3EO1 | pdb_00003eo1

Structure of the Fab Fragment of GC-1008 in Complex with Transforming Growth Factor-Beta 3

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
Thera-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)
C	d3eo1c_	Small proteins	Cystine-knot cytokines	Cystine-knot cytokines	Transforming growth factor (TGF)-beta	TGF-beta3	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
F	d3eo1f_	Small proteins	Cystine-knot cytokines	Cystine-knot cytokines	Transforming growth factor (TGF)-beta	TGF-beta3	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
I	d3eo1i_	Small proteins	Cystine-knot cytokines	Cystine-knot cytokines	Transforming growth factor (TGF)-beta	TGF-beta3	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
L	d3eo1l_	Small proteins	Cystine-knot cytokines	Cystine-knot cytokines	Transforming growth factor (TGF)-beta	TGF-beta3	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d3eo1a1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	(Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
A	d3eo1a2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	automated matches	(Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
D	d3eo1d1	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	d3eo1d2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	automated matches	(Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
G	d3eo1g1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	(Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
G	d3eo1g2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	automated matches	(Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
J	d3eo1j1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	(Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
J	d3eo1j2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	automated matches	(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)
C	SCOP2B Superfamily	Cystine-knot cytokines	8038775	3000846	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Cystine-knot cytokines	8038775	3000846	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	Cystine-knot cytokines	8038775	3000846	SCOP2B (2022-06-29)
L	SCOP2B Superfamily	Cystine-knot cytokines	8038775	3000846	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)
B	IL7	e3eo1B1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: IL7	ECOD (v294.1)
E	IL7	e3eo1E1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: IL7	ECOD (v294.1)
H	IL7	e3eo1H1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: IL7	ECOD (v294.1)
K	IL7	e3eo1K1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: IL7	ECOD (v294.1)
C	IL7	e3eo1C1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: IL7	ECOD (v294.1)
F	IL7	e3eo1F1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: IL7	ECOD (v294.1)
I	IL7	e3eo1I1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: IL7	ECOD (v294.1)
L	IL7	e3eo1L1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: IL7	ECOD (v294.1)
A	IL7	e3eo1A1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: IL7	ECOD (v294.1)
D	IL7	e3eo1D1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: IL7	ECOD (v294.1)
G	IL7	e3eo1G1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: IL7	ECOD (v294.1)
J	IL7	e3eo1J1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: IL7	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
E	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
H	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
K	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
C	2.10.90.10	Mainly Beta	Ribbon	Cystine Knot Cytokines, subunit B	Cystine-knot cytokines	CATH (4.3.0)
F	2.10.90.10	Mainly Beta	Ribbon	Cystine Knot Cytokines, subunit B	Cystine-knot cytokines	CATH (4.3.0)
I	2.10.90.10	Mainly Beta	Ribbon	Cystine Knot Cytokines, subunit B	Cystine-knot cytokines	CATH (4.3.0)
L	2.10.90.10	Mainly Beta	Ribbon	Cystine Knot Cytokines, subunit B	Cystine-knot cytokines	CATH (4.3.0)
A	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
D	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
G	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
J	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, E, H, K	Fab GC-1008	VH-CH1	Homo sapiens (human)	IGHV1-6901, IGHV1-6910, IGHV1-6912, IGHV1-6913, IGHV1-69D01, IGHJ301, IGHJ302, IGHG401, IGHG4*04	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-4_KAPPA	IMGT (202612-0)
A, D, G, J	Fab GC-1008	L-KAPPA	Homo sapiens (human)	IGKV3-2001, IGKJ501, IGKC*01	V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA	IG	FAB-GAMMA-4_KAPPA	IMGT (202612-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
B, E, H, K	Heavy Chain	IGHV1	-	transforming growth factor beta-3	SAbDab (2026-03-27)
A, D, G, J	Light Chain	IGKV8	Kappa	transforming growth factor beta-3	SAbDab (2026-03-27)

Thera-SAbDab Antibody Annotation Thera-SAbDab Database Homepage

Chain	Name	Target	Provenance Source
B, E, H, K	Fresolimumab	TGFB	Therapeutic SAbDab (2026-03-27)
A, D, G, J	Fresolimumab	TGFB	Therapeutic SAbDab (2026-03-27)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B, E, H, K	PF07654	Immunoglobulin C1-set domain (C1-set)	Immunoglobulin C1-set domain		Domain
