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- EMDB-24233: The cryoEM structure of LbpB from N. gonorrhoeae in complex with ... -

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Basic information

Entry
Database: EMDB / ID: EMD-24233
TitleThe cryoEM structure of LbpB from N. gonorrhoeae in complex with lactoferrin
Map data
Sample
  • Complex: complex between lactoferrin binding protein and lactoferrin
    • Complex: lactoferrin binding protein
      • Protein or peptide: Lactoferrin-binding protein B
    • Complex: lactoferrin
      • Protein or peptide: Lactotransferrin
  • Ligand: FE (III) ION
  • Ligand: BICARBONATE ION
Function / homology
Function and homology information


negative regulation by host of viral process / membrane destabilizing activity / Mtb iron assimilation by chelation / phagocytic vesicle lumen / positive regulation of toll-like receptor 4 signaling pathway / Metal sequestration by antimicrobial proteins / 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 / phagocytic vesicle lumen / positive regulation of toll-like receptor 4 signaling pathway / Metal sequestration by antimicrobial proteins / 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 / specific granule / negative regulation of osteoclast development / antifungal humoral response / positive regulation of chondrocyte proliferation / negative regulation of ATP-dependent activity / 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 / humoral immune response / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / positive regulation of osteoblast differentiation / regulation of cytokine production / protein serine/threonine kinase activator activity / ossification / innate immune response in mucosa / secretory granule / 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 / positive regulation of NF-kappaB transcription factor activity / heparin binding / iron ion transport / antibacterial humoral response / 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, C-lobe handle domain / TbpB, C-lobe handle domain superfamily / C-lobe handle domain of Tf-binding protein B / Transferrin-binding protein B, N-lobe handle / TbpB, N-lobe handle domain superfamily / N-Lobe handle Tf-binding protein B / 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, C-lobe handle domain / TbpB, C-lobe handle domain superfamily / C-lobe handle domain of Tf-binding protein B / Transferrin-binding protein B, N-lobe handle / TbpB, N-lobe handle domain superfamily / N-Lobe handle Tf-binding protein B / 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
Similarity search - Domain/homology
Lactotransferrin / Transferrin-binding protein B
Similarity search - Component
Biological speciesNeisseria gonorrhoeae (bacteria) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsYadav R / Noinaj N
Funding support United States, 1 items
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, 2021-
Header (metadata) releaseDec 1, 2021-
Map releaseDec 1, 2021-
UpdateDec 1, 2021-
Current statusDec 1, 2021Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.7
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.7
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7n88
  • Surface level: 0.7
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_24233.png

Downloads & links

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Map

FileDownload / File: emd_24233.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.08 Å
Density
Contour LevelBy AUTHOR: 0.7 / Movie #1: 0.7
Minimum - Maximum-2.4235923 - 4.014866
Average (Standard dev.)0.001979969 (±0.06683385)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 276.48 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.081.081.08
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z276.480276.480276.480
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-2.4244.0150.002

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Supplemental data

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Sample components

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Entire : complex between lactoferrin binding protein and lactoferrin

EntireName: complex between lactoferrin binding protein and lactoferrin
Components
  • Complex: complex between lactoferrin binding protein and lactoferrin
    • Complex: lactoferrin binding protein
      • Protein or peptide: Lactoferrin-binding protein B
    • Complex: lactoferrin
      • Protein or peptide: Lactotransferrin
  • Ligand: FE (III) ION
  • Ligand: BICARBONATE ION

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Supramolecule #1: complex between lactoferrin binding protein and lactoferrin

SupramoleculeName: complex between lactoferrin binding protein and lactoferrin
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2

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Supramolecule #2: lactoferrin binding protein

SupramoleculeName: lactoferrin binding protein / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Neisseria gonorrhoeae (bacteria)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)

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Supramolecule #3: lactoferrin

SupramoleculeName: lactoferrin / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Oryza sativa (Asian cultivated rice)

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Macromolecule #1: Lactoferrin-binding protein B

