3MJ9 | pdb_00003mj9

Crystal structure of JAML in complex with the stimulatory antibody HL4E10

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
IMGT Antibody Annotation
SAbDab Antibody Annotation
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)
C [auth H]	d3mj9h_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	(Nothocricetulus migratorius ) [TaxId: 3122392 ],	SCOPe (2.08)
B [auth L]	d3mj9l1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	(Nothocricetulus migratorius ) [TaxId: 3122392 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
C [auth H]	AAA	e3mj9H1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: AAA	ECOD (v294.1)
B [auth L]	AAA	e3mj9L1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: AAA	ECOD (v294.1)
A	HypA	e3mj9A1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Fibronectin type I module-like	T: Fibronectin type I module	F: HypA	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C [auth H]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
B [auth L]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
A	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)

IMGT Antibody Annotation IMGT Database Homepage

Chain	Protein Name	Description	Organism Name	Gene Allele Name(s)	Domain Name(s)	Receptor Type	Receptor Description	Provenance Source
C [auth H]	HL4E10 Fab	VH-CH1	Rattus norvegicus (Norway rat)	IGHV2-1901, IGHJ201, IGHG2B*01	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-2B_LAMBDA	IMGT (202612-0)
B [auth L]	HL4E10 Fab	L-LAMBDA	Rattus norvegicus (Norway rat)	IGLV4S101, IGLJ301, IGLJ101, IGLC201, IGLC4*01	V-DOMAIN V-LAMBDA, C-DOMAIN C-LAMBDA	IG	FAB-GAMMA-2B_LAMBDA	IMGT (202612-0)
A	JAML (Junctional adhesion molecule-like)	2V-LIKE	Mus musculus (house mouse)	AMICA1*01	V-LIKE-DOMAIN V-LIKE	RPI	2V-LIKE	IMGT (202612-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
C [auth H]	Heavy Chain	IGHV2	-	junctional adhesion molecule-like	SAbDab (2026-03-27)
B [auth L]	Light Chain	IGLV3	Lambda	junctional adhesion molecule-like	SAbDab (2026-03-27)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF07686	Immunoglobulin V-set domain (V-set)	Immunoglobulin V-set domain	This domain is found in antibodies as well as neural protein P0 and CTL4 amongst others.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C [auth H]	STIMULATORY HAMSTER ANTIBODY HL4E10 FAB HEAVY CHAIN	-	-	-
B [auth L]	STIMULATORY HAMSTER ANTIBODY HL4E10 FAB LIGHT CHAIN	-	-	-
A	Junctional adhesion molecule-like	cell adhesion molecule binding protein-containing complex binding protein binding binding integrin binding signaling receptor binding identical protein binding protein homodimerization activity protein dimerization activity	wound healing regulation of biological process cell population proliferation regulation of cellular process response to stimulus positive regulation of cell population proliferation positive regulation of epithelial cell proliferation biological regulation positive regulation of biological process response to stress regulation of cell population proliferation cellular process regulation of epithelial cell proliferation response to wounding wound healing regulation of biological process cell population proliferation regulation of cellular process response to stimulus positive regulation of cell population proliferation positive regulation of epithelial cell proliferation biological regulation positive regulation of biological process response to stress regulation of cell population proliferation cellular process regulation of epithelial cell proliferation response to wounding epithelial cell proliferation positive regulation of cellular process positive regulation of epithelial cell proliferation involved in wound healing leukocyte migration neutrophil extravasation immune system process myeloid leukocyte migration cellular extravasation cell migration neutrophil migration cell motility granulocyte migration multicellular organismal process gamma-delta T cell activation T cell activation cell activation lymphocyte activation leukocyte activation mononuclear cell migration monocyte extravasation cell chemotaxis cellular response to stimulus chemotaxis neutrophil chemotaxis response to external stimulus cellular response to chemical stimulus taxis granulocyte chemotaxis response to chemical leukocyte chemotaxis locomotion heterophilic cell-cell adhesion cell adhesion cell-cell adhesion	cell-cell junction apical junction complex bicellular tight junction cellular anatomical structure tight junction anchoring junction cell junction cell periphery plasma membrane membrane membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen cell-cell junction apical junction complex bicellular tight junction cellular anatomical structure tight junction anchoring junction cell junction cell periphery plasma membrane membrane membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
A	IPR003598	Immunoglobulin subtype 2	Domain
A	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
A	IPR000920	Myelin P0 protein-related	Family
A	IPR013106	Immunoglobulin V-set domain	Domain
A	IPR003599	Immunoglobulin domain subtype	Domain
A	IPR007110	Immunoglobulin-like domain	Domain

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.