6A78 | pdb_00006a78

Crystal structure of the fifth immunoglobulin domain (Ig5) of human Robo1 in complex with the scFv fragment of murine monoclonal antibody B5209B

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 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
Pharos: Disease Associations

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
F [auth I]	d6a78i_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	(Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
C [auth H]	d6a78h_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	(Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
E [auth M]	d6a78m_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	(Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
B [auth L]	d6a78l_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	(Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
D [auth B]	d6a78b1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D [auth B]	d6a78b2	Artifacts	Tags	Tags	Tags	N-terminal Tags	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d6a78a1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d6a78a2	Artifacts	Tags	Tags	Tags	N-terminal Tags	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)
D [auth B]	SCOP2B Superfamily	Immunoglobulin (Ig) domain-like	8077369	3000071	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Immunoglobulin (Ig) domain-like	8077369	3000071	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)
F [auth I]	C1-set	e6a78I1	A: a/b three-layered sandwiches	X: PriB N-terminal domain-like	H: Aconitase iron-sulfur domain	T: Aconitase iron-sulfur domain	F: C1-set	ECOD (v294.1)
C [auth H]	C1-set	e6a78H1	A: a/b three-layered sandwiches	X: PriB N-terminal domain-like	H: Aconitase iron-sulfur domain	T: Aconitase iron-sulfur domain	F: C1-set	ECOD (v294.1)
E [auth M]	C1-set	e6a78M1	A: a/b three-layered sandwiches	X: PriB N-terminal domain-like	H: Aconitase iron-sulfur domain	T: Aconitase iron-sulfur domain	F: C1-set	ECOD (v294.1)
B [auth L]	C1-set	e6a78L1	A: a/b three-layered sandwiches	X: PriB N-terminal domain-like	H: Aconitase iron-sulfur domain	T: Aconitase iron-sulfur domain	F: C1-set	ECOD (v294.1)
D [auth B]	C1-set	e6a78B1	A: a/b three-layered sandwiches	X: PriB N-terminal domain-like	H: Aconitase iron-sulfur domain	T: Aconitase iron-sulfur domain	F: C1-set	ECOD (v294.1)
A	C1-set	e6a78A1	A: a/b three-layered sandwiches	X: PriB N-terminal domain-like	H: Aconitase iron-sulfur domain	T: Aconitase iron-sulfur domain	F: C1-set	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D [auth B]	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], F [auth I]	scFv B5209B, anti-human Robo1	VH	Mus musculus (house mouse)	IGHV5-6-301, IGHJ401	V-DOMAIN VH	IG	FV-HEAVY_KAPPA	IMGT (202611-0)
B [auth L], E [auth M]	scFv B5209B, anti-human Robo1	V-KAPPA	Mus musculus (house mouse)	IGKV12-8901, IGKJ401	V-DOMAIN V-KAPPA	IG	FV-HEAVY_KAPPA	IMGT (202611-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
C [auth H], F [auth I]	Heavy Chain	IGHV5	-	roundabout homolog 1	SAbDab (2026-03-27)
B [auth L], E [auth M]	Light Chain	IGKV12	Kappa	roundabout homolog 1	SAbDab (2026-03-27)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, D [auth B]	PF13927	Immunoglobulin domain (Ig_3)	Immunoglobulin domain	This family contains immunoglobulin-like domains.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C [auth H], F [auth I]	Heavy chain and linker region of the anti-human Robo1 antibody B5209B scFv	-	-	-
B [auth L], E [auth M]	Light chain region of the anti-human Robo1 antibody B5209B scFv	-	-	-
A, D [auth B]	Roundabout homolog 1	molecular transducer activity transmembrane signaling receptor activity signaling receptor activity axon guidance receptor activity LRR domain binding protein binding binding protein domain specific binding identical protein binding	neuron recognition multicellular organismal process axonogenesis cellular developmental process cell projection organization plasma membrane bounded cell projection morphogenesis cell development neuron projection development axon choice point recognition cell morphogenesis cellular component organization neurogenesis multicellular organism development cell projection morphogenesis neuron differentiation neuron recognition multicellular organismal process axonogenesis cellular developmental process cell projection organization plasma membrane bounded cell projection morphogenesis cell development neuron projection development axon choice point recognition cell morphogenesis cellular component organization neurogenesis multicellular organism development cell projection morphogenesis neuron differentiation neuron projection morphogenesis cell differentiation anatomical structure development cell recognition cellular component organization or biogenesis system development developmental process plasma membrane bounded cell projection organization axon midline choice point recognition axon guidance nervous system development axon development cell morphogenesis involved in neuron differentiation generation of neurons anatomical structure morphogenesis neuron projection guidance neuron development cellular process heart development cardiac chamber morphogenesis animal organ development heart morphogenesis ventricular septum development circulatory system development cardiac septum development cardiac septum morphogenesis ventricular septum morphogenesis cardiac chamber development animal organ morphogenesis cardiac ventricle development regulation of biosynthetic process regulation of biological process regulation of cellular process biological regulation positive regulation of biological process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process positive regulation of macromolecule biosynthetic process regulation of gene expression positive regulation of metabolic process biosynthetic process positive regulation of gene expression positive regulation of biosynthetic process regulation of macromolecule biosynthetic process metabolic process positive regulation of macromolecule metabolic process macromolecule metabolic process regulation of metabolic process positive regulation of cellular process chemotaxis negative regulation of locomotion negative chemotaxis response to stimulus regulation of response to external stimulus negative regulation of response to stimulus negative regulation of biological process negative regulation of negative chemotaxis response to external stimulus negative regulation of chemotaxis regulation of chemotaxis regulation of negative chemotaxis taxis regulation of response to stimulus response to chemical regulation of locomotion negative regulation of response to external stimulus locomotion cellular response to stimulus positive regulation of cell communication cellular response to growth factor stimulus positive regulation of signal transduction signaling regulation of signal transduction cell surface receptor protein tyrosine kinase signaling pathway cell communication regulation of vascular endothelial growth factor receptor signaling pathway positive regulation of response to stimulus cellular response to endogenous stimulus signal