3BSZ

Crystal structure of the transthyretin-retinol binding protein-Fab complex

External Resource: Annotation

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: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Transthyretin (synonym: prealbumin)	8040289	3000848	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Transthyretin (synonym: prealbumin)	8040289	3000848	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Transthyretin (synonym: prealbumin)	8040289	3000848	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Transthyretin (synonym: prealbumin)	8040289	3000848	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Lipocalins	8042583	3001332	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Lipocalins	8042583	3001332	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	PF00576	e3bszA1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Prealbumin-like	F: PF00576	ECOD (1.6)
B	PF00576	e3bszB1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Prealbumin-like	F: PF00576	ECOD (1.6)
C	PF00576	e3bszC1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Prealbumin-like	F: PF00576	ECOD (1.6)
D	PF00576	e3bszD1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Prealbumin-like	F: PF00576	ECOD (1.6)
E	PF00061	e3bszE1	A: beta barrels	X: Lipocalins/Streptavidin	H: Lipocalins (From Topology)	T: Lipocalins	F: PF00061	ECOD (1.6)
F	PF00061	e3bszF1	A: beta barrels	X: Lipocalins/Streptavidin	H: Lipocalins (From Topology)	T: Lipocalins	F: PF00061	ECOD (1.6)
G [auth L]	PF07654	e3bszL2	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)
G [auth L]	PF07686	e3bszL1	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)
I [auth M]	PF07654	e3bszM2	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)
I [auth M]	PF07686	e3bszM1	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)
J [auth N]	PF07654	e3bszN2	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)
J [auth N]	PF07686	e3bszN1	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)
H	PF07654	e3bszH2	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)
H	PF07686	e3bszH1	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)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.60.40.180	Mainly Beta	Sandwich	Immunoglobulin-like	Transthyretin/hydroxyisourate hydrolase domain	CATH (4.3.0)
B	2.60.40.180	Mainly Beta	Sandwich	Immunoglobulin-like	Transthyretin/hydroxyisourate hydrolase domain	CATH (4.3.0)
C	2.60.40.180	Mainly Beta	Sandwich	Immunoglobulin-like	Transthyretin/hydroxyisourate hydrolase domain	CATH (4.3.0)
D	2.60.40.180	Mainly Beta	Sandwich	Immunoglobulin-like	Transthyretin/hydroxyisourate hydrolase domain	CATH (4.3.0)
E	2.40.128.20	Mainly Beta	Beta Barrel	Lipocalin	Calycin beta-barrel core domain	CATH (4.3.0)
F	2.40.128.20	Mainly Beta	Beta Barrel	Lipocalin	Calycin beta-barrel core domain	CATH (4.3.0)
G [auth L]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
I [auth M]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
J [auth N]	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)

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
G [auth L], I [auth M]	Anti-RBP Fab	L-KAPPA	Mus musculus (house mouse)	IGKV3-501, IGKJ102, IGKJ201, IGKC01, IGKC*02	V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA	IG	FAB-GAMMA-1_KAPPA	IMGT (202416-0)
H, J [auth N]	Anti-RBP Fab	VH-CH1	Mus musculus (house mouse)	IGHV1-501, IGHJ101, IGHJ102, IGHJ103, IGHG1*01	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-1_KAPPA	IMGT (202416-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
G [auth L], I [auth M]	Light Chain	IGKV3	Kappa	plasma retinol-binding protein	SAbDab (2024-04-26)
H, J [auth N]	Heavy Chain	IGHV1	-	plasma retinol-binding protein	SAbDab (2024-04-26)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF00576	HIUase/Transthyretin family (Transthyretin)	HIUase/Transthyretin family	This family includes transthyretin that is a thyroid hormone-binding protein that transports thyroxine from the bloodstream to the brain. However, most of the sequences listed in this family do not bind thyroid hormones. They are actually enzymes of ...	This family includes transthyretin that is a thyroid hormone-binding protein that transports thyroxine from the bloodstream to the brain. However, most of the sequences listed in this family do not bind thyroid hormones. They are actually enzymes of the purine catabolism that catalyse the conversion of 5-hydroxyisourate (HIU) to OHCU [2,3]. HIU hydrolysis is the original function of the family and is conserved from bacteria to mammals; transthyretins arose by gene duplications in the vertebrate lineage [4]. HIUases are distinguished in the alignment from the conserved C-terminal YRGS sequence.	Domain