C, F, I, L	PF00019	Transforming growth factor beta like domain (TGF_beta)	Transforming growth factor beta like domain		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B, E, H, K	GC-1008 Fab Heavy Chain	protein binding binding signaling receptor binding immunoglobulin receptor binding antigen binding	cellular response to stimulus immune response-regulating cell surface receptor signaling pathway regulation of cellular process response to stimulus signaling positive regulation of biological process cell communication positive regulation of response to stimulus immune response-activating signaling pathway immune response-regulating signaling pathway positive regulation of immune response regulation of immune system process signal transduction positive regulation of immune system process cellular response to stimulus immune response-regulating cell surface receptor signaling pathway regulation of cellular process response to stimulus signaling positive regulation of biological process cell communication positive regulation of response to stimulus immune response-activating signaling pathway immune response-regulating signaling pathway positive regulation of immune response regulation of immune system process signal transduction positive regulation of immune system process regulation of biological process cell surface receptor signaling pathway immune response-activating cell surface receptor signaling pathway immune response B cell receptor signaling pathway biological regulation regulation of response to stimulus immune system process regulation of immune response cellular process antigen receptor-mediated signaling pathway activation of immune response adaptive immune response adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains lymphocyte mediated immunity humoral immune response complement activation humoral immune response mediated by circulating immunoglobulin leukocyte mediated immunity complement activation, classical pathway immunoglobulin mediated immune response immune effector process B cell mediated immunity biological process involved in interspecies interaction between organisms response to other organism defense response antibacterial humoral response defense response to symbiont response to external stimulus antimicrobial humoral response response to biotic stimulus defense response to bacterium defense response to other organism response to stress response to bacterium response to external biotic stimulus	cellular anatomical structure extracellular region blood microparticle protein-containing complex extracellular protein-containing complex immunoglobulin complex, circulating immunoglobulin complex extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle organelle vesicle extracellular membrane-bounded organelle cellular anatomical structure extracellular region blood microparticle protein-containing complex extracellular protein-containing complex immunoglobulin complex, circulating immunoglobulin complex extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle organelle vesicle extracellular membrane-bounded organelle cell periphery plasma membrane membrane IgG immunoglobulin complex
C, F, I, L	Transforming growth factor beta-3	transforming growth factor beta receptor binding protein binding binding signaling receptor binding type I transforming growth factor beta receptor binding cytokine receptor binding molecular function activator activity molecular function regulator activity signaling receptor regulator activity growth factor activity receptor ligand activity signaling receptor activator activity identical protein binding transforming growth factor beta binding transforming growth factor beta receptor binding protein binding binding signaling receptor binding type I transforming growth factor beta receptor binding cytokine receptor binding molecular function activator activity molecular function regulator activity signaling receptor regulator activity growth factor activity receptor ligand activity signaling receptor activator activity identical protein binding transforming growth factor beta binding growth factor binding cytokine binding type II transforming growth factor beta receptor binding type III transforming growth factor beta receptor binding cytokine activity	cellular response to stimulus positive regulation of cell communication cell surface receptor protein serine/threonine kinase signaling pathway regulation of cellular process positive regulation of signal transduction response to stimulus signaling regulation of transmembrane receptor protein serine/threonine kinase signaling pathway positive regulation of biological process regulation of signal transduction intracellular signal transduction cell communication positive regulation of response to stimulus regulation of intracellular signal transduction intracellular signaling cassette cellular response to stimulus positive regulation of cell communication cell surface receptor protein serine/threonine kinase signaling pathway regulation of cellular process positive regulation of signal transduction response to stimulus signaling regulation of transmembrane receptor protein serine/threonine kinase signaling pathway positive regulation of biological process regulation of signal transduction intracellular signal transduction cell communication positive regulation of response to stimulus regulation of intracellular signal transduction intracellular signaling cassette signal transduction enzyme-linked receptor protein signaling pathway positive regulation of cellular process regulation of biological process regulation of signaling cell surface receptor signaling pathway biological regulation positive regulation of intracellular signal transduction positive regulation of transmembrane receptor protein serine/threonine kinase signaling pathway SMAD protein signal transduction regulation of response to stimulus regulation of cell communication cellular process regulation of SMAD protein signal transduction positive regulation of SMAD protein signal transduction positive regulation of signaling developmental process multicellular organismal process gland development animal organ development salivary gland