+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-2402 | |||||||||
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Title | 3D structure of a properdin vertex | |||||||||
Map data | Reconstruction of a vertex from a Properdin oligomer (tetramer) | |||||||||
Sample |
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Keywords | properdin / C3b / AP C3 convertase / complement / electron microscopy / EM | |||||||||
Function / homology | Function and homology information cytoplasmic side of Golgi membrane / positive regulation of opsonization / Defective B3GALTL causes PpS / O-glycosylation of TSR domain-containing proteins / regulation of complement activation / Alternative complement activation / Activation of C3 and C5 / complement activation / complement activation, alternative pathway / Regulation of Complement cascade ...cytoplasmic side of Golgi membrane / positive regulation of opsonization / Defective B3GALTL causes PpS / O-glycosylation of TSR domain-containing proteins / regulation of complement activation / Alternative complement activation / Activation of C3 and C5 / complement activation / complement activation, alternative pathway / Regulation of Complement cascade / specific granule lumen / positive regulation of immune response / tertiary granule lumen / defense response to bacterium / immune response / endoplasmic reticulum lumen / Neutrophil degranulation / extracellular space / extracellular region Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / negative staining / Resolution: 23.4 Å | |||||||||
Authors | Alcorlo M / Tortajada A / Rodriguez de Cordoba S / Llorca O | |||||||||
Citation | Journal: Proc Natl Acad Sci U S A / Year: 2013 Title: Structural basis for the stabilization of the complement alternative pathway C3 convertase by properdin. Authors: Martín Alcorlo / Agustín Tortajada / Santiago Rodríguez de Córdoba / Oscar Llorca / Abstract: Complement is an essential component of innate immunity. Its activation results in the assembly of unstable protease complexes, denominated C3/C5 convertases, leading to inflammation and lysis. ...Complement is an essential component of innate immunity. Its activation results in the assembly of unstable protease complexes, denominated C3/C5 convertases, leading to inflammation and lysis. Regulatory proteins inactivate C3/C5 convertases on host surfaces to avoid collateral tissue damage. On pathogen surfaces, properdin stabilizes C3/C5 convertases to efficiently fight infection. How properdin performs this function is, however, unclear. Using electron microscopy we show that the N- and C-terminal ends of adjacent monomers in properdin oligomers conform a curly vertex that holds together the AP convertase, interacting with both the C345C and vWA domains of C3b and Bb, respectively. Properdin also promotes a large displacement of the TED (thioester-containing domain) and CUB (complement protein subcomponents C1r/C1s, urchin embryonic growth factor and bone morphogenetic protein 1) domains of C3b, which likely impairs C3-convertase inactivation by regulatory proteins. The combined effect of molecular cross-linking and structural reorganization increases stability of the C3 convertase and facilitates recruitment of fluid-phase C3 convertase to the cell surfaces. Our model explains how properdin mediates the assembly of stabilized C3/C5-convertase clusters, which helps to localize complement amplification to pathogen surfaces. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_2402.map.gz | 514.9 KB | EMDB map data format | |
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Header (meta data) | emd-2402-v30.xml emd-2402.xml | 10.9 KB 10.9 KB | Display Display | EMDB header |
Images | emd_2402.jpg | 77.6 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-2402 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-2402 | HTTPS FTP |
-Validation report
Summary document | emd_2402_validation.pdf.gz | 198.2 KB | Display | EMDB validaton report |
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Full document | emd_2402_full_validation.pdf.gz | 197.3 KB | Display | |
Data in XML | emd_2402_validation.xml.gz | 5.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2402 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2402 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_2402.map.gz / Format: CCP4 / Size: 1.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Reconstruction of a vertex from a Properdin oligomer (tetramer) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.84 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Human Properdin purified from plasma
Entire | Name: Human Properdin purified from plasma |
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Components |
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-Supramolecule #1000: Human Properdin purified from plasma
Supramolecule | Name: Human Properdin purified from plasma / type: sample / ID: 1000 Details: The structure corresponds to a head-to-tail connection between two Properdin monomers (from a tetrameric species) Oligomeric state: dimer / Number unique components: 1 |
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Molecular weight | Theoretical: 45 KDa |
-Macromolecule #1: Complement Factor P
Macromolecule | Name: Complement Factor P / type: protein_or_peptide / ID: 1 / Name.synonym: Properdin / Number of copies: 2 / Oligomeric state: dimer / Recombinant expression: No |
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Source (natural) | Organism: Homo sapiens (human) / synonym: Human / Tissue: plasma |
Molecular weight | Experimental: 54 KDa / Theoretical: 53 KDa |
Sequence | UniProtKB: Properdin GO: extracellular space, complement activation, alternative pathway, defense response to bacterium, regulation of complement activation InterPro: Thrombospondin type-1 (TSP1) repeat |
-Experimental details
-Structure determination
Method | negative staining |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.01 mg/mL |
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Buffer | pH: 7.5 / Details: 20 mM Hepes, 75 mM NaCl and 5 mM MgCl2 |
Staining | Type: NEGATIVE Details: Grids with adsorbed protein floated on 1% w/v uranyl acetate for 15 seconds |
Grid | Details: 400 mesh copper carbon only (50ct), glow discharged |
Vitrification | Cryogen name: NONE / Instrument: OTHER |
-Electron microscopy
Microscope | JEOL 1230 |
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Alignment procedure | Legacy - Astigmatism: Objective lens astigmatism was corrected using a CMOS camera and the power spectrum |
Details | Micrographs were recorded using a low-dose protocol under control of the EM-TOOLS software (TVIPS) |
Date | Mar 21, 2012 |
Image recording | Category: CCD / Film or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Digitization - Sampling interval: 2.84 µm / Number real images: 625 / Average electron dose: 10 e/Å2 / Od range: 1.4 / Bits/pixel: 16 |
Tilt angle min | 0 |
Electron beam | Acceleration voltage: 100 kV / Electron source: TUNGSTEN HAIRPIN |
Electron optics | Calibrated magnification: 54926 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.9 mm / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 40000 |
Sample stage | Specimen holder model: JEOL / Tilt angle max: 40 |
-Image processing
Details | The particles were manually selected using Boxer (EMAN1). Images were classified and averaged using maximum-likelihood multi-reference methods as implemented in XMIPP. Ab initio templates for angular refinement were obtained using the command e2initial model in EMAN2. 3D reconstructions were obtained using angular refinement using EMAN. |
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CTF correction | Details: Each CCD Frame, estimated with CTFFIND and corrected using BSOFT |
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 23.4 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EMAN1, EMAN2, Xmipp-2.4 / Number images used: 6425 |
Final two d classification | Number classes: 30 |
-Atomic model buiding 1
Initial model | PDB ID: |
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Software | Name: UCSF Chimera |
Details | The domains were separately fitted using UCSF Chimera |
Refinement | Space: REAL / Protocol: RIGID BODY FIT / Target criteria: Cross correlation |