E, F	PF00061	Lipocalin / cytosolic fatty-acid binding protein family (Lipocalin)	Lipocalin / cytosolic fatty-acid binding protein family	Lipocalins are transporters for small hydrophobic molecules, such as lipids, steroid hormones, bilins, and retinoids. The family also encompasses the enzyme prostaglandin D synthase (EC:5.3.99.2). Alignment subsumes both the lipocalin and fatty acid ...	Lipocalins are transporters for small hydrophobic molecules, such as lipids, steroid hormones, bilins, and retinoids. The family also encompasses the enzyme prostaglandin D synthase (EC:5.3.99.2). Alignment subsumes both the lipocalin and fatty acid binding protein signatures from PROSITE. This is supported on structural and functional grounds. The structure is an eight-stranded beta barrel.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Transthyretin	hormone activity protein binding binding molecular function activator activity signaling receptor binding molecular function regulator activity signaling receptor regulator activity receptor ligand activity signaling receptor activator activity thyroid hormone binding hormone binding identical protein binding	organonitrogen compound metabolic process purine nucleobase metabolic process primary metabolic process purine-containing compound metabolic process nucleobase-containing compound metabolic process organic cyclic compound metabolic process organic substance metabolic process nucleobase-containing small molecule metabolic process nucleobase metabolic process small molecule metabolic process metabolic process	extracellular region cellular anatomical entity extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle organelle extracellular space vesicle extracellular membrane-bounded organelle intracellular anatomical structure lytic vacuole intracellular vesicle membrane-enclosed lumen extracellular region cellular anatomical entity extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle organelle extracellular space vesicle extracellular membrane-bounded organelle intracellular anatomical structure lytic vacuole intracellular vesicle membrane-enclosed lumen cytoplasmic vesicle lumen vacuolar lumen endomembrane system intracellular organelle lumen intracellular organelle cytoplasmic vesicle lysosome vesicle lumen azurophil granule vacuole intracellular membrane-bounded organelle secretory granule lumen azurophil granule lumen organelle lumen secretory granule primary lysosome secretory vesicle cytoplasm
E, F	Plasma retinol-binding protein	vitamin binding binding alcohol binding isoprenoid binding retinoid binding lipid binding retinol binding small molecule binding retinal binding alcohol transmembrane transporter activity retinol transmembrane transporter activity lipid transporter activity lipid transmembrane transporter activity organic hydroxy compound transmembrane transporter activity vitamin binding binding alcohol binding isoprenoid binding retinoid binding lipid binding retinol binding small molecule binding retinal binding alcohol transmembrane transporter activity retinol transmembrane transporter activity lipid transporter activity lipid transmembrane transporter activity organic hydroxy compound transmembrane transporter activity vitamin transmembrane transporter activity transporter activity transmembrane transporter activity	multicellular organismal process maintenance of gastrointestinal epithelium system process digestion multicellular organismal-level homeostasis epithelial structure maintenance homeostatic process digestive system process anatomical structure homeostasis tissue homeostasis developmental process heart development multicellular organism development anatomical structure development multicellular organismal process maintenance of gastrointestinal epithelium system process digestion multicellular organismal-level homeostasis epithelial structure maintenance homeostatic process digestive system process anatomical structure homeostasis tissue homeostasis developmental process heart development multicellular organism development anatomical structure development animal organ development circulatory system development system development camera-type eye morphogenesis sensory organ development eye development embryonic morphogenesis visual system development retina development in camera-type eye embryo development retina morphogenesis in camera-type eye anatomical structure morphogenesis eye morphogenesis embryonic retina morphogenesis in camera-type eye sensory organ morphogenesis camera-type eye development animal organ morphogenesis sensory system development urinary bladder development renal system development genitalia development reproductive system development reproductive process female genitalia development sex differentiation female sex differentiation developmental process involved in reproduction vagina development reproductive structure development embryonic organ morphogenesis embryonic organ development tube development respiratory tube development lung development respiratory system development genitalia morphogenesis female genitalia morphogenesis regulation of growth regulation of cellular process regulation of cardiac muscle tissue