3V89

The crystal structure of transferrin binding protein A (TbpA) from Neisseria meningitidis serogroup B in complex with the C-lobe of human transferrin

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
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: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	TonB_dep_Rec	e3v89A2	A: beta barrels	X: Outer membrane meander beta-barrels	H: Porins	T: Ligand-gated protein channel	F: TonB_dep_Rec	ECOD (1.6)
A	Plug	e3v89A1	A: a+b complex topology	X: N0 domain in phage tail proteins and secretins-like	H: TonB-dependent receptor plug domain (From Topology)	T: TonB-dependent receptor plug domain	F: Plug	ECOD (1.6)
B	Transferrin_2nd	e3v89B2	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II (From Topology)	H: Periplasmic binding protein-like II (From Topology)	T: Periplasmic binding protein-like II	F: Transferrin_2nd	ECOD (1.6)
B	Transferrin_1st	e3v89B1	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II (From Topology)	H: Periplasmic binding protein-like II (From Topology)	T: Periplasmic binding protein-like II	F: Transferrin_1st	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.170.130.10	Mainly Beta	Beta Complex	Ferric Hydroxamate Uptake Protein	Chain A, domain 1	CATH (4.3.0)
A	2.40.170.20	Mainly Beta	Beta Barrel	Maltoporin	Chain A	CATH (4.3.0)
B	3.40.190.10	Alpha Beta	3-Layer(aba) Sandwich	D-Maltodextrin-Binding Protein	domain 2	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF00593	TonB dependent receptor-like, beta-barrel (TonB_dep_Rec_b-barrel)	TonB dependent receptor-like, beta-barrel	This entry represents the beta-barrel domain of TonB-dependent receptors, such as BtuB, CirA, FatA, FcuT, FecA, FepA, among others [1].	Domain
A	PF07715	TonB-dependent Receptor Plug Domain (Plug)	TonB-dependent Receptor Plug Domain	The Plug domain has been shown to be an independently folding subunit of the TonB-dependent receptors ([1]). It acts as the channel gate, blocking the pore until the channel is bound by ligand. At this point it under goes conformational changes opens ...	The Plug domain has been shown to be an independently folding subunit of the TonB-dependent receptors ([1]). It acts as the channel gate, blocking the pore until the channel is bound by ligand. At this point it under goes conformational changes opens the channel.	Domain
B	PF00405	Transferrin (Transferrin)	Transferrin	-	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Transferrin-binding protein A	monoatomic cation transmembrane transporter activity ferric iron transmembrane transporter activity inorganic molecular entity transmembrane transporter activity iron ion transmembrane transporter activity inorganic cation transmembrane transporter activity monoatomic ion transmembrane transporter activity transporter activity transition metal ion transmembrane transporter activity metal ion transmembrane transporter activity transmembrane transporter activity siderophore-iron transmembrane transporter activity siderophore uptake transmembrane transporter activity	siderophore transport transport monoatomic ion transmembrane transport iron ion transport iron ion transmembrane transport inorganic ion transmembrane transport establishment of localization metal ion transport inorganic cation transmembrane transport siderophore transmembrane transport transmembrane transport monoatomic cation transmembrane transport localization transition metal ion transport monoatomic ion transport siderophore transport transport monoatomic ion transmembrane transport iron ion transport iron ion transmembrane transport inorganic ion transmembrane transport establishment of localization metal ion transport inorganic cation transmembrane transport siderophore transmembrane transport transmembrane transport monoatomic cation transmembrane transport localization transition metal ion transport monoatomic ion transport cellular process monoatomic cation transport iron coordination entity transport	cell periphery cell outer membrane cellular anatomical structure external encapsulating structure membrane cell envelope outer membrane
B	Serotransferrin	cation binding transition metal ion binding iron ion binding ion binding binding ferrous iron binding metal ion binding small molecule binding ferric iron binding transferrin receptor binding protein binding signaling receptor binding metallochaperone activity iron chaperone activity cation binding transition metal ion binding iron ion binding ion binding binding ferrous iron binding metal ion binding small molecule binding ferric iron binding transferrin receptor binding protein binding signaling receptor binding metallochaperone activity iron chaperone activity molecular carrier activity transmembrane transporter binding enzyme binding	intracellular iron ion homeostasis inorganic ion homeostasis cellular homeostasis chemical homeostasis homeostatic process intracellular monoatomic cation homeostasis monoatomic ion homeostasis intracellular chemical homeostasis monoatomic cation homeostasis intracellular monoatomic ion homeostasis localization transport iron ion transport transition metal ion transport intracellular iron ion homeostasis inorganic ion homeostasis cellular homeostasis chemical homeostasis homeostatic process intracellular monoatomic cation homeostasis monoatomic ion homeostasis intracellular chemical homeostasis monoatomic cation homeostasis intracellular monoatomic ion homeostasis localization transport iron ion transport transition metal ion transport monoatomic ion transport monoatomic cation transport establishment of localization metal ion transport cellular response to stimulus regulation of biological process regulation of cellular process response to stimulus signaling biological regulation intracellular signal transduction cell communication intracellular signaling cassette MAPK cascade cellular process ERK1 and ERK2 cascade signal transduction cellular response to iron ion cellular response to metal ion cellular response to chemical stimulus response to metal ion response to chemical response to iron ion humoral immune response biological process involved in interspecies interaction between organisms response