	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	RRM (RNA recognition motif) domain	CATH (4.3.0)
H	3.40.30.10	Alpha Beta	3-Layer(aba) Sandwich	Glutaredoxin	Glutaredoxin	CATH (4.3.0)
H	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, B, C, D, E A, B, C, D, E, F, G, H	PF00085	Thioredoxin (Thioredoxin)	Thioredoxin	Thioredoxins are small enzymes that participate in redox reactions, via the reversible oxidation of an active centre disulfide bond. Some members with only the active site are not separated from the noise.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E A, B, C, D, E, F, G, H	thioredoxin N-terminally fused to Puf60(UHM)	oxidoreductase activity, acting on a sulfur group of donors disulfide oxidoreductase activity oxidoreductase activity catalytic activity, acting on a protein protein-disulfide reductase activity catalytic activity DNA binding binding nucleic acid binding cell adhesion molecule binding cadherin binding protein binding RNA binding identical protein binding	cell redox homeostasis cellular homeostasis homeostatic process ribonucleoprotein complex biogenesis RNA metabolic process mRNA processing protein-RNA complex assembly cellular component organization cellular component biogenesis nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process spliceosomal complex assembly protein-RNA complex organization cell redox homeostasis cellular homeostasis homeostatic process ribonucleoprotein complex biogenesis RNA metabolic process mRNA processing protein-RNA complex assembly cellular component organization cellular component biogenesis nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process spliceosomal complex assembly protein-RNA complex organization cellular component assembly protein-containing complex assembly cellular component organization or biogenesis RNA processing mRNA splice site recognition RNA splicing protein-containing complex organization primary metabolic process gene expression nucleobase-containing compound biosynthetic process mRNA metabolic process macromolecule biosynthetic process nucleic acid 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 regulation of cellular process alternative mRNA splicing, via spliceosome regulation of mRNA splicing, via spliceosome regulation of primary metabolic process regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of biosynthetic process regulation of mRNA processing regulation of biological process biological regulation regulation of macromolecule metabolic process regulation of RNA splicing regulation of gene expression regulation of alternative mRNA splicing, via spliceosome regulation of macromolecule biosynthetic process regulation of mRNA metabolic process regulation of metabolic process apoptotic process cell death programmed cell death	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol cell junction protein-containing complex ribonucleoprotein complex membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm cellular anatomical structure intracellular anatomical structure cytoplasm cytosol cell junction protein-containing complex ribonucleoprotein complex 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, E A, B, C, D, E, F, G, H	IPR017937	Thioredoxin, conserved site	Conserved Site
A, B, C, D, E A, B, C, D, E, F, G, H	IPR013766	Thioredoxin domain	Domain
A, B, C, D, E A, B, C, D, E, F, G, H	IPR005746	Thioredoxin	Family
A, B, C, D, E A, B, C, D, E, F, G, H	IPR036249	Thioredoxin-like superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H	IPR000504	RNA recognition motif domain	Domain
A, B, C, D, E A, B, C, D, E, F, G, H	IPR034211	PUF60, RNA recognition motif 2	Domain
A, B, C, D, E A, B, C, D, E, F, G, H	IPR051974	Poly(U)-binding-splicing regulator	Family
A, B, C, D, E A, B, C, D, E, F, G, H	IPR003954	RNA recognition motif domain, eukaryotes	Domain
A, B, C, D, E A, B, C, D, E, F, G, H	IPR006532	Poly-U binding splicing factor, PUF60-like	Family
A, B, C, D, E A, B, C, D, E, F, G, H	IPR012677	Nucleotide-binding alpha-beta plait domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H	IPR034209	PUF60, RNA recognition motif 1	Domain
A, B, C, D, E A, B, C, D, E, F, G, H	IPR034212	PUF60, RNA recognition motif 3	Domain
A, B, C, D, E A, B, C, D, E, F, G, H	IPR035979	RNA-binding domain superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C, D, E A, B, C, D, E, F, G, H	Pharos: Q9UHX1	8q24.3 microdeletion syndrome Neoplasms, Experimental intellectual disability mesothelioma benign mesothelioma lung cancer microcephaly ovarian cancer malignant ependymoma

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.