growth regulation of developmental process developmental growth cardiac muscle cell proliferation negative regulation of biological process negative regulation of cardiac muscle tissue growth organ growth striated muscle tissue development negative regulation of organ growth negative regulation of growth regulation of organ growth regulation of heart growth negative regulation of cellular process regulation of cardiac muscle cell proliferation muscle cell proliferation regulation of multicellular organismal process cardiac muscle tissue growth muscle tissue development striated muscle cell proliferation negative regulation of cell population proliferation regulation of biological process heart growth regulation of multicellular organismal development cell population proliferation regulation of developmental growth negative regulation of heart growth cardiac muscle tissue development negative regulation of developmental process biological regulation growth tissue development negative regulation of developmental growth regulation of cell population proliferation cellular process negative regulation of multicellular organismal process negative regulation of cardiac muscle cell proliferation response to retinoic acid response to organic substance response to lipid response to stimulus response to chemical response to oxygen-containing compound cardiac chamber morphogenesis heart trabecula formation heart morphogenesis anatomical structure formation involved in morphogenesis cardiac chamber development heart trabecula morphogenesis trabecula formation trabecula morphogenesis uterus development regulation of immune effector process immunoglobulin production cellular biosynthetic process positive regulation of biological process positive regulation of cellular metabolic process positive regulation of macromolecule biosynthetic process positive regulation of metabolic process organic substance metabolic process positive regulation of biosynthetic process organic substance biosynthetic process positive regulation of immune effector process regulation of immune system process positive regulation of macromolecule metabolic process positive regulation of immune system process positive regulation of cellular process positive regulation of immunoglobulin production regulation of biosynthetic process production of molecular mediator of immune response cellular metabolic process regulation of cellular metabolic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process immune effector process regulation of cellular biosynthetic process regulation of gene expression biosynthetic process regulation of immunoglobulin production positive regulation of gene expression immune system process positive regulation of production of molecular mediator of immune response regulation of macromolecule biosynthetic process metabolic process regulation of production of molecular mediator of immune response macromolecule metabolic process regulation of metabolic process positive regulation of cellular biosynthetic process embryo development ending in birth or egg hatching skeletal system development chordate embryonic development embryonic skeletal system development monosaccharide metabolic process carbohydrate metabolic process small molecule biosynthetic process carbohydrate biosynthetic process hexose metabolic process primary metabolic process monosaccharide biosynthetic process gluconeogenesis hexose biosynthetic process small molecule metabolic process glucose metabolic process sensory perception of light stimulus sensory perception nervous system process visual perception transport organic substance transport lipid localization lipid transport organic hydroxy compound transport establishment of localization terpenoid transport localization macromolecule localization isoprenoid transport retinol transport protein localization positive regulation of cell communication regulation of localization establishment of protein localization nitrogen compound transport positive regulation of establishment of protein localization cell communication cellular macromolecule localization positive regulation of insulin secretion regulation of biological quality regulation of peptide hormone secretion regulation of hormone levels positive regulation of peptide hormone secretion establishment of protein localization to extracellular region protein secretion regulation of protein secretion regulation of secretion positive regulation of protein localization cellular localization regulation of hormone secretion regulation of protein localization regulation of peptide secretion signaling positive regulation of secretion by cell hormone secretion protein localization to extracellular region positive regulation of protein transport peptide secretion secretion by cell regulation of secretion by cell positive regulation of hormone secretion positive regulation of secretion amide transport signal release positive