3VE1

The 2.9 angstrom crystal structure of Transferrin binding protein B (TbpB) from serogroup B M982 Neisseria meningitidis in complex with human transferrin

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
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	TbpB N-lobe and C-lobe handle domains-like	8052221	3002099	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	TbpB N-lobe and C-lobe beta-barrel domains-like	8052220	3002098	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	TbpB N-lobe and C-lobe beta-barrel domains-like	8047030	3002098	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	TbpB N-lobe and C-lobe beta-barrel domains-like	8047030	3002098	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	TbpB N-lobe and C-lobe handle domains-like	8052221	3002099	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	TbpB N-lobe and C-lobe beta-barrel domains-like	8052220	3002098	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Type 2 solute binding protein-like	8041066	3000083	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Type 2 solute binding protein-like	8041066	3000083	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	TbpB_A	e3ve1A3	A: beta barrels	X: Handle domain in transferrin-binding protein B (From Topology)	H: Handle domain in transferrin-binding protein B (From Topology)	T: Handle domain in transferrin-binding protein B	F: TbpB_A	ECOD (1.6)
A	TbpB_B_D	e3ve1A1	A: beta barrels	X: Outer membrane meander beta-barrels	H: OMPA-like (From Topology)	T: OMPA-like	F: TbpB_B_D	ECOD (1.6)
C	TbpB_A	e3ve1C4	A: beta barrels	X: Handle domain in transferrin-binding protein B (From Topology)	H: Handle domain in transferrin-binding protein B (From Topology)	T: Handle domain in transferrin-binding protein B	F: TbpB_A	ECOD (1.6)
C	TbpB_C_1	e3ve1C3	A: beta barrels	X: Handle domain in transferrin-binding protein B (From Topology)	H: Handle domain in transferrin-binding protein B (From Topology)	T: Handle domain in transferrin-binding protein B	F: TbpB_C_1	ECOD (1.6)
C	TbpB_B_D	e3ve1C1	A: beta barrels	X: Outer membrane meander beta-barrels	H: OMPA-like (From Topology)	T: OMPA-like	F: TbpB_B_D	ECOD (1.6)
B	Transferrin_2nd	e3ve1B1	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	e3ve1B3	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)
D	Transferrin_2nd	e3ve1D1	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)
D	Transferrin_1st	e3ve1D3	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	2.40.128.250	Mainly Beta	Beta Barrel	Lipocalin		CATH (4.3.0)
A	2.40.160.90	Mainly Beta	Beta Barrel	Porin		CATH (4.3.0)
A	2.40.128.240	Mainly Beta	Beta Barrel	Lipocalin		CATH (4.3.0)
C	2.40.128.250	Mainly Beta	Beta Barrel	Lipocalin		CATH (4.3.0)
C	2.40.160.90	Mainly Beta	Beta Barrel	Porin		CATH (4.3.0)
C	2.40.128.240	Mainly Beta	Beta Barrel	Lipocalin		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)
D	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, C	PF17483	C-lobe handle domain of Tf-binding protein B (TbpB_C)	C-lobe handle domain of Tf-binding protein B	Bacterial lipoproteins represent a large group of specialised membrane proteins that perform a variety of functions including maintenance and stabilization of the cell envelope, protein targeting and transit to the outer membrane, membrane biogenesis ...	Bacterial lipoproteins represent a large group of specialised membrane proteins that perform a variety of functions including maintenance and stabilization of the cell envelope, protein targeting and transit to the outer membrane, membrane biogenesis, and cell adherence [1]. Pathogenic Gram-negative bacteria within the Neisseriaceae and Pasteurellaceae families rely on a specialised uptake system, characterized by an essential surface receptor complex that acquires iron from host transferrin (Tf) and transports the iron across the outer membrane. They have an iron uptake system composed of surface exposed lipoprotein, Tf-binding protein B (TbpB), and an integral outer-membrane protein, Tf-binding protein A (TbpA), that together function to extract iron from the host iron binding glycoprotein (Tf). TbpB is a bilobed (N and C lobe) lipid-anchored protein with each lobe consisting of an eight-stranded beta barrel flanked by a 'handle' domain made up of four (N lobe) or eight (C lobe) beta strands [2]. TbpB extends from the outer membrane surface by virtue of an N-terminal peptide region that is anchored to the outer membrane by fatty acyl chains on the N-terminal cysteine and is involved in the initial capture of iron-loaded Tf [3]. This domain family is found in the handle domain of the C lobe (domain C) of TbpB proteins. It consists of a squashed six-stranded beta sheet flanked by two antiparallel beta strands and has no supporting alpha helix as in the N lobe [2].	Domain
A, C	PF01298	C-lobe and N-lobe beta barrels of Tf-binding protein B (TbpB_B_D)	C-lobe and N-lobe beta barrels of Tf-binding protein B	Bacterial lipoproteins represent a large group of specialized membrane proteins that perform a variety of functions including maintenance and stabilization of the cell envelope, protein targeting and transit to the outer membrane, membrane biogenesis ...	Bacterial lipoproteins represent a large group of specialized membrane proteins that perform a variety of functions including maintenance and stabilization of the cell envelope, protein targeting and transit to the outer membrane, membrane biogenesis, and cell adherence [1]. Pathogenic Gram-negative bacteria within the Neisseriaceae and Pasteurellaceae families rely on a specialized uptake system, characterized by an essential surface receptor complex that acquires iron from host transferrin (Tf) and transports the iron across the outer membrane. They have an iron uptake system composed of surface exposed lipoprotein, Tf-binding protein B (TbpB), and an integral outer-membrane protein, Tf-binding protein A (TbpA), that together function to extract iron from the host iron binding glycoprotein (Tf). TbpB is a bilobed (N and C lobe) lipid-anchored protein with each lobe consisting of an eight-stranded beta barrel flanked by a "handle" domain made up of four (N lobe) or eight (C lobe) beta strands [2]. TbpB extends from the outer membrane surface by virtue of an N-terminal peptide region that is anchored to the outer membrane by fatty acyl chains on the N-terminal cysteine and is involved in the initial capture of iron-loaded Tf [3]. This domain family is found in C and N lobe eight stranded beta barrel region of TbpB proteins. The eight-stranded barrel domains in N and C lobe draw comparisons to eight-stranded beta barrel outer-membrane protein W (OmpW). However, the barrel domains of TbpB have the hydrophobic residues line the inner surface of the beta barrels to create a stable hydrophobic core [2].	Domain
B, D	PF00405	Transferrin (Transferrin)	Transferrin	-	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, C	Transferrin-binding protein 2	-	-	cell surface cellular anatomical structure cell periphery cell outer membrane external encapsulating structure membrane cell envelope outer membrane
B, D	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, C	IPR011250	Outer membrane protein/outer membrane enzyme PagP, beta-barrel	Homologous Superfamily
A, C	IPR001677	Transferrin-binding protein B, C-lobe/N-lobe beta-barrel domain	Domain
A, C	IPR035313	Transferrin-binding protein B, N-lobe handle	Domain
A, C	IPR038669	TbpB, N-lobe handle domain superfamily	Homologous Superfamily
A, C	IPR038197	TbpB, C-lobe handle domain superfamily	Homologous Superfamily
A, C	IPR035316	Transferrin-binding protein B, C-lobe handle domain	Domain
B, D	IPR016357	Transferrin	Family
B, D	IPR001156	Transferrin-like domain	Domain
B, D	IPR018195	Transferrin family, iron binding site	Binding Site
B, D	IPR030685	Serotransferrin, mammalian	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B, D	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

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.