3FMA | pdb_00003fma

Crystal structure of the GYF domain of Smy2 in complex with a proline-rich peptide from BBP/ScSF1

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
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)
E		e3fmaE1	A: Alpha-beta plaits	X: Phage tail protein-like	H: Transmembrane protein 14A	T: Pkinase, ABC1	F:	ECOD (20:10:01)
D		e3fmaD1	A: Alpha-beta plaits	X: Phage tail protein-like	H: Transmembrane protein 14A	T: Pkinase, ABC1	F:	ECOD (20:10:01)
C		e3fmaC1	A: Alpha-beta plaits	X: Phage tail protein-like	H: Transmembrane protein 14A	T: Pkinase, ABC1	F:	ECOD (20:10:01)
B		e3fmaB1	A: Alpha-beta plaits	X: Phage tail protein-like	H: Transmembrane protein 14A	T: Pkinase, ABC1	F:	ECOD (20:10:01)
A		e3fmaA1	A: OB-fold	X: Nucleic acid-binding protein	H: Nucleic acid-binding protein	T: Peptidase_M42	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
E	3.30.1490.40	Alpha Beta	2-Layer Sandwich	Dna Ligase	domain 1	CATH (4.3.0)
D	3.30.1490.40	Alpha Beta	2-Layer Sandwich	Dna Ligase	domain 1	CATH (4.3.0)
C	3.30.1490.40	Alpha Beta	2-Layer Sandwich	Dna Ligase	domain 1	CATH (4.3.0)
B	3.30.1490.40	Alpha Beta	2-Layer Sandwich	Dna Ligase	domain 1	CATH (4.3.0)
A	3.30.1490.40	Alpha Beta	2-Layer Sandwich	Dna Ligase	domain 1	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E	PF02213	GYF domain (GYF)	GYF domain	The GYF domain is named because of the presence of Gly-Tyr-Phe residues. The GYF domain is a proline-binding domain in CD2-binding protein Swiss:O95400.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
F [auth L], G [auth M], H [auth N], I [auth O], J [auth P]	Branchpoint-bridging protein	RNA binding binding nucleic acid binding mRNA binding pre-mRNA binding pre-mRNA branch point binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding	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 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 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 mRNA cis splicing, via spliceosome	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle U2-type spliceosomal complex protein-containing complex nucleus nuclear protein-containing complex intracellular membrane-bounded organelle intracellular organelle spliceosomal complex organelle ribonucleoprotein complex cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle U2-type spliceosomal complex protein-containing complex nucleus nuclear protein-containing complex intracellular membrane-bounded organelle intracellular organelle spliceosomal complex organelle ribonucleoprotein complex commitment complex
A, B, C, D, E	Protein SMY2	-	cellular response to stimulus catabolic process response to stimulus proteasome-mediated ubiquitin-dependent protein catabolic process macromolecule catabolic process cellular response to misfolded protein response to misfolded protein cellular response to stress modification-dependent macromolecule catabolic process response to stress protein metabolic process cellular response to topologically incorrect protein primary metabolic process proteasomal protein catabolic process cellular response to stimulus catabolic process response to stimulus proteasome-mediated ubiquitin-dependent protein catabolic process macromolecule catabolic process cellular response to misfolded protein response to misfolded protein cellular response to stress modification-dependent macromolecule catabolic process response to stress protein metabolic process cellular response to topologically incorrect protein primary metabolic process proteasomal protein catabolic process protein catabolic process nuclear protein quality control by the ubiquitin-proteasome system modification-dependent protein catabolic process response to topologically incorrect protein ubiquitin-dependent protein catabolic process metabolic process cellular process macromolecule metabolic process protein quality control for misfolded or incompletely synthesized proteins regulation of cellular process RNA metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process transcription by RNA polymerase II regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of transcription by RNA polymerase II regulation of biosynthetic process regulation of biological process biological regulation regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of gene expression biosynthetic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription regulation of metabolic process cellular component organization cellular component disassembly protein-containing complex organization protein-containing complex disassembly cellular component organization or biogenesis localization cellular localization transport establishment of localization in cell intracellular transport endoplasmic reticulum to Golgi vesicle-mediated transport establishment of localization Golgi vesicle transport vesicle-mediated transport	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle intracellular organelle organelle nucleus intracellular membrane-bounded organelle organelle subcompartment membrane endomembrane system endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle intracellular organelle organelle nucleus intracellular membrane-bounded organelle organelle subcompartment membrane endomembrane system endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum organelle membrane endoplasmic reticulum membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
F [auth L], G [auth M], H [auth N], I [auth O], J [auth P]	IPR036875	Zinc finger, CCHC-type superfamily	Homologous Superfamily
F [auth L], G [auth M], H [auth N], I [auth O], J [auth P]	IPR032570	Splicing factor 1, helix-hairpin domain	Domain
F [auth L], G [auth M], H [auth N], I [auth O], J [auth P]	IPR013041	Clathrin adaptor, appendage, Ig-like subdomain superfamily	Homologous Superfamily
F [auth L], G [auth M], H [auth N], I [auth O], J [auth P]	IPR004087	K Homology domain	Domain
F [auth L], G [auth M], H [auth N], I [auth O], J [auth P]	IPR047086	Splicing factor 1, helix-hairpin domain superfamily	Homologous Superfamily
F [auth L], G [auth M], H [auth N], I [auth O], J [auth P]	IPR001878	Zinc finger, CCHC-type	Domain
F [auth L], G [auth M], H [auth N], I [auth O], J [auth P]	IPR036612	K Homology domain, type 1 superfamily	Homologous Superfamily
F [auth L], G [auth M], H [auth N], I [auth O], J [auth P]	IPR045071	KH domain-containing BBP-like	Family
F [auth L], G [auth M], H [auth N], I [auth O], J [auth P]	IPR055256	KHDC4/BBP-like, KH-domain type I	Domain
A, B, C, D, E	IPR003169	GYF domain	Domain
A, B, C, D, E	IPR035445	GYF-like domain superfamily	Homologous Superfamily
A, B, C, D, E	IPR051640	GRB10-interacting GYF	Family

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.