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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 / 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 / positive regulation of immune response / specific granule lumen / 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 / CFP-like, C-terminal thrombospondin type 1 domain / : / 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
  • Download
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)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.84 Å/pix.
x 72 pix.
= 204.48 Å		2.84 Å/pix.
x 72 pix.
= 204.48 Å		2.84 Å/pix.
x 72 pix.
= 204.48 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.84 Å
Density

Histogram

Histogram (log scale)
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
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
Electron beamAcceleration voltage: 100 kV / Electron source: TUNGSTEN HAIRPIN
Electron opticsCalibrated 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 stageSpecimen holder model: JEOL / Tilt angle max: 40

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Image processing

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.
CTF correctionDetails: Each CCD Frame, estimated with CTFFIND and corrected using BSOFT
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
Final two d classificationNumber classes: 30

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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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