1T77

Crystal structure of the PH-BEACH domains of human LRBA/BGL

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 Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1t77a1	All alpha proteins	BEACH domain	BEACH domain	BEACH domain	Lipopolysaccharide-responsive and beige-like anchor protein LRBA	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d1t77a2	All beta proteins	PH domain-like barrel	PH domain-like	PreBEACH PH-like domain	Lipopolysaccharide-responsive and beige-like anchor protein LRBA	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d1t77b1	All alpha proteins	BEACH domain	BEACH domain	BEACH domain	Lipopolysaccharide-responsive and beige-like anchor protein LRBA	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d1t77b2	All beta proteins	PH domain-like barrel	PH domain-like	PreBEACH PH-like domain	Lipopolysaccharide-responsive and beige-like anchor protein LRBA	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d1t77c1	All alpha proteins	BEACH domain	BEACH domain	BEACH domain	Lipopolysaccharide-responsive and beige-like anchor protein LRBA	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d1t77c2	All beta proteins	PH domain-like barrel	PH domain-like	PreBEACH PH-like domain	Lipopolysaccharide-responsive and beige-like anchor protein LRBA	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d1t77d1	All alpha proteins	BEACH domain	BEACH domain	BEACH domain	Lipopolysaccharide-responsive and beige-like anchor protein LRBA	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d1t77d2	All beta proteins	PH domain-like barrel	PH domain-like	PreBEACH PH-like domain	Lipopolysaccharide-responsive and beige-like anchor protein LRBA	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)
A	SCOP2 Family	BEACH domain	8030038	4002423	SCOP2 (2022-06-29)
A	SCOP2 Family	PreBEACH PH-like domain	8030039	4002719	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	BEACH domain	8042417	3001218	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	PH domain-like	8042418	3000134	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	BEACH domain	8042417	3001218	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	PH domain-like	8042418	3000134	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	BEACH domain	8042417	3001218	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	PH domain-like	8042418	3000134	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	PH domain-like	8042418	3000134	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	BEACH domain	8042417	3001218	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	PH_BEACH	e1t77A1	A: beta barrels	X: PH domain-like	H: PH domain-like (From Topology)	T: PH domain-like	F: PH_BEACH	ECOD (1.6)
A	Beach	e1t77A2	A: alpha arrays	X: BEACH domain (From Topology)	H: BEACH domain (From Topology)	T: BEACH domain	F: Beach	ECOD (1.6)
B	PH_BEACH	e1t77B1	A: beta barrels	X: PH domain-like	H: PH domain-like (From Topology)	T: PH domain-like	F: PH_BEACH	ECOD (1.6)
B	Beach	e1t77B2	A: alpha arrays	X: BEACH domain (From Topology)	H: BEACH domain (From Topology)	T: BEACH domain	F: Beach	ECOD (1.6)
C	PH_BEACH	e1t77C1	A: beta barrels	X: PH domain-like	H: PH domain-like (From Topology)	T: PH domain-like	F: PH_BEACH	ECOD (1.6)
C	Beach	e1t77C2	A: alpha arrays	X: BEACH domain (From Topology)	H: BEACH domain (From Topology)	T: BEACH domain	F: Beach	ECOD (1.6)
D	PH_BEACH	e1t77D1	A: beta barrels	X: PH domain-like	H: PH domain-like (From Topology)	T: PH domain-like	F: PH_BEACH	ECOD (1.6)
D	Beach	e1t77D2	A: alpha arrays	X: BEACH domain (From Topology)	H: BEACH domain (From Topology)	T: BEACH domain	F: Beach	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
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)
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)
C	2.30.29.30	Mainly Beta	Roll	PH-domain like	Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB)	CATH (4.3.0)
C	1.10.1540.10	Mainly Alpha	Orthogonal Bundle	Neurobeachin	Chain: A, domain 1	CATH (4.3.0)
D	2.30.29.30	Mainly Beta	Roll	PH-domain like	Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB)	CATH (4.3.0)
D	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, C, D	PF02138	Beige/BEACH domain (Beach)	Beige/BEACH domain	-	Family
