1MI1 | pdb_00001mi1

Crystal Structure of the PH-BEACH Domain of Human Neurobeachin

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
Pharos: Disease Associations

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
B	d1mi1b1	All alpha proteins	BEACH domain	BEACH domain	BEACH domain	BEACH domain of neurobeachin	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d1mi1b2	All beta proteins	PH domain-like barrel	PH domain-like	PreBEACH PH-like domain	PH-like domain of neurobeachin	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d1mi1a1	All alpha proteins	BEACH domain	BEACH domain	BEACH domain	BEACH domain of neurobeachin	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d1mi1a2	All beta proteins	PH domain-like barrel	PH domain-like	PreBEACH PH-like domain	PH-like domain of neurobeachin	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	PH domain-like	8043567	3000134	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	BEACH domain	8043565	3001218	SCOP2B (2022-06-29)
A	SCOP2 Family	BEACH domain	8031187	4002423	SCOP2 (2022-06-29)
A	SCOP2 Family	PreBEACH PH-like domain	8031189	4002719	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	BEACH domain	8043565	3001218	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	PH domain-like	8043567	3000134	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)
B	Rieske	e1mi1B1	A: a/b three-layered sandwiches	X: Phage tail fiber protein trimerization domain	H: beta-Prism I	T: beta-Prism I	F: Rieske	ECOD (v294.1)
B		e1mi1B2	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: alpha-2-Macroglobulin receptor associated protein (RAP) domain 1	T: alpha-2-Macroglobulin receptor associated protein (RAP) domain 1	F:	ECOD (v294.1)
A	Rieske	e1mi1A1	A: a/b three-layered sandwiches	X: Phage tail fiber protein trimerization domain	H: beta-Prism I	T: beta-Prism I	F: Rieske	ECOD (v294.1)
A		e1mi1A2	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: alpha-2-Macroglobulin receptor associated protein (RAP) domain 1	T: alpha-2-Macroglobulin receptor associated protein (RAP) domain 1	F:	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	2.30.29.30	Mainly Beta	Roll	PH-domain like	Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB)	CATH (4.3.0)
B	1.10.1540.10	Mainly Alpha	Orthogonal Bundle	Neurobeachin	Chain: A, domain 1	CATH (4.3.0)
A	2.30.29.30	Mainly Beta	Roll	PH-domain like	Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB)	CATH (4.3.0)
A	1.10.1540.10	Mainly Alpha	Orthogonal Bundle	Neurobeachin	Chain: A, domain 1	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF14844	PH domain associated with Beige/BEACH (PH_BEACH)	PH domain associated with Beige/BEACH	This PH domain is found in proteins containing the Beige/BEACH domain (Pfam:PF02138), it immediately precedes the Beige/BEACH domain [1].	Domain
A, B	PF02138	Beige/BEACH domain (Beach)	Beige/BEACH domain	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Neurobeachin	protein binding binding kinase binding enzyme binding protein kinase binding	localization macromolecule localization intracellular protein localization	cellular anatomical structure endomembrane system membrane membrane-bounded organelle intracellular anatomical structure Golgi apparatus subcompartment Golgi apparatus organelle subcompartment intracellular membrane-bounded organelle intracellular organelle organelle trans-Golgi network cytoplasm cytosol cellular anatomical structure endomembrane system membrane membrane-bounded organelle intracellular anatomical structure Golgi apparatus subcompartment Golgi apparatus organelle subcompartment intracellular membrane-bounded organelle intracellular organelle organelle trans-Golgi network cytoplasm cytosol cell periphery plasma membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR046852	Neurobeachin, alpha-solenoid region	Domain
A, B	IPR016024	Armadillo-type fold	Homologous Superfamily
A, B	IPR050865	BEACH Domain-Containing	Family
A, B	IPR000409	BEACH domain	Domain
A, B	IPR036322	WD40-repeat-containing domain superfamily	Homologous Superfamily
A, B	IPR013320	Concanavalin A-like lectin/glucanase domain superfamily	Homologous Superfamily
A, B	IPR001680	WD40 repeat	Repeat
A, B	IPR011993	PH-like domain superfamily	Homologous Superfamily
A, B	IPR046851	Neurobeachin, beta-propeller domain	Domain
A, B	IPR036372	BEACH domain superfamily	Homologous Superfamily
A, B	IPR031570	Neurobeachin/BDCP, DUF4704	Domain
A, B	IPR015943	WD40/YVTN repeat-like-containing domain superfamily	Homologous Superfamily
A, B	IPR010508	Neurobeachin-like, DUF1088	Domain
A, B	IPR023362	PH-BEACH domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	Pharos: Q8NFP9	Liver Cirrhosis, Experimental nasopharyngeal carcinoma pancreatic intraductal papillary-mucinous carcinoma progressive supranuclear palsy subependymal giant cell astrocytoma adrenal cortex carcinoma atypical teratoid rhabdoid tumor breast cancer epilepsy large cell medulloblastoma malignant colon neoplasm malignant mesothelioma oligodendroglioma pilocytic astrocytoma psoriasis Liver Cirrhosis, Experimental nasopharyngeal carcinoma pancreatic intraductal papillary-mucinous carcinoma progressive supranuclear palsy subependymal giant cell astrocytoma adrenal cortex carcinoma atypical teratoid rhabdoid tumor breast cancer epilepsy large cell medulloblastoma malignant colon neoplasm malignant mesothelioma oligodendroglioma pilocytic astrocytoma psoriasis tuberculosis astrocytic tumor autism cystic fibrosis glioblastoma malignant ependymoma medulloblastoma ovarian cancer primitive neuroectodermal tumor sinusitis attention deficit hyperactivity disorder, inattentive type diabetes mellitus invasive ductal breast carcinoma lung carcinoma malignant glioma

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.