development anatomical structure morphogenesis multicellular organism development gland morphogenesis salivary gland morphogenesis anatomical structure development animal organ morphogenesis exocrine system development system development heart development circulatory system development response to ketone response to lipid response to hormone response to steroid hormone response to chemical response to endogenous stimulus response to progesterone response to oxygen-containing compound positive regulation of programmed cell death regulation of apoptotic process regulation of programmed cell death cell death positive regulation of apoptotic process apoptotic process programmed cell death mammary gland development response to decreased oxygen levels detection of hypoxia detection of stimulus response to hypoxia response to stress detection of chemical stimulus response to oxygen levels response to abiotic stimulus detection of oxygen positive regulation of cell division cell division regulation of cell division embryo development ending in birth or egg hatching chordate embryonic development embryo development in utero embryonic development cellular component disassembly regulation of tight junction disassembly positive regulation of cellular component organization regulation of cellular component organization cell junction disassembly tight junction organization positive regulation of tight junction disassembly cellular component organization tight junction disassembly cell junction organization cell-cell junction disassembly cellular component organization or biogenesis cell-cell junction organization secondary palate development roof of mouth development odontogenesis regulation of immune effector process negative regulation of biological process negative regulation of macrophage cytokine production cytokine production regulation of cytokine production negative regulation of cellular process regulation of immune system process regulation of multicellular organismal process myeloid leukocyte cytokine production cytokine production involved in immune response negative regulation of macromolecule metabolic process production of molecular mediator of immune response regulation of biosynthetic process negative regulation of cytokine production involved in immune response regulation of cytokine production involved in immune response immune response negative regulation of metabolic process negative regulation of immune effector process negative regulation of cytokine production regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process immune effector process regulation of gene expression negative regulation of production of molecular mediator of immune response negative regulation of gene expression biosynthetic process regulation of macrophage cytokine production negative regulation of immune system process negative regulation of biosynthetic process immune system process negative regulation of macromolecule biosynthetic process metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of production of molecular mediator of immune response negative regulation of multicellular organismal process regulation of metabolic process macrophage cytokine production collagen biosynthetic process regulation of collagen biosynthetic process regulation of collagen metabolic process positive regulation of metabolic process positive regulation of collagen metabolic process positive regulation of biosynthetic process positive regulation of collagen biosynthetic process collagen metabolic process positive regulation of DNA-templated transcription RNA metabolic process positive regulation of macromolecule biosynthetic 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 positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of transcription by RNA polymerase II 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 regulation of vascular associated smooth muscle cell proliferation negative regulation of cell population proliferation cell population proliferation regulation of smooth muscle cell proliferation negative regulation of vascular associated smooth muscle cell proliferation smooth muscle cell proliferation negative regulation of smooth muscle cell proliferation regulation of cell population proliferation muscle cell proliferation vascular associated smooth muscle cell proliferation cellular response to growth factor stimulus cellular response to transforming growth factor beta stimulus cellular response to endogenous stimulus response to transforming growth factor beta transforming growth factor beta receptor signaling pathway response to growth factor transforming growth factor beta receptor superfamily signaling pathway head development face morphogenesis head morphogenesis face development body morphogenesis regulation of epithelial to mesenchymal transition regulation of developmental process cellular developmental process positive regulation of epithelial to mesenchymal transition regulation of cell differentiation mesenchyme development positive regulation of developmental process positive regulation of cell differentiation cell differentiation tissue development epithelial to mesenchymal transition positive regulation of multicellular organismal process mesenchymal cell differentiation neuron apoptotic process negative regulation of neuron apoptotic process negative regulation of programmed cell death negative regulation of apoptotic process regulation of neuron apoptotic process positive regulation of cell population proliferation regulation of localization establishment of protein localization regulation of protein localization transport positive regulation of