5F3X

Crystal structure of Harmonin NPDZ1 in complex with ANKS4B SAM-PBM

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	PDZ domain-like	8091810	3000388	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	PAH2 domain-like	8091808	3000467	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	PAH2 domain-like	8091808	3000467	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	PDZ domain-like	8091810	3000388	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)
B	PF00536	e5f3xB1	A: alpha arrays	X: HhH/H2TH	H: SAM/DNA-glycosylase	T: SAM domain-like	F: PF00536	ECOD (1.6)
D	PF00536	e5f3xD1	A: alpha arrays	X: HhH/H2TH	H: SAM/DNA-glycosylase	T: SAM domain-like	F: PF00536	ECOD (1.6)
A	PF00595	e5f3xA2	A: beta barrels	X: PDZ domain (From Topology)	H: PDZ domain (From Topology)	T: PDZ domain	F: PF00595	ECOD (1.6)
A	PF21219	e5f3xA1	A: alpha bundles	X: PAH2 domain (From Topology)	H: PAH2 domain (From Topology)	T: PAH2 domain	F: PF21219	ECOD (1.6)
C	PF00595	e5f3xC2	A: beta barrels	X: PDZ domain (From Topology)	H: PDZ domain (From Topology)	T: PDZ domain	F: PF00595	ECOD (1.6)
C	PF21219	e5f3xC1	A: alpha bundles	X: PAH2 domain (From Topology)	H: PAH2 domain (From Topology)	T: PAH2 domain	F: PF21219	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	1.10.150.50	Mainly Alpha	Orthogonal Bundle	DNA polymerase	domain 1	CATH (4.3.0)
D	1.10.150.50	Mainly Alpha	Orthogonal Bundle	DNA polymerase	domain 1	CATH (4.3.0)
A	1.20.1160.20	Mainly Alpha	Up-down Bundle	Paired amphipathic helix 2 (pah2 repeat)		CATH (4.3.0)
A	2.30.42.10	Mainly Beta	Roll	Pdz3 Domain	PDZ domain	CATH (4.3.0)
C	1.20.1160.20	Mainly Alpha	Up-down Bundle	Paired amphipathic helix 2 (pah2 repeat)		CATH (4.3.0)
C	2.30.42.10	Mainly Beta	Roll	Pdz3 Domain	PDZ domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B, D	PF00536	SAM domain (Sterile alpha motif) (SAM_1)	SAM domain (Sterile alpha motif)	It has been suggested that SAM is an evolutionarily conserved protein binding domain that is involved in the regulation of numerous developmental processes in diverse eukaryotes. The SAM domain can potentially function as a protein interaction module ...	It has been suggested that SAM is an evolutionarily conserved protein binding domain that is involved in the regulation of numerous developmental processes in diverse eukaryotes. The SAM domain can potentially function as a protein interaction module through its ability to homo- and heterooligomerise with other SAM domains.	Domain
A, C	PF21219	Harmonin, N-terminal domain (USH1C_N)	Harmonin, N-terminal domain	This domain is found at the N-terminal end of Harmonin from humans (USH1C) and similar proteins from vertebrates. Harmonin is a master scaffold in the assembly of the Usher protein complexes present in the inner ear and the retina. Defects in these p ...	This domain is found at the N-terminal end of Harmonin from humans (USH1C) and similar proteins from vertebrates. Harmonin is a master scaffold in the assembly of the Usher protein complexes present in the inner ear and the retina. Defects in these proteins are related to a hereditary hearing-vision loss disease, Usher syndrome I (USH1). The N-terminal domain of USH1C, which precedes the first PDZ protein- binding domain (Pfam:PF00595), adopts a compact five-helix-bundle structure [1,3].	Domain
A, C	PF00595	PDZ domain (PDZ)	PDZ domain	PDZ domains are found in diverse signaling proteins.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B, D	Ankyrin repeat and SAM domain-containing protein 4B	-	cellular component organization cellular component biogenesis cellular component assembly protein-containing complex organization protein-containing complex assembly cellular process cellular component organization or biogenesis developmental process cellular developmental process cell differentiation protein localization localization cellular localization cellular macromolecule localization cellular component organization cellular component biogenesis cellular component assembly protein-containing complex organization protein-containing complex assembly cellular process cellular component organization or biogenesis developmental process cellular developmental process cell differentiation protein localization localization cellular localization cellular macromolecule localization macromolecule localization protein localization to microvillus brush border assembly cellular response to stimulus cellular response to stress response to stimulus response to stress response to endoplasmic reticulum stress	cell projection actin-based cell projection microvillus cellular anatomical entity plasma membrane bounded cell projection cell periphery plasma membrane membrane cluster of actin-based cell projections brush border membrane-bounded organelle intracellular anatomical structure organelle subcompartment intracellular membrane-bounded organelle cell projection actin-based cell projection microvillus cellular anatomical entity plasma membrane bounded cell projection cell periphery plasma membrane membrane cluster of actin-based cell projections brush border membrane-bounded organelle intracellular anatomical structure organelle subcompartment intracellular membrane-bounded organelle endomembrane system endoplasmic reticulum subcompartment intracellular organelle organelle nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum cytoplasm organelle membrane endoplasmic reticulum membrane
A, C	Harmonin	cytoskeletal protein binding spectrin binding protein-containing complex binding protein binding binding	cellular component organization cellular component biogenesis cellular component assembly protein-containing complex organization protein-containing complex assembly cellular process cellular component organization or biogenesis developmental process ear morphogenesis embryonic organ morphogenesis multicellular organismal process ear development sensory organ development animal organ development cellular component organization cellular component biogenesis cellular component assembly protein-containing complex organization protein-containing complex assembly cellular process cellular component organization or biogenesis developmental process ear morphogenesis embryonic organ morphogenesis multicellular organismal process ear development sensory organ development animal organ development embryonic morphogenesis embryo development multicellular organism development anatomical structure morphogenesis sensory organ morphogenesis inner ear development inner ear morphogenesis anatomical structure development animal organ morphogenesis embryonic organ development sensory perception of light stimulus system process sensory perception nervous system process actin cytoskeleton organization actin filament organization organelle organization parallel actin filament bundle assembly actin filament bundle organization actin filament bundle assembly actin filament-based process supramolecular fiber organization cytoskeleton organization brush border assembly protein localization localization cellular localization cellular macromolecule localization macromolecule localization protein localization to microvillus multicellular organismal-level homeostasis homeostatic process anatomical structure homeostasis tissue homeostasis retina homeostasis photoreceptor cell maintenance neuromuscular process equilibrioception neuromuscular process controlling balance inner ear receptor cell development cellular developmental process cell projection organization cell development neuron projection development neurogenesis neuron differentiation cell differentiation system development mechanoreceptor differentiation plasma membrane bounded cell projection organization nervous system development inner ear receptor cell differentiation generation of neurons neuron development inner ear receptor cell stereocilium organization sensory perception of sound sensory perception of mechanical stimulus epidermis development epithelial cell differentiation hair cell differentiation epithelium development epidermal cell differentiation inner ear auditory receptor cell differentiation tissue development cell cycle G2/M phase transition mitotic cell cycle process G2/M transition of mitotic cell cycle cell cycle phase transition cell cycle mitotic cell cycle cell cycle process mitotic cell cycle phase transition photoreceptor cell differentiation visual system development retina development in camera-type eye neural retina development eye morphogenesis retinal cone cell differentiation eye photoreceptor cell differentiation sensory system development photoreceptor cell development camera-type eye morphogenesis eye development eye photoreceptor cell development retinal cone cell development camera-type eye photoreceptor cell differentiation retina morphogenesis in camera-type eye camera-type eye development regulation of biological process regulation of cellular component organization regulation of cellular process regulation of cellular component size regulation of cell projection organization biological regulation regulation of cell projection size regulation of microvillus length microvillus organization regulation of microvillus organization regulation of biological quality regulation of plasma membrane bounded cell projection organization regulation of anatomical structure size	membrane-bounded organelle cell projection organelle cilium cellular anatomical entity plasma membrane bounded cell projection apical part of cell photoreceptor inner segment protein-containing complex stereocilia ankle link stereocilia ankle link complex stereocilium bundle stereocilia coupling link cluster of actin-based cell projections membrane-bounded organelle cell projection organelle cilium cellular anatomical entity plasma membrane bounded cell projection apical part of cell photoreceptor inner segment protein-containing complex stereocilia ankle link stereocilia ankle link complex stereocilium bundle stereocilia coupling link cluster of actin-based cell projections stereocilium actin-based cell projection stereocilium tip neuron projection intracellular anatomical structure cytoplasm cytosol cell periphery plasma membrane membrane brush border non-motile cilium 9+0 non-motile cilium photoreceptor outer segment photoreceptor cell cilium intracellular organelle cytoskeleton intracellular non-membrane-bounded organelle non-membrane-bounded organelle synapse cell junction microvillus

