3KJ4 | pdb_00003kj4

Structure of rat Nogo receptor bound to 1D9 antagonist antibody

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

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
F [auth D]	d3kj4d_	Alpha and beta proteins (a/b)	Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)	L domain-like	Ngr ectodomain-like	automated matches	rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
C [auth A]	d3kj4a_	Alpha and beta proteins (a/b)	Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)	L domain-like	Ngr ectodomain-like	automated matches	rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
E [auth C]	d3kj4c_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
B [auth H]	d3kj4h_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
D [auth B]	d3kj4b2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	automated matches	mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
D [auth B]	d3kj4b1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
A [auth L]	d3kj4l2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	automated matches	mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
A [auth L]	d3kj4l1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
F [auth D]	SCOP2B Superfamily	L domain-like	8088501	3001010	SCOP2B (2022-06-29)
C [auth A]	SCOP2 Family	Ngr ectodomain-like	8088500	4002278	SCOP2 (2022-06-29)
C [auth A]	SCOP2 Superfamily	L domain-like	8088501	3001010	SCOP2 (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 D]	LRR_8_1	e3kj4D1	A: beta duplicates or obligate multimers	X: Single-stranded right-handed beta-helix	H: Leucine-rich repeats (From Topology)	T: Leucine-rich repeats	F: LRR_8_1	ECOD (1.6)
C [auth A]	LRR_8_1	e3kj4A1	A: beta duplicates or obligate multimers	X: Single-stranded right-handed beta-helix	H: Leucine-rich repeats (From Topology)	T: Leucine-rich repeats	F: LRR_8_1	ECOD (1.6)
E [auth C]	V-set_8	e3kj4C1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_8	ECOD (1.6)
E [auth C]	C1-set_1	e3kj4C2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_1	ECOD (1.6)
B [auth H]	V-set_8	e3kj4H1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_8	ECOD (1.6)
B [auth H]	C1-set_1	e3kj4H2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_1	ECOD (1.6)
D [auth B]	C1-set_4	e3kj4B2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_4	ECOD (1.6)
D [auth B]	V-set	e3kj4B1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set	ECOD (1.6)
A [auth L]	C1-set_4	e3kj4L2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_4	ECOD (1.6)
A [auth L]	V-set	e3kj4L1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
F [auth D]	3.80.10.10	Alpha Beta	Alpha-Beta Horseshoe	Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)	Ribonuclease Inhibitor	CATH (4.3.0)
C [auth A]	3.80.10.10	Alpha Beta	Alpha-Beta Horseshoe	Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)	Ribonuclease Inhibitor	CATH (4.3.0)
E [auth C]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
B [auth H]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
D [auth B]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
A [auth L]	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
B [auth H], E [auth C]	1D9 Fab	VH-CH1	Mus musculus (house mouse)	IGHV2-902, IGHJ301, IGHG1*02	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-1_KAPPA	IMGT (202547-0)
A [auth L], D [auth B]	1D9 Fab	L-KAPPA	Mus musculus (house mouse)	IGKV8-2101, IGKJ401, IGKC01, IGKC02	V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA	IG	FAB-GAMMA-1_KAPPA	IMGT (202547-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
B [auth H], E [auth C]	Heavy Chain	IGHV2	-	reticulon-4 receptor	SAbDab (2025-12-05)
A [auth L], D [auth B]	Light Chain	IGKV8	Kappa	reticulon-4 receptor	SAbDab (2025-12-05)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C [auth A], F [auth D]	PF13855	Leucine rich repeat (LRR_8)	Leucine rich repeat	-	Repeat