MacromoleculeName: Lactoferrin-binding protein B / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Neisseria gonorrhoeae (bacteria)
Molecular weightTheoretical: 78.432734 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: GAMGGNFGVQ PVVESTPTAY PVTFKSKDVP TSPPPAEPSV ETTPVNRPAV GAAMRLLRRN TAFHREDGTA IPDSKQAEEK LSFKEGDVL FLYGSKGNKL QQLKSEIHKR DSDVEIRTSE KENKKYGYEF VDAGYVYTKN GKDEIEQNSG GKRFTHRFGY D GFVYYSGE ...String:
GAMGGNFGVQ PVVESTPTAY PVTFKSKDVP TSPPPAEPSV ETTPVNRPAV GAAMRLLRRN TAFHREDGTA IPDSKQAEEK LSFKEGDVL FLYGSKGNKL QQLKSEIHKR DSDVEIRTSE KENKKYGYEF VDAGYVYTKN GKDEIEQNSG GKRFTHRFGY D GFVYYSGE RPSQSLPSAG TVKYFGNWQY MTDAKRHRTG KAVASDDLGY ITFYGNDIGA TSYAAKDADD REKHPAEYTV DF DKKILKG ELIKNQYVQK KNDPKKPLTI YNITADLNGN RFTGSAKVNT EVKTRHADKE YLFFHTDADQ RLEGGFFGDN GEE LAGRFI SNDNGVFGVF AGKQKTNASG TNPAMPFGKH TKILDSLKIS VDEATDENPR PFEVSTMPDF GHPDKLLVEG REIP LVSKE KTIDLADGRK MTVSACCDFL TYVKLGRIKT ERPAVKPKAQ DEEDSGINNG EESEDEEEIA EESEDEVSED DNGED EDEI VEEEADEAEE IEEEAEEEEP EEESPEEGNG VSDGIPPAPE ALKGRDIDLF LKGIRTAEAD IPKTGTAHYT GTWEAR IGE PIQWDNKADK AAKAEFDVDF GNKSISGTLT EQNGVEPAFR IENGVIEGNG FHATARTRDN GINLSGNGST NPQSFKA DN LLVTGGFYGP QAAELGGTIF NKDGKSLGIT EDIENEVENE ADVGEQLEPE VKPQFGVVFG AKKDNKEVEK

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Macromolecule #2: Lactotransferrin

MacromoleculeName: Lactotransferrin / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
EC number: Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 76.263266 KDa
Recombinant expressionOrganism: Oryza sativa (Asian cultivated rice)
SequenceString: GRRRSVQWCA VSQPEATKCF QWQRNMRKVR GPPVSCIKRD SPIQCIQAIA ENRADAVTLD GGFIYEAGLA PYKLRPVAAE VYGTERQPR THYYAVAVVK KGGSFQLNEL QGLKSCHTGL RRTAGWNVPI GTLRPFLNWT GPPEPIEAAV ARFFSASCVP G ADKGQFPN ...String:
GRRRSVQWCA VSQPEATKCF QWQRNMRKVR GPPVSCIKRD SPIQCIQAIA ENRADAVTLD GGFIYEAGLA PYKLRPVAAE VYGTERQPR THYYAVAVVK KGGSFQLNEL QGLKSCHTGL RRTAGWNVPI GTLRPFLNWT GPPEPIEAAV ARFFSASCVP G ADKGQFPN LCRLCAGTGE NKCAFSSQEP YFSYSGAFKC LRDGAGDVAF IRESTVFEDL SDEAERDEYE LLCPDNTRKP VD KFKDCHL ARVPSHAVVA RSVNGKEDAI WNLLRQAQEK FGKDKSPKFQ LFGSPSGQKD LLFKDSAIGF SRVPPRIDSG LYL GSGYFT AIQNLRKSEE EVAARRARVV WCAVGEQELR KCNQWSGLSE GSVTCSSAST TEDCIALVLK GEADAMSLDG GYVY TAGKC GLVPVLAENY KSQQSSDPDP NCVDRPVEGY LAVAVVRRSD TSLTWNSVKG KKSCHTAVDR TAGWNIPMGL LFNQT GSCK FDEYFSQSCA PGSDPRSNLC ALCIGDEQGE NKCVPNSNER YYGYTGAFRC LAENAGDVAF VKDVTVLQNT DGNNNE AWA KDLKLADFAL LCLDGKRKPV TEARSCHLAM APNHAVVSRM DKVERLKQVL LHQQAKFGRN GSDCPDKFCL FQSETKN LL FNDNTECLAR LHGKTTYEKY LGPQYVAGIT NLKKCSTSPL LEACEFLRK

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Macromolecule #3: FE (III) ION

MacromoleculeName: FE (III) ION / type: ligand / ID: 3 / Number of copies: 2 / Formula: FE
Molecular weightTheoretical: 55.845 Da

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Macromolecule #4: BICARBONATE ION

MacromoleculeName: BICARBONATE ION / type: ligand / ID: 4 / Number of copies: 2 / Formula: BCT
Molecular weightTheoretical: 61.017 Da
Chemical component information

ChemComp-BCT:
BICARBONATE ION / pH buffer*YM

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 53.68 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY / Details: 4U9C; 2BJJ
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 127832
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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