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B, D	IPR002110	Ankyrin repeat	Repeat
B, D	IPR013761	Sterile alpha motif/pointed domain superfamily	Homologous Superfamily
B, D	IPR036770	Ankyrin repeat-containing domain superfamily	Homologous Superfamily
B, D	IPR037601	ANKS4B, SAM domain	Domain
B, D	IPR001660	Sterile alpha motif domain	Domain
A, C	IPR030237	Harmonin, N-terminal	Domain
A, C	IPR036034	PDZ superfamily	Homologous Superfamily
A, C	IPR001478	PDZ domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, C	Pharos: Q9Y6N9	nonsyndromic genetic deafness autosomal recessive nonsyndromic deafness 18A Usher syndrome type 1C Usher syndrome Usher syndrome, type 1C retinitis pigmentosa Usher syndrome type 1B lung cancer nephrosclerosis pancreatic intraductal papillary-mucinous carcinoma pituitary cancer cone-rod dystrophy lung carcinoma pancreatic intraductal papillary-mucinous neoplasm psoriasis nonsyndromic genetic deafness autosomal recessive nonsyndromic deafness 18A Usher syndrome type 1C Usher syndrome Usher syndrome, type 1C retinitis pigmentosa Usher syndrome type 1B lung cancer nephrosclerosis pancreatic intraductal papillary-mucinous carcinoma pituitary cancer cone-rod dystrophy lung carcinoma pancreatic intraductal papillary-mucinous neoplasm psoriasis esophageal adenocarcinoma malignant pancreatic neoplasm osteosarcoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia retinal degeneration

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 R01GM133198.