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C [auth A], F [auth D]	Reticulon-4 receptor	glycosaminoglycan binding chondroitin sulfate binding binding carbohydrate derivative binding sulfur compound binding protein binding signaling receptor binding Roundabout binding molecular transducer activity signaling receptor activity transmembrane signaling receptor activity neuregulin receptor activity ganglioside GM1 binding amide binding glycosaminoglycan binding chondroitin sulfate binding binding carbohydrate derivative binding sulfur compound binding protein binding signaling receptor binding Roundabout binding molecular transducer activity signaling receptor activity transmembrane signaling receptor activity neuregulin receptor activity ganglioside GM1 binding amide binding organic acid binding ceramide binding sphingolipid binding glycolipid binding ion binding glycosphingolipid binding ganglioside binding anion binding lipid binding carboxylic acid binding small molecule binding ganglioside GT1b binding protein-containing complex binding heparin binding	developmental process corpus callosum development multicellular organismal process head development forebrain development animal organ development brain development nervous system development multicellular organism development central nervous system development anatomical structure development telencephalon development system development axon extension developmental process corpus callosum development multicellular organismal process head development forebrain development animal organ development brain development nervous system development multicellular organism development central nervous system development anatomical structure development telencephalon development system development axon extension regulation of growth regulation of cellular process axonogenesis regulation of cellular component size developmental growth cell projection organization negative regulation of biological process regulation of cell differentiation regulation of neurogenesis neuron projection development regulation of cell development cell projection morphogenesis neuron differentiation negative regulation of growth neuron projection morphogenesis cell differentiation regulation of biological quality regulation of biological process negative regulation of cellular component organization regulation of cell projection organization negative regulation of cell growth developmental growth involved in morphogenesis generation of neurons negative regulation of axonogenesis negative regulation of developmental growth negative regulation of multicellular organismal process regulation of neuron projection development regulation of cellular component organization cellular developmental process regulation of developmental process plasma membrane bounded cell projection morphogenesis cell development cell growth cell morphogenesis regulation of axon extension cellular component organization regulation of nervous system development neurogenesis negative regulation of neurogenesis regulation of extent of cell growth regulation of axonogenesis negative regulation of cellular process negative regulation of nervous system development regulation of multicellular organismal process negative regulation of cell differentiation cellular component organization or biogenesis negative regulation of cell projection organization regulation of anatomical structure morphogenesis regulation of cell size neuron projection extension regulation of multicellular organismal development regulation of developmental growth plasma membrane bounded cell projection organization developmental cell growth negative regulation of developmental process biological regulation growth negative regulation of axon extension axon development regulation of cell growth cell morphogenesis involved in neuron differentiation negative regulation of neuron projection development anatomical structure morphogenesis negative regulation of cell development neuron development cellular process regulation of plasma membrane bounded cell projection organization regulation of anatomical structure size positive regulation of molecular function regulation of molecular function positive regulation of hydrolase activity regulation of catalytic activity regulation of hydrolase activity positive regulation of catalytic activity regulation of GTPase activity positive regulation of GTPase activity cellular response to stimulus positive regulation of cell communication small GTPase-mediated signal transduction positive regulation of signal transduction response to stimulus signaling regulation of small GTPase mediated signal transduction positive regulation of biological process regulation of signal transduction intracellular signal transduction Rho protein signal transduction cell communication positive regulation of response to stimulus regulation of intracellular signal transduction intracellular signaling cassette signal transduction positive regulation of cellular process regulation of signaling positive regulation of intracellular signal transduction regulation of Rho protein signal transduction positive regulation of Rho protein signal transduction regulation of response to stimulus regulation of cell communication positive regulation of small GTPase mediated signal transduction positive regulation of signaling regulation of cellular response to stress negative regulation of neuron projection regeneration regeneration neuron projection regeneration response to wounding regulation of axon regeneration response to external stimulus negative regulation of response to external stimulus regulation of neuron projection regeneration negative regulation of axon regeneration regulation of response to external stimulus response to axon injury regulation of response to wounding cellular response to stress axon regeneration regulation of response to stress response to stress negative regulation of response to stimulus negative regulation of response to wounding cell surface receptor signaling pathway cellular component biogenesis cellular component assembly regulation of postsynapse assembly cell junction assembly regulation of synapse structure or activity synapse organization regulation of synapse assembly postsynapse organization postsynapse assembly regulation of postsynapse organization regulation of cellular component biogenesis regulation of cell junction assembly regulation of synapse organization cell junction organization synapse assembly chemotaxis negative chemotaxis taxis response to chemical locomotion neuronal signal transduction	somatodendritic compartment cell body cellular anatomical structure perikaryon neuronal cell body cell periphery cell surface membrane plasma membrane external side of plasma membrane side of membrane growth cone axon cell projection somatodendritic compartment cell body cellular anatomical structure perikaryon neuronal cell body cell periphery cell surface membrane plasma membrane external side of plasma membrane side of membrane growth cone axon cell projection distal axon neuron projection axonal growth cone plasma membrane bounded cell projection site of polarized growth membrane microdomain membrane raft presynapse synapse cell junction glutamatergic synapse dendrite dendritic tree dendritic shaft
B [auth H], E [auth C]	Fab fragment 1D9 heavy chain	-	-	-
A [auth L], D [auth B]	Fab fragment 1D9 light chain	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C [auth A], F [auth D]	IPR003591	Leucine-rich repeat, typical subtype	Repeat
C [auth A], F [auth D]	IPR001611	Leucine-rich repeat	Repeat
C [auth A], F [auth D]	IPR050541	Leucine-rich repeat and transmembrane domain-containing protein	Family
C [auth A], F [auth D]	IPR032675	Leucine-rich repeat domain superfamily	Homologous Superfamily
C [auth A], F [auth D]	IPR000483	Cysteine-rich flanking region, C-terminal	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.