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- EMDB-2402: 3D structure of a properdin vertex -

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Basic information

Entry
Database: EMDB / ID: EMD-2402
Title3D structure of a properdin vertex
Map dataReconstruction of a vertex from a Properdin oligomer (tetramer)
Sample
  • Sample: Human Properdin purified from plasma
  • Protein or peptide: Complement Factor P
Keywordsproperdin / 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, alternative pathway / complement activation / 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, alternative pathway / complement activation / 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
: / Thrombospondin type 1 repeat / Thrombospondin type 1 domain / Thrombospondin type-1 (TSP1) repeat superfamily / Thrombospondin type-1 (TSP1) repeat profile. / Thrombospondin type 1 repeats / Thrombospondin type-1 (TSP1) repeat / Thrombospondin type-1 (TSP1) repeat
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / negative staining / Resolution: 23.4 Å
AuthorsAlcorlo M / Tortajada A / Rodriguez de Cordoba S / Llorca O
CitationJournal: 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
DepositionJun 25, 2013-
Header (metadata) releaseJul 24, 2013-
Map releaseJul 24, 2013-
UpdateAug 21, 2013-
Current statusAug 21, 2013Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 2
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_2402.jpg

Downloads & links

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Map

FileDownload / File: emd_2402.map.gz / Format: CCP4 / Size: 1.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of a vertex from a Properdin oligomer (tetramer)
Voxel sizeX=Y=Z: 2.84 Å
Density
Contour LevelBy AUTHOR: 2.0 / Movie #1: 2
Minimum - Maximum-14.58631611 - 11.318551060000001
Average (Standard dev.)0.0 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-36-36-36
Dimensions727272
Spacing727272
CellA=B=C: 204.48 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.842.842.84
M x/y/z727272
origin x/y/z0.0000.0000.000
length x/y/z204.480204.480204.480
α/β/γ90.00090.00090.000
start NX/NY/NZ00-40
NX/NY/NZ555581
MAP C/R/S123
start NC/NR/NS-36-36-36
NC/NR/NS727272
D min/max/mean-14.58611.319-0.000

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Supplemental data

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Sample components

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Entire : Human Properdin purified from plasma

EntireName: Human Properdin purified from plasma
Components
  • Sample: Human Properdin purified from plasma
  • Protein or peptide: Complement Factor P

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Supramolecule #1000: Human Properdin purified from plasma

SupramoleculeName: 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
Molecular weightTheoretical: 45 KDa

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Macromolecule #1: Complement Factor P

MacromoleculeName: Complement Factor P / type: protein_or_peptide / ID: 1 / Name.synonym: Properdin / Number of copies: 2 / Oligomeric state: dimer / Recombinant expression: No
Source (natural)Organism: Homo sapiens (human) / synonym: Human / Tissue: plasma
Molecular weightExperimental: 54 KDa / Theoretical: 53 KDa
SequenceUniProtKB: Properdin
GO: extracellular space, complement activation, alternative pathway, defense response to bacterium, regulation of complement activation
InterPro: Thrombospondin type-1 (TSP1) repeat

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Experimental details

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Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.01 mg/mL
BufferpH: 7.5 / Details: 20 mM Hepes, 75 mM NaCl and 5 mM MgCl2
StainingType: NEGATIVE
Details: Grids with adsorbed protein floated on 1% w/v uranyl acetate for 15 seconds
GridDetails: 400 mesh copper carbon only (50ct), glow discharged
VitrificationCryogen name: NONE / Instrument: OTHER

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Electron microscopy

MicroscopeJEOL 1230
Electron beamAcceleration voltage: 100 kV / Electron source: TUNGSTEN HAIRPIN
Electron opticsCalibrated magnification: 54926 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.9 mm / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 40000
Sample stageSpecimen holder model: JEOL / Tilt angle max: 40
Alignment procedureLegacy - Astigmatism: Objective lens astigmatism was corrected using a CMOS camera and the power spectrum
DetailsMicrographs were recorded using a low-dose protocol under control of the EM-TOOLS software (TVIPS)
DateMar 21, 2012
Image recordingCategory: 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 min0

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Image processing

CTF correctionDetails: Each CCD Frame, estimated with CTFFIND and corrected using BSOFT
Final two d classificationNumber classes: 30
Final reconstructionApplied 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
DetailsThe 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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Atomic model buiding 1

Initial modelPDB ID:

3r6b

SoftwareName: UCSF Chimera
DetailsThe domains were separately fitted using UCSF Chimera
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: Cross correlation

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