2J3W | pdb_00002j3w

The crystal structure of the bet3-trs31-sedlin complex.

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
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: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
E	d2j3we_	Alpha and beta proteins (a+b)	Ligand-binding domain in the NO signalling and Golgi transport	Ligand-binding domain in the NO signalling and Golgi transport	TRAPP components	automated matches	HOUSE MOUSE (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
D	d2j3wd_	Alpha and beta proteins (a+b)	Ligand-binding domain in the NO signalling and Golgi transport	Ligand-binding domain in the NO signalling and Golgi transport	TRAPP components	automated matches	HOUSE MOUSE (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
F	d2j3wf_	Alpha and beta proteins (a+b)	Ligand-binding domain in the NO signalling and Golgi transport	Ligand-binding domain in the NO signalling and Golgi transport	TRAPP components	TRAPPC5, similar to trafficking protein particle complex 5	ZEBRAFISH (Danio rerio ) [TaxId: 7955 ],	SCOPe (2.08)
B	d2j3wb1	Alpha and beta proteins (a+b)	Ligand-binding domain in the NO signalling and Golgi transport	Ligand-binding domain in the NO signalling and Golgi transport	TRAPP components	TRAPPC5, similar to trafficking protein particle complex 5	ZEBRAFISH (Danio rerio ) [TaxId: 7955 ],	SCOPe (2.08)
C	d2j3wc_	Alpha and beta proteins (a+b)	Profilin-like	SNARE-like	Sedlin (SEDL)	Sedlin (SEDL)	HOUSE MOUSE (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
A	d2j3wa_	Alpha and beta proteins (a+b)	Profilin-like	SNARE-like	Sedlin (SEDL)	Sedlin (SEDL)	HOUSE MOUSE (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
E	SCOP2B Superfamily	Ligand-binding domain in the NO signalling and Golgi transport	8043404	3001668	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Ligand-binding domain in the NO signalling and Golgi transport	8043404	3001668	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Ligand-binding domain in the NO signalling and Golgi transport	8033250	3001668	SCOP2B (2022-06-29)
B	SCOP2 Family	TRAPP components	8020870	4003802	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	Ligand-binding domain in the NO signalling and Golgi transport	8033250	3001668	SCOP2 (2022-06-29)
C	SCOP2B Superfamily	SNARE-like	8043017	3001113	SCOP2B (2022-06-29)
A	SCOP2 Family	Sedlin (SEDL)	8030638	4003315	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	SNARE-like	8043017	3001113	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
E	MarR	e2j3wE1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: winged helix domain	F: MarR	ECOD (v294.1)
D	MarR	e2j3wD1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: winged helix domain	F: MarR	ECOD (v294.1)
F	LRR_6,LRR_RI_capping	e2j3wF1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: LRR_6,LRR_RI_capping	ECOD (v294.1)
B	TRAPP	e2j3wB1	A: beta duplicates or obligate multimers	X: H-NOX domain	H: H-NOX domain	T: H-NOX domain	F: TRAPP	ECOD (v294.1)
C	Transpeptidase	e2j3wC1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: Transpeptidase	ECOD (v294.1)
A	Sedlin_N	e2j3wA1	A: a+b three layers	X: Profilin-like	H: profilin-like	T: profilin-like	F: Sedlin_N	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
E	3.30.1380.20	Alpha Beta	2-Layer Sandwich	Muramoyl-pentapeptide Carboxypeptidase	domain 2	CATH (4.3.0)
D	3.30.1380.20	Alpha Beta	2-Layer Sandwich	Muramoyl-pentapeptide Carboxypeptidase	domain 2	CATH (4.3.0)
F	3.30.1380.20	Alpha Beta	2-Layer Sandwich	Muramoyl-pentapeptide Carboxypeptidase	domain 2	CATH (4.3.0)
B	3.30.1380.20	Alpha Beta	2-Layer Sandwich	Muramoyl-pentapeptide Carboxypeptidase	domain 2	CATH (4.3.0)
C	3.30.450.70	Alpha Beta	2-Layer Sandwich	Beta-Lactamase		CATH (4.3.0)
A	3.30.450.70	Alpha Beta	2-Layer Sandwich	Beta-Lactamase		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
D, E	PF04051	Transport protein particle (TRAPP) component (TRAPP)	Transport protein particle (TRAPP) component	-	Family
B, F	PF04051	Transport protein particle (TRAPP) component (TRAPP)	Transport protein particle (TRAPP) component	-	Family
A, C	PF04628	Sedlin, N-terminal conserved region (Sedlin_N)	Sedlin, N-terminal conserved region	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
D, E	TRAFFICKING PROTEIN PARTICLE COMPLEX SUBUNIT 3	-	localization transport cellular process establishment of localization Golgi vesicle transport vesicle-mediated transport intra-Golgi vesicle-mediated transport vesicle localization establishment of organelle localization cellular localization establishment of vesicle localization vesicle targeting cellular component organization organelle localization localization transport cellular process establishment of localization Golgi vesicle transport vesicle-mediated transport intra-Golgi vesicle-mediated transport vesicle localization establishment of organelle localization cellular localization establishment of vesicle localization vesicle targeting cellular component organization organelle localization establishment of localization in cell cellular component organization or biogenesis vesicle tethering vesicle budding from membrane vesicle targeting, to, from or within Golgi vesicle organization cellular component biogenesis cellular component assembly protein-containing complex assembly vesicle coating vesicle targeting, rough ER to cis-Golgi membrane organization protein-containing complex organization intracellular transport endoplasmic reticulum to Golgi vesicle-mediated transport organelle organization COPII-coated vesicle budding COPII vesicle coating	membrane-bounded organelle intracellular anatomical structure cis-Golgi network membrane Golgi apparatus membrane intracellular membrane-bounded organelle endomembrane system intracellular organelle cellular anatomical structure bounding membrane of organelle cis-Golgi network organelle cytoplasm organelle membrane membrane-bounded organelle intracellular anatomical structure cis-Golgi network membrane Golgi apparatus membrane intracellular membrane-bounded organelle endomembrane system intracellular organelle cellular anatomical structure bounding membrane of organelle cis-Golgi network organelle cytoplasm organelle membrane protein-containing complex intracellular protein-containing complex TRAPP complex vesicle tethering complex Golgi membrane endosome intracellular vesicle TRAPPII protein complex cytoplasmic vesicle vesicle TRAPPIII protein complex cytosol endoplasmic reticulum
