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- PDB-7n88: The cryoEM structure of LbpB from N. gonorrhoeae in complex with ... -

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Basic information

Entry
Database: PDB / ID: 7n88
TitleThe cryoEM structure of LbpB from N. gonorrhoeae in complex with lactoferrin
Components
  • Lactoferrin-binding protein B
  • Lactotransferrin
KeywordsMEMBRANE PROTEIN/TRANSPORT PROTEIN / lactoferrin / lipoprotein / neisseria / iron import / MEMBRANE PROTEIN / MEMBRANE PROTEIN-TRANSPORT PROTEIN complex
Function / homology
Function and homology information


negative regulation by host of viral process / membrane destabilizing activity / Mtb iron assimilation by chelation / Metal sequestration by antimicrobial proteins / phagocytic vesicle lumen / positive regulation of toll-like receptor 4 signaling pathway / negative regulation of viral process / negative regulation of cysteine-type endopeptidase activity / negative regulation of tumor necrosis factor (ligand) superfamily member 11 production / negative regulation of single-species biofilm formation in or on host organism ...negative regulation by host of viral process / membrane destabilizing activity / Mtb iron assimilation by chelation / Metal sequestration by antimicrobial proteins / phagocytic vesicle lumen / positive regulation of toll-like receptor 4 signaling pathway / negative regulation of viral process / negative regulation of cysteine-type endopeptidase activity / negative regulation of tumor necrosis factor (ligand) superfamily member 11 production / negative regulation of single-species biofilm formation in or on host organism / positive regulation of bone mineralization involved in bone maturation / negative regulation of lipopolysaccharide-mediated signaling pathway / negative regulation of osteoclast development / specific granule / antifungal humoral response / negative regulation of ATP-dependent activity / positive regulation of chondrocyte proliferation / regulation of tumor necrosis factor production / bone morphogenesis / Antimicrobial peptides / cysteine-type endopeptidase inhibitor activity / negative regulation of viral genome replication / positive regulation of osteoblast proliferation / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / humoral immune response / positive regulation of osteoblast differentiation / regulation of cytokine production / ossification / protein serine/threonine kinase activator activity / secretory granule / innate immune response in mucosa / lipopolysaccharide binding / cell outer membrane / positive regulation of protein serine/threonine kinase activity / recycling endosome / specific granule lumen / antimicrobial humoral immune response mediated by antimicrobial peptide / tertiary granule lumen / antibacterial humoral response / heparin binding / positive regulation of NF-kappaB transcription factor activity / iron ion transport / positive regulation of canonical NF-kappaB signal transduction / defense response to Gram-negative bacterium / killing of cells of another organism / early endosome / iron ion binding / Amyloid fiber formation / serine-type endopeptidase activity / Neutrophil degranulation / negative regulation of apoptotic process / cell surface / protein-containing complex / proteolysis / DNA binding / extracellular space / extracellular exosome / extracellular region / nucleus / plasma membrane / cytoplasm
Similarity search - Function
Transferrin-binding protein B, N-lobe handle / N-Lobe handle Tf-binding protein B / Transferrin-binding protein B, C-lobe handle domain / TbpB, C-lobe handle domain superfamily / C-lobe handle domain of Tf-binding protein B / TbpB, N-lobe handle domain superfamily / Transferrin-binding protein B, C-lobe/N-lobe beta barrel domain / C-lobe and N-lobe beta barrels of Tf-binding protein B / Lactotransferrin / Transferrin-like domain signature 2. ...Transferrin-binding protein B, N-lobe handle / N-Lobe handle Tf-binding protein B / Transferrin-binding protein B, C-lobe handle domain / TbpB, C-lobe handle domain superfamily / C-lobe handle domain of Tf-binding protein B / TbpB, N-lobe handle domain superfamily / Transferrin-binding protein B, C-lobe/N-lobe beta barrel domain / C-lobe and N-lobe beta barrels of Tf-binding protein B / Lactotransferrin / Transferrin-like domain signature 2. / Transferrin family, iron binding site / Transferrin-like domain signature 1. / Transferrin-like domain signature 3. / Transferrin-like domain / Transferrin / Transferrin / Transferrin-like domain profile. / Transferrin / Outer membrane protein/outer membrane enzyme PagP, beta-barrel / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
BICARBONATE ION / : / Lactotransferrin / Transferrin-binding protein B
Similarity search - Component
Biological speciesNeisseria gonorrhoeae (bacteria)
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsYadav, R. / Noinaj, N.
Funding support United States, 1items
OrganizationGrant numberCountry
Other governmentPurdue University United States
CitationJournal: Elife / Year: 2021
Title: Structural insight into the dual function of LbpB in mediating Neisserial pathogenesis.
Authors: Ravi Yadav / Srinivas Govindan / Courtney Daczkowski / Andrew Mesecar / Srinivas Chakravarthy / Nicholas Noinaj /
Abstract: Lactoferrin-binding protein B (LbpB) is a lipoprotein present on the surface of that has been postulated to serve dual functions during pathogenesis in both iron acquisition from lactoferrin (Lf), ...Lactoferrin-binding protein B (LbpB) is a lipoprotein present on the surface of that has been postulated to serve dual functions during pathogenesis in both iron acquisition from lactoferrin (Lf), and in providing protection against the cationic antimicrobial peptide lactoferricin (Lfcn). While previous studies support a dual role for LbpB, exactly how these ligands interact with LbpB has remained unknown. Here, we present the structures of LbpB from and in complex with human holo-Lf, forming a 1:1 complex and confirmed by size-exclusion chromatography small-angle X-ray scattering. LbpB consists of N- and C-lobes with the N-lobe interacting extensively with the C-lobe of Lf. Our structures provide insight into LbpB's preference towards holo-Lf, and our mutagenesis and binding studies show that Lf and Lfcn bind independently. Our studies provide the molecular details for how LbpB serves to capture and preserve Lf in an iron-bound state for delivery to the membrane transporter LbpA for iron piracy, and as an antimicrobial peptide sink to evade host immune defenses.
History
DepositionJun 14, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 1, 2021Provider: repository / Type: Initial release

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Assembly

Deposited unit
A: Lactoferrin-binding protein B
B: Lactotransferrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)154,9306
Polymers154,6962
Non-polymers2344
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Lactoferrin-binding protein B


Mass: 78432.734 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria gonorrhoeae (bacteria) / Gene: lbpB / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9Z4N2
#2: Protein Lactotransferrin / Lactoferrin / Growth-inhibiting protein 12 / Talalactoferrin


Mass: 76263.266 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LTF, GIG12, LF / Production host: Oryza sativa (Asian cultivated rice)
References: UniProt: P02788, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#3: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#4: Chemical ChemComp-BCT / BICARBONATE ION


Mass: 61.017 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CHO3 / Comment: pH buffer*YM
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1complex between lactoferrin binding protein and lactoferrinCOMPLEX#1-#20MULTIPLE SOURCES
2lactoferrin binding proteinCOMPLEX#11RECOMBINANT
3lactoferrinCOMPLEX#21RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
12Neisseria gonorrhoeae (bacteria)485
23Homo sapiens (human)9606
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
12Escherichia coli BL21(DE3) (bacteria)469008
23Oryza sativa (Asian cultivated rice)4530
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 53.68 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.18rc1_3777: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 127832 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0089596
ELECTRON MICROSCOPYf_angle_d0.97412963
ELECTRON MICROSCOPYf_dihedral_angle_d21.5741318
ELECTRON MICROSCOPYf_chiral_restr0.0541383
ELECTRON MICROSCOPYf_plane_restr0.0061724

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