6O39

Crystal structure of Frizzled 5 CRD in complex with F2.I Fab

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)
A	d6o39a2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	automated matches	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d6o39a1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d6o39b_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d6o39c_	All alpha proteins	Frizzled cysteine-rich domain	Frizzled cysteine-rich domain	Frizzled cysteine-rich domain	automated matches	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)
C	SCOP2B Superfamily	Frizzled domain-like	8083828	3001950	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)
A	C1-set_4	e6o39A2	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	V-set	e6o39A1	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)
B	V-set_8	e6o39B1	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	C1-set_1	e6o39B2	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)
C	Fz	e6o39C1	A: few secondary structure elements	X: Frizzled cysteine-rich domain-related (From Topology)	H: Frizzled cysteine-rich domain-related (From Topology)	T: Frizzled cysteine-rich domain-related	F: Fz	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)
B	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)
C	1.10.2000.10	Mainly Alpha	Orthogonal Bundle	Frizzled cysteine-rich domain	Frizzled cysteine-rich domain	CATH (utative)

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
A	Fab F2.I	L-KAPPA	Homo sapiens (human)	IGKV1-3901, IGKV1D-3901, IGKJ101, IGKC01	V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA	IG	FAB-GAMMA-1_KAPPA	IMGT (202447-0)
B	Fab F2.I	VH-CH1	Homo sapiens (human)	IGHV3-6601, IGHV3-6602, IGHV3-6604, IGHJ401, IGHJ402, IGHJ403, IGHG101, IGHG102, IGHG104, IGHG105, IGHG112, IGHG114, IGHG113, IGHG109, IGHG110, IGHG107, IGHG1*11	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-1_KAPPA	IMGT (202447-0)
C	Frizzled-5	FZD8	Homo sapiens (human)	FDZ8*01	R-LIKE-DOMAIN FZD8 (Pr28-158)	FPIA	FZD8	IMGT (202447-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
A	Light Chain	IGKV1	Kappa	frizzled-5	SAbDab (2024-11-29)
B	Heavy Chain	IGHV3	-	frizzled-5	SAbDab (2024-11-29)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C	PF01392	Fz domain (Fz)	Fz domain	Also known as the CRD (cysteine rich domain), the C6 box in MuSK receptor. This domain of unknown function has been independently identified by several groups [1,2,3,4]. The domain contains 10 conserved cysteines.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Antibody F2.I Fab, Light chain	-	-	-
B	Antibody F2.I Fab, Heavy chain	-	-	-
C	Frizzled-5	molecular transducer activity transmembrane signaling receptor activity signaling receptor activity Wnt receptor activity amide binding amyloid-beta binding binding peptide binding protein-containing complex binding ubiquitin protein ligase binding protein binding ubiquitin-like protein ligase binding enzyme binding Wnt-protein binding molecular transducer activity transmembrane signaling receptor activity signaling receptor activity Wnt receptor activity amide binding amyloid-beta binding binding peptide binding protein-containing complex binding ubiquitin protein ligase binding protein binding ubiquitin-like protein ligase binding enzyme binding Wnt-protein binding G protein-coupled receptor activity kinase binding protein kinase binding lipid binding	developmental process multicellular organismal process sensory organ development post-embryonic camera-type eye development eye development animal organ development visual system development multicellular organism development camera-type eye development anatomical structure development post-embryonic development sensory system development system development adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains developmental process multicellular organismal process sensory organ development post-embryonic camera-type eye development eye development animal organ development visual system development multicellular organism development camera-type eye development anatomical structure development post-embryonic development sensory system development system development adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains regulation of immune effector process lymphocyte mediated immunity T cell mediated immunity positive regulation of leukocyte mediated immunity regulation of cellular process response to stimulus T cell cytokine production positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of immune response cytokine production leukocyte mediated immunity regulation of immune system process positive regulation of macromolecule metabolic process positive regulation of adaptive immune response positive regulation of T cell cytokine production positive regulation of immune system process regulation of T cell mediated immunity regulation of biological process regulation of cytokine production involved in immune response immune response regulation of adaptive immune response immune effector process regulation of gene expression regulation of leukocyte mediated immunity biosynthetic process regulation of response to stimulus positive regulation of production of molecular mediator of immune response positive regulation of multicellular organismal process regulation of immune response metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of production of molecular mediator of immune response positive regulation of cytokine production regulation of metabolic process positive regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains positive regulation of lymphocyte mediated immunity positive regulation of biological process positive regulation of response to stimulus regulation of T cell cytokine production regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains positive regulation of biosynthetic process regulation of cytokine production positive regulation of immune effector process regulation of multicellular organismal process cytokine production involved in immune response positive regulation of cellular process production of molecular mediator of immune response regulation of biosynthetic process biological regulation regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process adaptive immune response regulation of lymphocyte mediated immunity positive regulation of gene expression immune system process positive regulation of T cell mediated immunity positive regulation of cytokine production involved in immune response cellular process cellular response to stimulus cell surface receptor signaling pathway signaling canonical Wnt signaling pathway cell communication signal transduction Wnt signaling pathway cell differentiation involved in embryonic placenta development cellular developmental process placenta development reproductive process syncytiotrophoblast cell differentiation involved in labyrinthine layer development chordate embryonic development labyrinthine layer development developmental process involved in reproduction embryo development in utero embryonic development embryonic placenta development embryo development ending in birth or egg hatching cell differentiation embryonic organ development cell development epithelial cell differentiation intestinal epithelial cell maturation columnar/cuboidal epithelial cell development cell maturation epithelium development digestive system