B, F	ZGC 92866	-	localization cellular localization transport establishment of localization in cell intracellular transport cellular process endoplasmic reticulum to Golgi vesicle-mediated transport establishment of localization Golgi vesicle transport vesicle-mediated transport	membrane-bounded organelle protein-containing complex intracellular anatomical structure intracellular membrane-bounded organelle TRAPPI protein complex TRAPP complex vesicle tethering complex intracellular organelle cellular anatomical structure organelle endoplasmic reticulum-Golgi intermediate compartment cytoplasm intracellular protein-containing complex endoplasmic reticulum membrane-bounded organelle protein-containing complex intracellular anatomical structure intracellular membrane-bounded organelle TRAPPI protein complex TRAPP complex vesicle tethering complex intracellular organelle cellular anatomical structure organelle endoplasmic reticulum-Golgi intermediate compartment cytoplasm intracellular protein-containing complex endoplasmic reticulum endomembrane system Golgi apparatus endosome intracellular vesicle TRAPPII protein complex cytoplasmic vesicle vesicle TRAPPIII protein complex
A, C	TRAFFICKING PROTEIN PARTICLE COMPLEX PROTEIN 2	transcription factor binding transcription coregulator binding transcription corepressor binding protein binding binding transmembrane transporter binding	developmental process multicellular organism development multicellular organismal process skeletal system development anatomical structure development system development regulation of biosynthetic process regulation of biological process regulation of cellular process biological regulation positive regulation of biological process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process developmental process multicellular organism development multicellular organismal process skeletal system development anatomical structure development system development regulation of biosynthetic process regulation of biological process regulation of cellular process biological regulation positive regulation of biological process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process positive regulation of macromolecule biosynthetic process regulation of gene expression positive regulation of metabolic process biosynthetic process positive regulation of gene expression positive regulation of biosynthetic process regulation of macromolecule biosynthetic process metabolic process cellular process positive regulation of macromolecule metabolic process macromolecule metabolic process regulation of metabolic process positive regulation of cellular process vesicle localization establishment of organelle localization cellular localization transport establishment of vesicle localization establishment of localization vesicle targeting vesicle-mediated transport cellular component organization localization organelle localization establishment of localization in cell cellular component organization or biogenesis vesicle tethering vesicle budding from membrane vesicle targeting, to, from or within Golgi vesicle organization cellular component biogenesis cellular component assembly protein-containing complex assembly vesicle coating vesicle targeting, rough ER to cis-Golgi membrane organization protein-containing complex organization intracellular transport endoplasmic reticulum to Golgi vesicle-mediated transport organelle organization COPII-coated vesicle budding COPII vesicle coating Golgi vesicle transport	protein-containing complex intracellular protein-containing complex TRAPP complex vesicle tethering complex membrane-bounded organelle intracellular anatomical structure Golgi apparatus endosome intracellular vesicle intracellular membrane-bounded organelle endomembrane system intracellular organelle cellular anatomical structure TRAPPII protein complex protein-containing complex intracellular protein-containing complex TRAPP complex vesicle tethering complex membrane-bounded organelle intracellular anatomical structure Golgi apparatus endosome intracellular vesicle intracellular membrane-bounded organelle endomembrane system intracellular organelle cellular anatomical structure TRAPPII protein complex cytoplasmic vesicle organelle cytoplasm vesicle TRAPPIII protein complex perinuclear region of cytoplasm endoplasmic reticulum-Golgi intermediate compartment nucleus membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen endoplasmic reticulum

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
D, E	IPR024096	NO signalling/Golgi transport ligand-binding domain superfamily	Homologous Superfamily
D, E	IPR007194	Transport protein particle (TRAPP) component	Family
D, E	IPR016721	Bet3 family	Family
B, F	IPR024096	NO signalling/Golgi transport ligand-binding domain superfamily	Homologous Superfamily
B, F	IPR016696	TRAPP I complex, subunit 5	Family
B, F	IPR007194	Transport protein particle (TRAPP) component	Family
A, C	IPR011012	Longin-like domain superfamily	Homologous Superfamily
A, C	IPR006722	Trafficking protein particle complex subunit 2	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.