6WW2

Structure of human Frizzled5 by fiducial-assisted cryo-EM

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
IMGT Antibody Annotation
SAbDab Antibody Annotation
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations
Membrane Protein Annotation: OPM
Membrane Protein Annotation: PDBTM
Membrane Protein Annotation: MemProtMD
Membrane Protein Annotation: mpstruc

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D [auth R]	SCOP2B Superfamily	Cytochromes	8057879	3001526	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)
C [auth L]	PF07654	e6ww2L2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07654	ECOD (1.6)
C [auth L]	PF07686	e6ww2L1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)
A [auth H]	PF07654	e6ww2H1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07654	ECOD (1.6)
A [auth H]	PF07686	e6ww2H2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)
B [auth K]	PF07686	e6ww2K1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)
D [auth R]	PF01534	e6ww2R2	A: alpha bundles	X: Family A G protein-coupled receptor-like (From Topology)	H: Family A G protein-coupled receptor-like (From Topology)	T: Family A G protein-coupled receptor-like	F: PF01534	ECOD (1.6)
D [auth R]	PF07361	e6ww2R1	A: alpha bundles	X: Four-helical up-and-down bundle	H: Cytochromes (From Topology)	T: Cytochromes	F: PF07361	ECOD (1.6)

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 L]	Fab, anti-BRIL	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 (202421-0)
A [auth H]	Fab, anti-BRIL	VH-CH1	Homo sapiens (human)	IGHV3-4801, IGHV3-4804, IGHJ401, IGHJ402, IGHJ403, IGHG101, IGHG102, IGHG104, IGHG105, IGHG112, IGHG114, IGHG113, IGHG109, IGHG110, IGHG107, IGHG111	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-1_KAPPA	IMGT (202421-0)
B [auth K]	synthetic VH	VH	Homo sapiens (human)	IGHV3-2301, IGHV3-23D01, IGHJ401, IGHJ402, IGHJ4*03	V-DOMAIN VH	IG	VH	IMGT (202421-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
C [auth L]	Light Chain	IGKV1	Kappa	frizzled-5,soluble cytochrome b562	SAbDab (2024-05-31)
A [auth H]	Heavy Chain	IGHV3	-	frizzled-5,soluble cytochrome b562	SAbDab (2024-05-31)
B [auth K]	Heavy Chain	IGHV1	-	-	SAbDab (2024-05-31)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
D [auth R]	PF07361	Cytochrome b562 (Cytochrom_B562)	Cytochrome b562	-	Family
D [auth R]	PF01534	Frizzled/Smoothened family membrane region (Frizzled)	Frizzled/Smoothened family membrane region	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C [auth L]	anti-BRIL Fab Light chain	-	-	-
A [auth H]	anti-BRIL Fab Heavy chain	-	-	-
B [auth K]	anti-Fab Nanobody	-	-	-
D [auth R]	Frizzled-5,Soluble cytochrome b562	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 organic cyclic compound binding tetrapyrrole binding heme binding electron transfer activity cation binding transition metal ion binding iron ion binding ion binding metal ion binding small molecule 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 organic substance biosynthetic process 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 cellular metabolic process regulation of cellular metabolic process 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 cellular biosynthetic process positive regulation of biological process positive regulation of cellular metabolic process positive regulation of response to stimulus regulation of T cell cytokine production organic substance metabolic process 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 cellular biosynthetic process 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 positive regulation of cellular biosynthetic 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 regulation of cellular component organization macroautophagy autophagy regulation of autophagy cellular catabolic process cellular component organization mitophagy organelle disassembly regulation of autophagy of mitochondrion cellular component organization or biogenesis process utilizing autophagic mechanism mitochondrion organization cellular component disassembly regulation of mitophagy regulation of catabolic process regulation of organelle organization organelle organization regulation of macroautophagy regulation of cellular catabolic process regulation of mitochondrion organization 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 biogenesis cell junction organization cellular component assembly cell junction assembly synapse organization synapse assembly regulation of primary metabolic process nucleobase-containing compound metabolic process DNA-templated transcription regulation of RNA metabolic process transcription by RNA polymerase II regulation of nucleobase-containing compound metabolic 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 positive regulation of RNA metabolic process organic cyclic compound metabolic process organic cyclic compound biosynthetic process regulation of DNA-templated transcription positive regulation of DNA-templated transcription RNA metabolic process RNA biosynthetic process nucleic acid biosynthetic process regulation of RNA biosynthetic process nucleobase-containing compound biosynthetic process nucleic acid metabolic process positive regulation of RNA biosynthetic process 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 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 response to organic substance 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 chemical 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 electron transport chain generation of precursor metabolites and energy	somatodendritic compartment cell body perikaryon neuronal cell body cellular anatomical entity 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 perikaryon neuronal cell body cellular anatomical entity 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 periplasmic space

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
D [auth R]	IPR036790	Frizzled cysteine-rich domain superfamily	Homologous Superfamily
D [auth R]	IPR017981	GPCR, family 2-like, 7TM	Domain
D [auth R]	IPR000539	Frizzled/Smoothened, 7TM	Domain
D [auth R]	IPR020067	Frizzled domain	Domain
D [auth R]	IPR037441	Frizzled-5, CRD domain	Domain
D [auth R]	IPR015526	Frizzled/secreted frizzled-related protein	Family
D [auth R]	IPR010980	Cytochrome c/b562	Homologous Superfamily
D [auth R]	IPR009155	Cytochrome b562	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
D [auth R]	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

Membrane Protein Annotation: OPM OPM Database Homepage

Chains	External Link	Type	Class	Superfamily	Family
D [auth R]	OPM	Transmembrane	Alpha-helical polytopic	Rhodopsin-like receptors and pumps	Frizzled/Smoothened family

Membrane Protein Annotation: PDBTM PDBTM Database Homepage

Chains	External Link	Comment
D [auth R]	PDBTM	Annotated as membrane protein by PDBTM

Membrane Protein Annotation: MemProtMD MemProtMD Database Homepage

Chains	External Link	Comment
D [auth R]	MemProtMD	Annotated as membrane protein by MemProtMD

Membrane Protein Annotation: mpstruc mpstruc Database Homepage

Chains	Resource Link	Group	Subgroup	Protein
D [auth R]	mpstruc	TRANSMEMBRANE PROTEINS: ALPHA-HELICAL	G Protein-Coupled Receptors: Class F	Frizzled 5 (FZD5) receptor in the ligand-free state

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 R01GM133198.