development intestinal epithelial cell differentiation tube development intestinal epithelial cell development developmental maturation tissue development digestive tract development epithelial cell development anatomical structure maturation columnar/cuboidal epithelial cell differentiation epithelial cell maturation columnar/cuboidal epithelial cell maturation embryonic morphogenesis morphogenesis of an epithelium branching involved in labyrinthine layer morphogenesis embryonic placenta morphogenesis anatomical structure morphogenesis labyrinthine layer morphogenesis tissue morphogenesis morphogenesis of a branching structure morphogenesis of a branching epithelium interleukin-1 production regulation of interleukin-1 beta production positive regulation of interleukin-1 beta production positive regulation of interleukin-1 production regulation of interleukin-1 production interleukin-1 beta production hemopoiesis cell activation mononuclear cell differentiation lymphocyte activation lymphocyte differentiation leukocyte activation T cell differentiation in thymus T cell activation T cell differentiation leukocyte differentiation catabolic process macroautophagy autophagy regulation of mitophagy regulation of catabolic process regulation of autophagy regulation of macroautophagy mitophagy regulation of autophagy of mitochondrion process utilizing autophagic mechanism autophagy of mitochondrion glandular epithelial cell development glandular epithelial cell maturation glandular epithelial cell differentiation embryonic eye morphogenesis embryonic camera-type eye development eye morphogenesis animal organ morphogenesis embryonic organ morphogenesis camera-type eye morphogenesis embryonic camera-type eye morphogenesis sensory organ morphogenesis nervous system development cellular component organization cellular component biogenesis cell junction organization cellular component assembly cell junction assembly synapse organization cellular component organization or biogenesis synapse assembly positive regulation of DNA-templated transcription RNA metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process transcription by RNA polymerase II regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of transcription by RNA polymerase II positive regulation of nucleobase-containing compound metabolic process primary metabolic process positive regulation of transcription by RNA polymerase II nucleobase-containing compound biosynthetic process nucleic acid metabolic process positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process regulation of DNA-templated transcription apoptotic process involved in development apoptotic process involved in morphogenesis apoptotic process cell death programmed cell death labyrinthine layer blood vessel development placenta blood vessel development vasculature development circulatory system development blood vessel development blood vessel morphogenesis angiogenesis tube morphogenesis anatomical structure formation involved in morphogenesis cell population proliferation regulation of cell population proliferation regulation of chorionic trophoblast cell proliferation chorionic trophoblast cell proliferation non-canonical Wnt signaling pathway blastoderm segmentation embryonic pattern specification anterior/posterior axis specification, embryo anterior/posterior pattern specification segmentation pattern specification process regionalization tripartite regional subdivision embryonic axis specification anterior/posterior axis specification axis specification extraembryonic membrane development chorion development chorionic trophoblast cell differentiation generation of neurons neurogenesis neuron differentiation bicellular tight junction assembly regulation of bicellular tight junction assembly regulation of cellular component organization tight junction organization apical junction assembly regulation of cellular component biogenesis regulation of cell junction assembly tight junction assembly cell-cell junction assembly cell-cell junction organization protein localization regulation of localization establishment of protein localization cellular localization regulation of protein localization protein targeting regulation of protein targeting to mitochondrion positive regulation of establishment of protein localization localization cellular macromolecule localization positive regulation of protein targeting to mitochondrion regulation of establishment of protein localization establishment of localization regulation of establishment of protein localization to mitochondrion establishment of protein localization to organelle regulation of protein targeting regulation of cellular localization macromolecule localization protein localization to organelle protein localization to mitochondrion positive regulation of protein localization protein targeting to mitochondrion establishment of protein localization to mitochondrion positive regulation of establishment of protein localization to mitochondrion biological process involved in interspecies interaction between organisms response to other organism response to external stimulus cellular response to molecule of bacterial origin response to biotic stimulus cellular response to biotic stimulus response to bacterium response to external biotic stimulus response to molecule of bacterial origin negative regulation of cell population proliferation negative regulation of cellular process negative regulation of biological process Spemann organizer formation developmental induction regulation of tumor necrosis factor production positive regulation of tumor necrosis factor superfamily cytokine production tumor necrosis factor superfamily cytokine production positive regulation of tumor necrosis factor production tumor necrosis factor production regulation of tumor necrosis factor superfamily cytokine production regulation of type II interferon production type II interferon production positive regulation of type II interferon production	somatodendritic compartment cell body cellular anatomical structure perikaryon neuronal cell body membrane-bounded organelle intracellular anatomical structure intracellular vesicle intracellular organelle bounding membrane of organelle cytoplasmic vesicle vesicle membrane clathrin-coated vesicle endocytic vesicle membrane somatodendritic compartment cell body cellular anatomical structure perikaryon neuronal cell body membrane-bounded organelle intracellular anatomical structure intracellular vesicle intracellular organelle bounding membrane of organelle cytoplasmic vesicle vesicle membrane clathrin-coated vesicle endocytic vesicle membrane coated vesicle vesicle endocytic vesicle clathrin-coated vesicle membrane clathrin-coated endocytic vesicle membrane membrane intracellular membrane-bounded organelle clathrin-coated endocytic vesicle cytoplasmic vesicle membrane coated vesicle membrane organelle cytoplasm organelle membrane cell projection dendrite dendritic tree neuron projection plasma membrane bounded cell projection Golgi membrane Golgi apparatus endomembrane system perinuclear region of cytoplasm axon cell surface cell periphery plasma membrane endosome membrane early endosome endosome early endosome membrane synapse cell junction cell-cell junction apical junction complex bicellular tight junction tight junction anchoring junction

