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- EMDB-1583: 3D structure of the C3bB complex provides insights into the activ... -

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Basic information

Entry
Database: EMDB / ID: EMD-1583
Title3D structure of the C3bB complex provides insights into the activation and regulation of the complement alternative pathway convertase
Map dataStructure of the C3bB pro-convertase.
Sample
  • Sample: C3bB
  • Protein or peptide: C3bB
KeywordsC3bB / complement alternative pathway
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / negative staining / Resolution: 28.0 Å
AuthorsTorreira E / Tortajada A / Montes T / Rodriguez de Cordoba S / Llorca O
CitationJournal: Proc Natl Acad Sci U S A / Year: 2009
Title: 3D structure of the C3bB complex provides insights into the activation and regulation of the complement alternative pathway convertase.
Authors: Eva Torreira / Agustín Tortajada / Tamara Montes / Santiago Rodríguez de Córdoba / Oscar Llorca /
Abstract: Generation of the alternative pathway C3-convertase, the central amplification enzyme of the complement cascade, initiates by the binding of factor B (fB) to C3b to form the proconvertase, C3bB. C3bB ...Generation of the alternative pathway C3-convertase, the central amplification enzyme of the complement cascade, initiates by the binding of factor B (fB) to C3b to form the proconvertase, C3bB. C3bB is subsequently cleaved by factor D (fD) at a single site in fB, producing Ba and Bb fragments. Ba dissociates from the complex, while Bb remains bound to C3b, forming the active alternative pathway convertase, C3bBb. Using single-particle electron microscopy we have determined the 3-dimensional structures of the C3bB and the C3bBb complexes at approximately 27A resolution. The C3bB structure shows that fB undergoes a dramatic conformational change upon binding to C3b. However, the C3b-bound fB structure was easily interpreted after independently fitting the atomic structures of the isolated Bb and Ba fragments. Interestingly, the divalent cation-binding site in the von Willebrand type A domain in Bb faces the C345C domain of C3b, whereas the serine-protease domain of Bb points outwards. The structure also shows that the Ba fragment interacts with C3b separately from Bb at the level of the alpha'NT and CUB domains. Within this conformation, the long and flexible linker between Bb and Ba is likely exposed and accessible for cleavage by fD to form the active convertase, C3bBb. The architecture of the C3bB and C3bBb complexes reveals that C3b could promote cleavage and activation of fB by actively displacing the Ba domain from the von Willebrand type A domain in free fB. These structures provide a structural basis to understand fundamental aspects of the activation and regulation of the alternative pathway C3-convertase.
History
DepositionNov 24, 2008-
Header (metadata) releaseDec 3, 2008-
Map releaseApr 1, 2009-
UpdateOct 31, 2012-
Current statusOct 31, 2012Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 4.665481014
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 4.665481014
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-2i07
  • Surface level: 4.665481014
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1583.gif

Downloads & links

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Map

FileDownload / File: emd_1583.map.gz / Format: CCP4 / Size: 1.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationStructure of the C3bB pro-convertase.
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 Level1: 4.75 / Movie #1: 4.665481
Minimum - Maximum-3.26826 - 12.711600000000001
Average (Standard dev.)0.152448 (±0.975135)
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 °

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-100-100-99
NX/NY/NZ200200200
MAP C/R/S123
start NC/NR/NS-9-9-9
NC/NR/NS727272
D min/max/mean-3.26812.7120.152

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Supplemental data

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Sample components

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Entire : C3bB

EntireName: C3bB
Components
  • Sample: C3bB
  • Protein or peptide: C3bB

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Supramolecule #1000: C3bB

SupramoleculeName: C3bB / type: sample / ID: 1000
Oligomeric state: One monomer of C3b binds to one monomer of Fb
Number unique components: 2
Molecular weightExperimental: 270 KDa / Theoretical: 270 KDa

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Macromolecule #1: C3bB

MacromoleculeName: C3bB / type: protein_or_peptide / ID: 1 / Name.synonym: complement pro-convertase / Number of copies: 1 / Oligomeric state: dimer / Recombinant expression: No
Source (natural)Organism: Homo sapiens (human) / synonym: Human

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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

BufferDetails: 25mM TrisHCl pH8.0, 50mM NaCl, 5 mM NiCl2
StainingType: NEGATIVE / Details: 1% uranyl formate
GridDetails: 400 mesh Copper/Palladium grid
VitrificationCryogen name: NONE / Instrument: OTHER

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Electron microscopy

MicroscopeJEOL 1230
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: OTHER / Digitization - Sampling interval: 10.5 µm
Details: images scanned with a 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 magnification: 50000
Sample stageSpecimen holder: Eucentric / Specimen holder model: OTHER / Tilt angle max: 35

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Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 28.0 Å / Resolution method: FSC 0.5 CUT-OFF / Number images used: 6000

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Atomic model buiding 1

Initial modelPDB ID:

2i07

RefinementSpace: RECIPROCAL

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