regulation of peptide secretion regulation of signaling secretion regulation of transport regulation of peptide transport regulation of establishment of protein localization cell-cell signaling export from cell regulation of protein transport positive regulation of protein secretion peptide transport positive regulation of transport protein transport regulation of cellular localization regulation of insulin secretion peptide hormone secretion hormone transport regulation of cell communication insulin secretion positive regulation of signaling chemical homeostasis glucose homeostasis carbohydrate homeostasis diterpenoid metabolic process organic hydroxy compound metabolic process alcohol metabolic process hormone metabolic process retinoid metabolic process cellular lipid metabolic process olefinic compound metabolic process retinol metabolic process terpenoid metabolic process isoprenoid metabolic process lipid metabolic process primary alcohol metabolic process	extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space cellular anatomical entity vesicle extracellular membrane-bounded organelle
G [auth L], I [auth M]	Fab fragment heavy chain	-	-	-
H, J [auth N]	Fab fragment light chain	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR036817	Transthyretin/hydroxyisourate hydrolase domain superfamily	Homologous Superfamily
A, B, C, D	IPR023418	Transthyretin, thyroxine binding site	Binding Site
A, B, C, D	IPR023419	Transthyretin, conserved site	Conserved Site
A, B, C, D	IPR023416	Transthyretin/hydroxyisourate hydrolase domain	Domain
A, B, C, D	IPR000895	Transthyretin/hydroxyisourate hydrolase	Family
E, F	IPR012674	Calycin	Homologous Superfamily
E, F	IPR000566	Lipocalin/cytosolic fatty-acid binding domain	Domain
E, F	IPR022272	Lipocalin family conserved site	Conserved Site
E, F	IPR022271	Lipocalin, ApoD type	Family
E, F	IPR002449	Retinol binding protein/Purpurin	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C, D	Pharos: P02766	amyloidosis familial amyloid neuropathy carpal tunnel syndrome hyperthyroxinemia, dystransthyretinemic lattice corneal dystrophy peripheral neuropathy Transthyretin related familial amyloid cardiomyopathy carpal tunnel syndrome 1 diabetes mellitus pancreatic intraductal papillary-mucinous carcinoma drug-induced liver injury peripheral nervous system disease Riley-Day syndrome acquired metabolic disease hydrocephalus amyloidosis familial amyloid neuropathy carpal tunnel syndrome hyperthyroxinemia, dystransthyretinemic lattice corneal dystrophy peripheral neuropathy Transthyretin related familial amyloid cardiomyopathy carpal tunnel syndrome 1 diabetes mellitus pancreatic intraductal papillary-mucinous carcinoma drug-induced liver injury peripheral nervous system disease Riley-Day syndrome acquired metabolic disease hydrocephalus intellectual disability Charcot-Marie-Tooth disease medulloblastoma dilated cardiomyopathy osteosarcoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia psoriasis schizophrenia acute kidney failure kidney disease lung benign neoplasm lymphatic system disease depressive disorder periodic fever syndrome polyneuropathy rheumatoid arthritis heart disease Sjogren syndrome hereditary amyloidosis hypertrophic cardiomyopathy lung carcinoma
E, F	Pharos: P02753	microphthalmia, isolated, with coloboma 10 progressive retinal dystrophy due to retinol transport defect keratomalacia vitamin A deficiency polycystic ovary syndrome Necrosis sarcomatoid carcinoma microphthalmia congestive heart failure kidney disease alcoholic liver diseases carcinoma gastric cancer oligodendroglioma hereditary diffuse gastric adenocarcinoma microphthalmia, isolated, with coloboma 10 progressive retinal dystrophy due to retinol transport defect keratomalacia vitamin A deficiency polycystic ovary syndrome Necrosis sarcomatoid carcinoma microphthalmia congestive heart failure kidney disease alcoholic liver diseases carcinoma gastric cancer oligodendroglioma hereditary diffuse gastric adenocarcinoma pilocytic astrocytoma invasive ductal breast carcinoma psoriasis adrenal cortex adenoma lung carcinoma malignant mesothelioma atopic eczema mammary neoplasms, animal undifferentiated carcinoma breast carcinoma ductal breast carcinoma in situ gastric neoplasm non-small cell lung carcinoma heart failure ovarian cancer inborn carbohydrate metabolic disorder pituitary cancer primitive neuroectodermal tumor lung adenocarcinoma adrenal cortex carcinoma malignant ependymoma type 2 diabetes mellitus atypical teratoid rhabdoid tumor breast fibroadenoma coloboma cystic fibrosis Emery-Dreifuss muscular dystrophy myopathy glioblastoma obesity disorder Pick disease interstitial cystitis adenoma lung cancer sarcoidosis malignant glioma Sjogren syndrome astrocytic tumor ulcerative colitis breast cancer medulloblastoma microphthalmia with coloboma 1

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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.