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C	IPR036790	Frizzled cysteine-rich domain superfamily	Homologous Superfamily
C	IPR017981	GPCR, family 2-like, 7TM	Domain
C	IPR000539	Frizzled/Smoothened, 7TM	Domain
C	IPR020067	Frizzled domain	Domain
C	IPR037441	Frizzled-5, CRD domain	Domain
C	IPR015526	Frizzled/secreted frizzled-related protein	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
C	Pharos: Q13467	lung adenocarcinoma medulloblastoma pancreatic intraductal papillary-mucinous carcinoma psoriasis adrenal cortex carcinoma breast fibroadenoma Coloboma of lens esophageal adenocarcinoma invasive ductal breast carcinoma lung cancer non-small cell lung carcinoma pancreatic intraductal papillary-mucinous neoplasm ulcerative colitis atypical teratoid rhabdoid tumor coloboma lung adenocarcinoma medulloblastoma pancreatic intraductal papillary-mucinous carcinoma psoriasis adrenal cortex carcinoma breast fibroadenoma Coloboma of lens esophageal adenocarcinoma invasive ductal breast carcinoma lung cancer non-small cell lung carcinoma pancreatic intraductal papillary-mucinous neoplasm ulcerative colitis atypical teratoid rhabdoid tumor coloboma coloboma of macula cutaneous lupus erythematosus Gaucher disease interstitial cystitis large cell medulloblastoma malignant ependymoma ovarian cancer pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia breast carcinoma coloboma of eyelid coloboma of optic disc ductal breast carcinoma in situ glioblastoma interstitial lung disease

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.