establishment of protein localization positive regulation of secretion by cell protein localization to extracellular region positive regulation of protein transport localization regulation of secretion by cell secretion by cell positive regulation of secretion intracellular protein localization regulation of transport secretion regulation of establishment of protein localization establishment of protein localization to extracellular region export from cell regulation of protein transport protein secretion establishment of localization positive regulation of protein secretion regulation of protein secretion regulation of secretion positive regulation of transport protein transport macromolecule localization positive regulation of protein localization rhythmic process ovulation cycle ovulation cycle process reproductive process multicellular organismal reproductive process uterine wall breakdown filopodium assembly cell projection organization regulation of filopodium assembly plasma membrane bounded cell projection assembly cellular component biogenesis cellular component assembly positive regulation of cell projection organization positive regulation of filopodium assembly plasma membrane bounded cell projection organization positive regulation of cellular component biogenesis regulation of cell projection organization regulation of cell projection assembly regulation of cellular component biogenesis regulation of plasma membrane bounded cell projection assembly cell projection assembly regulation of plasma membrane bounded cell projection organization positive regulation of plasma membrane bounded cell projection assembly positive regulation of organelle organization regulation of cytoskeleton organization regulation of actin filament-based process regulation of actin filament bundle assembly positive regulation of actin filament bundle assembly actin filament bundle organization positive regulation of stress fiber assembly actin filament-based process stress fiber assembly regulation of actin filament organization actin cytoskeleton organization actomyosin structure organization positive regulation of cytoskeleton organization actin filament organization positive regulation of supramolecular fiber organization regulation of organelle organization regulation of stress fiber assembly organelle organization contractile actin filament bundle assembly regulation of actomyosin structure organization regulation of actin cytoskeleton organization actin filament bundle assembly regulation of supramolecular fiber organization supramolecular fiber organization cytoskeleton organization tube development respiratory tube development lung development respiratory system development lung alveolus development	membrane-bounded organelle vesicle lumen intracellular anatomical structure intracellular vesicle membrane-enclosed lumen cytoplasmic vesicle lumen intracellular membrane-bounded organelle secretory granule lumen endomembrane system intracellular organelle lumen intracellular organelle cellular anatomical structure cytoplasmic vesicle organelle lumen membrane-bounded organelle vesicle lumen intracellular anatomical structure intracellular vesicle membrane-enclosed lumen cytoplasmic vesicle lumen intracellular membrane-bounded organelle secretory granule lumen endomembrane system intracellular organelle lumen intracellular organelle cellular anatomical structure cytoplasmic vesicle organelle lumen organelle secretory granule secretory vesicle cytoplasm platelet alpha granule vesicle platelet alpha granule lumen cell periphery plasma membrane membrane extracellular matrix external encapsulating structure extracellular region
A, D, G, J	GC-1008 Fab Light Chain	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B, E, H, K	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
B, E, H, K	IPR050380	Immune Recognition and Response Modulators	Family
B, E, H, K	IPR003597	Immunoglobulin C1-set	Domain
B, E, H, K	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
B, E, H, K	IPR007110	Immunoglobulin-like domain	Domain
B, E, H, K	IPR003006	Immunoglobulin/major histocompatibility complex, conserved site	Conserved Site
C, F, I, L	IPR029034	Cystine-knot cytokine	Homologous Superfamily
C, F, I, L	IPR017948	Transforming growth factor beta, conserved site	Conserved Site
C, F, I, L	IPR015615	Transforming growth factor-beta-like	Family
C, F, I, L	IPR001839	Transforming growth factor-beta, C-terminal	Domain
C, F, I, L	IPR016319	Transforming growth factor-beta	Family
C, F, I, L	IPR015618	Transforming growth factor beta-3	Family
C, F, I, L	IPR001111	TGF-beta, propeptide	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B, E, H, K	Pharos: P01861	psoriasis Renal transplant rejection
C, F, I, L	Pharos: P10600	cleft palate arrhythmogenic right ventricular cardiomyopathy Rienhoff syndrome arrhythmogenic right ventricular dysplasia 1 Loeys-Dietz syndrome Liver Cirrhosis, Experimental cardiomyopathy medulloblastoma arthrogryposis Ehlers-Danlos syndrome Loeys-Dietz syndrome 4 breast cancer diabetes mellitus familial thoracic aortic aneurysm and aortic dissection Marfan syndrome cleft palate arrhythmogenic right ventricular cardiomyopathy Rienhoff syndrome arrhythmogenic right ventricular dysplasia 1 Loeys-Dietz syndrome Liver Cirrhosis, Experimental cardiomyopathy medulloblastoma arthrogryposis Ehlers-Danlos syndrome Loeys-Dietz syndrome 4 breast cancer diabetes mellitus familial thoracic aortic aneurysm and aortic dissection Marfan syndrome nonsyndromic genetic deafness thoracic aortic aneurysm ductal breast carcinoma in situ intellectual disability

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.