A, B, C, D	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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Lipopolysaccharide-responsive and beige-like anchor protein	protein binding binding kinase binding enzyme binding protein kinase binding	protein localization localization cellular localization cellular macromolecule localization macromolecule localization cellular process cellular component disassembly catabolic process macroautophagy cellular metabolic process autophagy cellular catabolic process cellular component organization organelle organization protein localization localization cellular localization cellular macromolecule localization macromolecule localization cellular process cellular component disassembly catabolic process macroautophagy cellular metabolic process autophagy cellular catabolic process cellular component organization organelle organization mitophagy organelle disassembly metabolic process cellular component organization or biogenesis autophagy of mitochondrion process utilizing autophagic mechanism mitochondrion organization autophagosome organization cellular component biogenesis cellular component assembly autophagosome assembly organelle assembly vacuole organization protein localization to phagophore assembly site	vacuolar membrane membrane-bounded organelle intracellular anatomical structure membrane lytic vacuole vacuole cellular anatomical entity intracellular membrane-bounded organelle intracellular organelle lytic vacuole membrane bounding membrane of organelle organelle lysosomal membrane cytoplasm vacuolar membrane membrane-bounded organelle intracellular anatomical structure membrane lytic vacuole vacuole cellular anatomical entity intracellular membrane-bounded organelle intracellular organelle lytic vacuole membrane bounding membrane of organelle organelle lysosomal membrane cytoplasm organelle membrane lysosome Golgi apparatus endomembrane system cytosol cell periphery plasma membrane organelle subcompartment endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum endoplasmic reticulum membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR046852	Neurobeachin, alpha-solenoid region	Domain
A, B, C, D	IPR016024	Armadillo-type fold	Homologous Superfamily
A, B, C, D	IPR000409	BEACH domain	Domain
A, B, C, D	IPR036322	WD40-repeat-containing domain superfamily	Homologous Superfamily
A, B, C, D	IPR013320	Concanavalin A-like lectin/glucanase domain superfamily	Homologous Superfamily
A, B, C, D	IPR011989	Armadillo-like helical	Homologous Superfamily
A, B, C, D	IPR001680	WD40 repeat	Repeat
A, B, C, D	IPR011993	PH-like domain superfamily	Homologous Superfamily
A, B, C, D	IPR046851	Neurobeachin, beta-propeller domain	Domain
A, B, C, D	IPR036372	BEACH domain superfamily	Homologous Superfamily
A, B, C, D	IPR031570	Neurobeachin/BDCP, DUF4704	Domain
A, B, C, D	IPR015943	WD40/YVTN repeat-like-containing domain superfamily	Homologous Superfamily
A, B, C, D	IPR010508	Neurobeachin-like, DUF1088	Domain
A, B, C, D	IPR023362	PH-BEACH domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C, D	Pharos: P50851	common variable immunodeficiency combined immunodeficiency due to LRBA deficiency malignant ependymoma malignant pancreatic neoplasm ovarian cancer primitive neuroectodermal tumor agammaglobulinemia cholelithiasis ductal breast carcinoma in situ gastric cancer invasive ductal breast carcinoma lung cancer malignant mesothelioma medulloblastoma pancreatic intraductal papillary-mucinous neoplasm common variable immunodeficiency combined immunodeficiency due to LRBA deficiency malignant ependymoma malignant pancreatic neoplasm ovarian cancer primitive neuroectodermal tumor agammaglobulinemia cholelithiasis ductal breast carcinoma in situ gastric cancer invasive ductal breast carcinoma lung cancer malignant mesothelioma medulloblastoma pancreatic intraductal papillary-mucinous neoplasm tuberculosis atypical teratoid rhabdoid tumor colobomatous microphthalmia-rhizomelic dysplasia syndrome cystic fibrosis exocrine pancreatic carcinoma gastric carcinoma large cell medulloblastoma lung carcinoma Malignant neoplasm of breast osteosarcoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia B cell deficiency diabetes mellitus gallbladder disease interstitial cystitis liver disease

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.