transduction enzyme-linked receptor protein signaling pathway regulation of signaling cell surface receptor signaling pathway response to endogenous stimulus regulation of cellular response to growth factor stimulus vascular endothelial growth factor receptor signaling pathway positive regulation of vascular endothelial growth factor receptor signaling pathway regulation of cell communication response to growth factor positive regulation of signaling positive regulation of nervous system development regulation of cell differentiation regulation of neurogenesis regulation of cell development positive regulation of developmental process positive regulation of cell projection organization regulation of cell projection organization positive regulation of cell development positive regulation of multicellular organismal process regulation of neuron projection development regulation of cellular component organization positive regulation of cellular component organization regulation of developmental process regulation of nervous system development positive regulation of cell differentiation regulation of axonogenesis positive regulation of neurogenesis regulation of multicellular organismal process positive regulation of axonogenesis regulation of anatomical structure morphogenesis regulation of multicellular organismal development regulation of plasma membrane bounded cell projection organization small GTPase-mediated signal transduction regulation of small GTPase mediated signal transduction intracellular signal transduction Rho protein signal transduction regulation of intracellular signal transduction intracellular signaling cassette positive regulation of intracellular signal transduction regulation of Rho protein signal transduction positive regulation of Rho protein signal transduction positive regulation of small GTPase mediated signal transduction regulation of vascular endothelial growth factor signaling pathway regulation of cellular response to vascular endothelial growth factor stimulus positive regulation of vascular endothelial growth factor signaling pathway vascular endothelial growth factor signaling pathway cellular response to vascular endothelial growth factor stimulus cell migration involved in sprouting angiogenesis blood vessel morphogenesis tube development endothelial cell migration angiogenesis sprouting angiogenesis vasculature development tube morphogenesis anatomical structure formation involved in morphogenesis blood vessel endothelial cell migration cell migration cell motility blood vessel development mesenchyme morphogenesis endocardial cushion morphogenesis mesenchyme development tissue development endocardial cushion formation tissue morphogenesis endocardial cushion development mammary gland development gland development negative regulation of mammary gland epithelial cell proliferation negative regulation of cellular process epithelial cell proliferation negative regulation of cell population proliferation epithelium development cell population proliferation regulation of mammary gland epithelial cell proliferation mammary gland epithelium development regulation of cell population proliferation regulation of epithelial cell proliferation negative regulation of multicellular organismal process negative regulation of epithelial cell proliferation mammary gland epithelial cell proliferation artery development aorta development outflow tract septum morphogenesis outflow tract morphogenesis heart valve development aortic valve development heart valve morphogenesis semi-lunar valve development aortic valve morphogenesis negative regulation of signaling regulation of chemokine-mediated signaling pathway response to cytokine response to chemokine negative regulation of cell communication cytokine-mediated signaling pathway cellular response to chemokine negative regulation of G protein-coupled receptor signaling pathway chemokine-mediated signaling pathway cellular response to cytokine stimulus regulation of G protein-coupled receptor signaling pathway regulation of cytokine-mediated signaling pathway negative regulation of chemokine-mediated signaling pathway negative regulation of signal transduction response to peptide regulation of response to cytokine stimulus negative regulation of response to cytokine stimulus negative regulation of cytokine-mediated signaling pathway G protein-coupled receptor signaling pathway positive regulation of MAPK cascade regulation of MAPK cascade MAPK cascade pulmonary valve morphogenesis pulmonary valve development regulation of cell motility regulation of cell migration negative regulation of cell motility negative regulation of cell migration cell adhesion telencephalon cell migration head development brain development tangential migration from the subventricular zone to the olfactory bulb central nervous system development substrate-dependent cell migration olfactory bulb interneuron differentiation forebrain development central nervous system neuron development cerebral cortex development central nervous system neuron differentiation cerebral cortex tangential migration using cell-cell interactions forebrain cell migration olfactory bulb development substrate-dependent cerebral cortex tangential migration cerebral cortex cell migration forebrain generation of neurons olfactory lobe development chemorepulsion involved in postnatal olfactory bulb interneuron migration pallium development cerebral cortex tangential migration forebrain neuron development olfactory bulb interneuron development telencephalon development forebrain neuron differentiation postnatal olfactory bulb interneuron migration cell-cell adhesion homophilic cell-cell adhesion Notch signaling pathway regulation of Notch signaling pathway positive regulation of Notch signaling pathway negative regulation of metabolic process negative regulation of gene expression negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of macromolecule metabolic process Roundabout signaling pathway heart induction specification of animal organ identity pattern specification process developmental induction animal organ formation regulation of animal organ morphogenesis heart formation regionalization positive regulation of animal organ morphogenesis regulation of animal organ formation organ induction regulation of heart morphogenesis heart field specification	membrane-bounded organelle cell projection cellular anatomical structure organelle cilium plasma membrane bounded cell projection cell surface intracellular anatomical structure cytoplasm cytosol cell periphery plasma membrane membrane intracellular membrane-bounded organelle membrane-bounded organelle cell projection cellular anatomical structure organelle cilium plasma membrane bounded cell projection cell surface intracellular anatomical structure cytoplasm cytosol cell periphery plasma membrane membrane intracellular membrane-bounded organelle intracellular organelle bounding membrane of organelle endoplasmic reticulum-Golgi intermediate compartment membrane endoplasmic reticulum-Golgi intermediate compartment organelle membrane axon neuron projection

