Annotations: 9BIA

Cryo-EM structure of NINJ1 K45Q bound to Nb538

External Resource: Annotation

Domain Annotation: ECOD Classification
SAbDab Antibody Annotation
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Membrane Protein Annotation: PDBTM

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
E	MIT	e9biaE01	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: MIT	ECOD (v294.2)
F	WD40	e9biaF1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: WD40	ECOD (v294.2)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
E, F	Heavy Chain	IGHV3	-	ninjurin-1 \| ninjurin-1	SAbDab (2026-06-12)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth B], B [auth C], C [auth A], D	PF04923	Ninjurin (Ninjurin)	Ninjurin	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
E, F	Nb538	-	-	-
A [auth B], B [auth C], C [auth A], D	Ninjurin-1	binding lipid binding lipopolysaccharide binding carbohydrate derivative binding cell adhesion molecule binding protein binding cell adhesion mediator activity cell-cell adhesion mediator activity membrane destabilizing activity	ferroptosis cellular process cell death programmed cell death developmental process multicellular organismal process regulation of multicellular organismal development regulation of biological process regulation of developmental process blood vessel morphogenesis tube development biological regulation angiogenesis vasculature development ferroptosis cellular process cell death programmed cell death developmental process multicellular organismal process regulation of multicellular organismal development regulation of biological process regulation of developmental process blood vessel morphogenesis tube development biological regulation angiogenesis vasculature development regulation of vasculature development circulatory system development anatomical structure morphogenesis multicellular organism development tube morphogenesis regulation of angiogenesis anatomical structure formation involved in morphogenesis anatomical structure development regulation of multicellular organismal process regulation of anatomical structure morphogenesis blood vessel development system development cellular response to stimulus positive regulation of cell communication positive regulation of response to biotic stimulus immune response-regulating cell surface receptor signaling pathway regulation of cellular process positive regulation of signal transduction response to stimulus pattern recognition receptor signaling pathway regulation of signal transduction response to biotic stimulus cell communication immune response-activating signaling pathway positive regulation of immune response regulation of immune system process signal transduction positive regulation of immune system process cell surface toll-like receptor signaling pathway innate immune response-activating signaling pathway positive regulation of pattern recognition receptor signaling pathway immune response response to other organism immune response-activating cell surface receptor signaling pathway regulation of innate immune response response to external stimulus regulation of toll-like receptor 4 signaling pathway positive regulation of toll-like receptor 4 signaling pathway regulation of response to stimulus defense response to other organism regulation of pattern recognition receptor signaling pathway positive regulation of defense response activation of innate immune response regulation of immune response activation of immune response regulation of defense response regulation of response to biotic stimulus biological process involved in interspecies interaction between organisms regulation of response to external stimulus signaling positive regulation of biological process innate immune response activating cell surface receptor signaling pathway positive regulation of response to stimulus positive regulation of response to external stimulus immune response-regulating signaling pathway regulation of response to stress response to stress innate immune response response to external biotic stimulus positive regulation of cellular process cell surface pattern recognition receptor signaling pathway regulation of signaling positive regulation of innate immune response cell surface receptor signaling pathway defense response defense response to symbiont immune system process toll-like receptor 4 signaling pathway regulation of cell communication positive regulation of signaling regulation of inflammatory response positive regulation of inflammatory response inflammatory response regulation of cell-substrate adhesion positive regulation of cell adhesion regulation of cell adhesion cell-substrate adhesion positive regulation of cell-matrix adhesion cell adhesion cell-matrix adhesion positive regulation of cell-substrate adhesion regulation of cell-matrix adhesion sensory organ development eye development animal organ development visual system development anatomical structure regression hyaloid vascular plexus regression camera-type eye development sensory system development tissue regeneration developmental growth growth regeneration response to osmotic stress cellular response to chemical stress cellular response to osmotic stress cellular response to environmental stimulus cellular response to chemical stimulus hyperosmotic response cellular hyperosmotic response cellular response to stress response to chemical response to abiotic stimulus cellular response to abiotic stimulus pericyte cell migration cell migration cell motility positive regulation of developmental process positive regulation of angiogenesis positive regulation of vasculature development positive regulation of multicellular organismal process programmed necrotic cell death regulation of cell motility regulation of monocyte chemotaxis taxis regulation of cell migration myeloid leukocyte migration regulation of mononuclear cell migration locomotion cell chemotaxis chemotaxis regulation of leukocyte chemotaxis regulation of leukocyte migration regulation of chemotaxis monocyte chemotaxis leukocyte migration regulation of locomotion mononuclear cell migration leukocyte chemotaxis leukocyte chemotaxis involved in inflammatory response leukocyte migration involved in inflammatory response cytolysis macrophage chemotaxis macrophage migration pyroptotic cell death pyroptotic inflammatory response muscle structure development cellular developmental process cell differentiation muscle cell differentiation disruption of cell in another organism disruption of anatomical structure in another organism killing of cells of another organism cell killing regulation of leukocyte differentiation regulation of cell differentiation regulation of cell development skeletal system development regulation of osteoclast development positive regulation of cell development regulation of myeloid leukocyte differentiation osteoclast development positive regulation of myeloid leukocyte differentiation leukocyte differentiation myeloid leukocyte differentiation cell development positive regulation of osteoclast differentiation regulation of osteoclast differentiation positive regulation of cell differentiation positive regulation of hemopoiesis bone cell development osteoclast differentiation bone development positive regulation of osteoclast development hemopoiesis regulation of myeloid cell differentiation myeloid cell differentiation myeloid cell development positive regulation of myeloid cell differentiation regulation of hemopoiesis positive regulation of leukocyte differentiation heterotypic cell-cell adhesion cell-cell adhesion cellular component organization cellular component biogenesis cellular component assembly protein-containing complex organization protein complex oligomerization protein-containing complex assembly protein homooligomerization cellular component organization or biogenesis	cell periphery cellular anatomical structure membrane plasma membrane synapse cell junction plasma membrane region synaptic membrane extracellular region filopodium membrane intracellular anatomical structure intracellular membraneless organelle actin cytoskeleton plasma membrane bounded cell projection cell periphery cellular anatomical structure membrane plasma membrane synapse cell junction plasma membrane region synaptic membrane extracellular region filopodium membrane intracellular anatomical structure intracellular membraneless organelle actin cytoskeleton plasma membrane bounded cell projection intracellular organelle cell projection actin-based cell projection cytoskeleton organelle membraneless organelle filopodium cell projection membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth B], B [auth C], C [auth A], D	IPR007007	Ninjurin	Family

Membrane Protein Annotation: PDBTM PDBTM Database Homepage

Chains	External Link	Comment
A [auth B], B [auth C], C [auth A], D	PDBTM	Annotated as membrane protein by PDBTM

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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.