to other organism defense response immune 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 immune system process response to bacterium response to external biotic stimulus multicellular organismal-level iron ion homeostasis multicellular organismal process multicellular organismal-level homeostasis multicellular organismal-level chemical homeostasis positive regulation of proteasomal protein catabolic process catabolic process positive regulation of protein metabolic process proteolysis involved in protein catabolic process positive regulation of biological process proteasome-mediated ubiquitin-dependent protein catabolic process macromolecule catabolic process regulation of ubiquitin-dependent protein catabolic process regulation of primary metabolic process positive regulation of metabolic process positive regulation of ubiquitin-dependent protein catabolic process regulation of proteolysis regulation of proteolysis involved in protein catabolic process modification-dependent macromolecule catabolic process proteolysis positive regulation of macromolecule metabolic process protein metabolic process positive regulation of cellular process regulation of protein metabolic process primary metabolic process proteasomal protein catabolic process regulation of macromolecule metabolic process protein catabolic process regulation of catabolic process positive regulation of protein catabolic process positive regulation of proteolysis involved in protein catabolic process positive regulation of catabolic process regulation of proteasomal ubiquitin-dependent protein catabolic process modification-dependent protein catabolic process positive regulation of proteolysis regulation of proteasomal protein catabolic process positive regulation of proteasomal ubiquitin-dependent protein catabolic process metabolic process ubiquitin-dependent protein catabolic process macromolecule metabolic process regulation of metabolic process regulation of protein catabolic process regulation of protein stability regulation of biological quality regulation of localization import into cell positive regulation of cellular component organization regulation of cellular component organization vesicle-mediated transport cellular component organization positive regulation of endocytosis cellular component organization or biogenesis positive regulation of receptor-mediated endocytosis regulation of endocytosis regulation of transport regulation of receptor-mediated endocytosis regulation of vesicle-mediated transport positive regulation of transport endocytosis receptor-mediated endocytosis positive regulation of DNA-templated transcription RNA metabolic process positive regulation of macromolecule biosynthetic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process positive regulation of biosynthetic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process positive regulation of nucleobase-containing compound metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process positive regulation of RNA metabolic process regulation of gene expression biosynthetic process positive regulation of RNA biosynthetic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription developmental process myeloid leukocyte differentiation cellular developmental process hemopoiesis cell development myeloid cell differentiation cell differentiation osteoclast differentiation anatomical structure development leukocyte differentiation regulation of bone remodeling tissue homeostasis regulation of tissue remodeling regulation of bone resorption bone resorption tissue remodeling bone remodeling anatomical structure homeostasis positive regulation of multicellular organismal process regulation of multicellular organismal process positive regulation of bone resorption positive regulation of phosphorylation positive regulation of phosphorus metabolic process phosphorylation positive regulation of phosphate metabolic process regulation of phosphate metabolic process phosphate-containing compound metabolic process regulation of phosphorus metabolic process regulation of phosphorylation phosphorus metabolic process positive regulation of locomotion regulation of cell motility regulation of locomotion positive regulation of cell motility cell motility locomotion organelle organization actin cytoskeleton organization actin filament organization actin filament-based process supramolecular fiber organization cytoskeleton organization regulation of monoatomic ion transport regulation of iron ion transport regulation of metal ion transport	cellular anatomical structure clathrin-coated pit membrane endomembrane system membrane-bounded organelle organelle vesicle cell periphery apical part of cell plasma membrane plasma membrane region apical plasma membrane basal part of cell basal plasma membrane cellular anatomical structure clathrin-coated pit membrane endomembrane system membrane-bounded organelle organelle vesicle cell periphery apical part of cell plasma membrane plasma membrane region apical plasma membrane basal part of cell basal plasma membrane intracellular anatomical structure intracellular vesicle intracellular organelle bounding membrane of organelle cytoplasmic vesicle vesicle membrane clathrin-coated vesicle endocytic vesicle membrane coated vesicle endocytic vesicle clathrin-coated vesicle membrane clathrin-coated endocytic vesicle membrane intracellular membrane-bounded organelle clathrin-coated endocytic vesicle cytoplasmic vesicle membrane coated vesicle membrane cytoplasm organelle membrane extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular space extracellular membrane-bounded organelle protein-containing complex plasma membrane protein complex plasma membrane signaling receptor complex membrane protein complex HFE-transferrin receptor complex receptor complex cell surface early endosome endosome blood microparticle membrane-enclosed lumen intracellular organelle lumen endoplasmic reticulum lumen organelle lumen endoplasmic reticulum recycling endosome vesicle lumen cytoplasmic vesicle lumen secretory granule lumen secretory granule secretory vesicle perinuclear region of cytoplasm endosome membrane late endosome