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, D [auth B]	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
A, D [auth B]	IPR003598	Immunoglobulin subtype 2	Domain
A, D [auth B]	IPR051170	Neural and epithelial cell adhesion domain-containing protein	Family
A, D [auth B]	IPR013106	Immunoglobulin V-set domain	Domain
A, D [auth B]	IPR003599	Immunoglobulin domain subtype	Domain
A, D [auth B]	IPR013098	Immunoglobulin I-set	Domain
A, D [auth B]	IPR003961	Fibronectin type III	Domain
A, D [auth B]	IPR032986	Roundabout homologue 1, immunoglobulin-like domain 3	Domain
A, D [auth B]	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
A, D [auth B]	IPR007110	Immunoglobulin-like domain	Domain
A, D [auth B]	IPR036116	Fibronectin type III superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, D [auth B]	Pharos: Q9Y6N7	adenocarcinoma prostate cancer tubular adenocarcinoma granular cell carcinoma malignant ependymoma Malignant neoplasm of lung nasopharyngeal carcinoma pancreatic ductal adenocarcinoma autism cribriform carcinoma cystic fibrosis gastric carcinoma lung benign neoplasm malignant mesothelioma malignant pancreatic neoplasm adenocarcinoma prostate cancer tubular adenocarcinoma granular cell carcinoma malignant ependymoma Malignant neoplasm of lung nasopharyngeal carcinoma pancreatic ductal adenocarcinoma autism cribriform carcinoma cystic fibrosis gastric carcinoma lung benign neoplasm malignant mesothelioma malignant pancreatic neoplasm osteosarcoma pilocytic astrocytoma ulcerative colitis cribriform carcinoma of breast dyslexia lung cancer malignant colon neoplasm medulloblastoma ovarian cancer pituitary stalk interruption syndrome sarcoidosis breast cancer Crohn disease endogenous depression hepatocellular carcinoma lung carcinoma

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.