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- EMDB-1908: Unique structure of iC3b by 3D-Electron Microscopy -

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Basic information

Entry
Database: EMDB / ID: EMD-1908
TitleUnique structure of iC3b by 3D-Electron Microscopy
Map data3D structure of iC3b, a component of the complement alternative pathway
Sample
  • Sample: Human iC3b
  • Protein or peptide: Complement component iC3b
KeywordsiC3b / C3b / complement / 3D-electron microscopy / SAXS
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / negative staining / Resolution: 24.0 Å
AuthorsAlcorlo M / Martinez-Barricarte R / Fernandez FJ / Rodriguez-Gallego C / Round A / Vega MC / Harris CL / Rodriguez-de-Cordoba S / Llorca O
CitationJournal: Proc Natl Acad Sci U S A / Year: 2011
Title: Unique structure of iC3b resolved at a resolution of 24 Å by 3D-electron microscopy.
Authors: Martin Alcorlo / Ruben Martínez-Barricarte / Francisco J Fernández / César Rodríguez-Gallego / Adam Round / M Cristina Vega / Claire L Harris / Santiago Rodríguez de Cordoba / Oscar Llorca /
Abstract: Activation of C3, deposition of C3b on the target surface, and subsequent amplification by formation of a C3-cleaving enzyme (C3-convertase; C3bBb) triggers the effector functions of complement that ...Activation of C3, deposition of C3b on the target surface, and subsequent amplification by formation of a C3-cleaving enzyme (C3-convertase; C3bBb) triggers the effector functions of complement that result in inflammation and cell lysis. Concurrently, surface-bound C3b is proteolyzed to iC3b by factor I and appropriate cofactors. iC3b then interacts with the complement receptors (CR) of the Ig superfamily, CR2 (CD21), CR3 (CD11b/CD18), and CR4 (CD11c/CD18) on leukocytes, down-modulating inflammation, enhancing B cell-mediated immunity, and targeting pathogens for clearance by phagocytosis. Using EM and small-angle X-ray scattering, we now present a medium-resolution structure of iC3b (24 Å). iC3b displays a unique conformation with structural features distinct from any other C3 fragment. The macroglobulin ring in iC3b is similar to that in C3b, whereas the TED (thioester-containing domain) domain and the remnants of the CUB (complement protein subcomponents C1r/C1s, urchin embryonic growth factor and bone morphogenetic protein 1) domain have moved to locations more similar to where they were in native C3. A consequence of this large conformational change is the disruption of the factor B binding site, which renders iC3b unable to assemble a C3-convertase. This structural model also justifies the decreased interaction between iC3b and complement regulators and the recognition of iC3b by the CR of the Ig superfamily, CR2, CR3, and CR4. These data further illustrate the extraordinary conformational versatility of C3 to accommodate a great diversity of functional activities.
History
DepositionJun 10, 2011-
Header (metadata) releaseJul 6, 2011-
Map releaseJul 6, 2011-
UpdateNov 26, 2014-
Current statusNov 26, 2014Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 4.59
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 4.59
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMDB-1908_im...

Downloads & links

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Map

FileDownload / File: emd_1908.map.gz / Format: CCP4 / Size: 1.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation3D structure of iC3b, a component of the complement alternative pathway
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
4.2 Å/pix.
x 72 pix.
= 302.4 Å		4.2 Å/pix.
x 72 pix.
= 302.4 Å		4.2 Å/pix.
x 72 pix.
= 302.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 4.2 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 4.59 / Movie #1: 4.59
Minimum - Maximum-13.079293249999999 - 13.85720444
Average (Standard dev.)0.0 (±0.97025698)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-9-9-9
Dimensions727272
Spacing727272
CellA=B=C: 302.4 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.24.24.2
M x/y/z727272
origin x/y/z0.0000.0000.000
length x/y/z302.400302.400302.400
α/β/γ90.00090.00090.000
start NX/NY/NZ-56-56-55
NX/NY/NZ112112112
MAP C/R/S123
start NC/NR/NS-9-9-9
NC/NR/NS727272
D min/max/mean-13.07913.8570.000

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Supplemental data

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Sample components

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Entire : Human iC3b

EntireName: Human iC3b
Components
  • Sample: Human iC3b
  • Protein or peptide: Complement component iC3b

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Supramolecule #1000: Human iC3b

SupramoleculeName: Human iC3b / type: sample / ID: 1000 / Oligomeric state: Monomer / Number unique components: 1
Molecular weightTheoretical: 181 KDa

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Macromolecule #1: Complement component iC3b

MacromoleculeName: Complement component iC3b / type: protein_or_peptide / ID: 1 / Name.synonym: iC3b / Number of copies: 1 / Oligomeric state: Monomer / Recombinant expression: No
Source (natural)Organism: Homo sapiens (human) / synonym: Human / Tissue: Plasma
Molecular weightTheoretical: 181 KDa

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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

Concentration1.1 mg/mL
BufferpH: 7.4 / Details: 150 mM NaCl, 20 mM Tris-HCL
StainingType: NEGATIVE / Details: 1% w/v uranyl acetate
GridDetails: Carbon-coated 400 mesh copper grid
VitrificationCryogen name: NONE / Instrument: OTHER

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Electron microscopy

MicroscopeJEOL 1230
Alignment procedureLegacy - Astigmatism: Objective lens astigmatism was corrected at 80,000 times magnification
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: OTHER / Digitization - Sampling interval: 10.5 µm / Number real images: 112 / Average electron dose: 10 e/Å2
Details: Images scanned with Minolta Dimage Scan Multi Pro scanner at 2400 dpi and averaged to a final 4.2 Angstroms pixel at the specimen
Bits/pixel: 16
Tilt angle min0
Electron beamAcceleration voltage: 100 kV / Electron source: TUNGSTEN HAIRPIN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.9 mm / Nominal defocus max: 1.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 50000
Sample stageSpecimen holder: Eucentric / Specimen holder model: JEOL / Tilt angle max: 47

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Image processing

DetailsThe particles were selected manually with Boxer (Eman)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 24.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: Xmipp,EMAN / Number images used: 29730

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Atomic model buiding 1

Initial modelPDB ID:

2i07

SoftwareName: Situs
DetailsProtocol: Rigid Body
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: Cross-correlation

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