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR039426	TonB-dependent receptor-like	Family
A	IPR037066	TonB-dependent receptor, plug domain superfamily	Homologous Superfamily
A	IPR010917	TonB-dependent receptor, conserved site	Conserved Site
A	IPR010949	TonB-dependent haemoglobin/transferrin/lactoferrin receptor	Family
A	IPR036942	TonB-dependent receptor-like, beta-barrel domain superfamily	Homologous Superfamily
A	IPR012910	TonB-dependent receptor, plug domain	Domain
A	IPR010916	TonB box, conserved site	Conserved Site
A	IPR010948	TonB-dependent lactoferrin/transferrin receptor	Family
A	IPR000531	TonB-dependent receptor-like, beta-barrel	Domain
B	IPR016357	Transferrin	Family
B	IPR001156	Transferrin-like domain	Domain
B	IPR018195	Transferrin family, iron binding site	Binding Site
B	IPR030685	Serotransferrin, mammalian	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B	Pharos: P02787	atransferrinemia Alzheimer disease echinococcosis nephrotic syndrome hypochromic microcytic anemia obesity disorder alcohol abuse restless legs syndrome Inflammation malignant mesothelioma sarcomatoid carcinoma carcinoma paratuberculosis hepatitis breast cancer atransferrinemia Alzheimer disease echinococcosis nephrotic syndrome hypochromic microcytic anemia obesity disorder alcohol abuse restless legs syndrome Inflammation malignant mesothelioma sarcomatoid carcinoma carcinoma paratuberculosis hepatitis breast cancer malignant glioma medulloblastoma cystic fibrosis pancreatic intraductal papillary-mucinous carcinoma ductal breast carcinoma in situ Pick disease primitive neuroectodermal tumor glioblastoma schizophrenia subependymal giant cell astrocytoma atopic eczema autism lung cancer breast carcinoma mammary neoplasms, animal oligodendroglioma drug-induced liver injury pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia acute kidney failure pituitary cancer progressive supranuclear palsy hemochromatosis type 1 sinusitis invasive ductal breast carcinoma large cell medulloblastoma malignant ependymoma malignant pancreatic neoplasm osteosarcoma esophageal adenocarcinoma fatty liver disease psoriasis schizoaffective disorder undifferentiated carcinoma atypical teratoid rhabdoid tumor lung adenocarcinoma

Membrane Protein Annotation: OPM OPM Database Homepage

Chains	External Link	Type	Class	Superfamily	Family
A, B	OPM	Transmembrane	Beta-barrel transmembrane	Ligand-gated protein channels (n=22,S=24)	Outer Membrane Receptor (OMR)

Membrane Protein Annotation: PDBTM PDBTM Database Homepage

Chains	External Link	Comment
A, B	PDBTM	Annotated as membrane protein by PDBTM

Membrane Protein Annotation: MemProtMD MemProtMD Database Homepage

Chains	External Link	Comment
A, B	MemProtMD	Annotated as membrane protein by MemProtMD

Membrane Protein Annotation: mpstruc mpstruc Database Homepage

Chains	Resource Link	Group	Subgroup	Protein
A, B	mpstruc	TRANSMEMBRANE PROTEINS: BETA-BARREL	Beta-Barrel Membrane Proteins: Monomeric/Dimeric	Transferrin binding protein A (TbpA) in complex with human transferrin

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.