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- EMDB-4231: C1-IgG1 complex on liposomes -

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Basic information

Entry
Database: EMDB / ID: EMD-4231
TitleC1-IgG1 complex on liposomes
Map dataC1-IgG1 complex observed on liposomes
Sample
  • Complex: C1-IgG1 complex on liposomes
    • Complex: IgG1 antibodies
    • Complex: C1 complex
Function / homology
Function and homology information


complement component C1 complex / complement component C1q complex / negative regulation of macrophage differentiation / synapse pruning / negative regulation of granulocyte differentiation / vertebrate eye-specific patterning / complement-mediated synapse pruning / collagen trimer / complement activation / Classical antibody-mediated complement activation ...complement component C1 complex / complement component C1q complex / negative regulation of macrophage differentiation / synapse pruning / negative regulation of granulocyte differentiation / vertebrate eye-specific patterning / complement-mediated synapse pruning / collagen trimer / complement activation / Classical antibody-mediated complement activation / neuron remodeling / Initial triggering of complement / immunoglobulin complex / complement activation, classical pathway / Regulation of Complement cascade / astrocyte activation / synapse organization / microglial cell activation / cell-cell signaling / amyloid-beta binding / postsynapse / collagen-containing extracellular matrix / blood microparticle / adaptive immune response / immune response / innate immune response / synapse / extracellular space / extracellular region / plasma membrane
Similarity search - Function
C1q domain / C1q domain / C1q domain profile. / Complement component C1q domain. / Tumour necrosis factor-like domain superfamily / Collagen triple helix repeat / Collagen triple helix repeat (20 copies) / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain ...C1q domain / C1q domain / C1q domain profile. / Complement component C1q domain. / Tumour necrosis factor-like domain superfamily / Collagen triple helix repeat / Collagen triple helix repeat (20 copies) / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Complement C1q subcomponent subunit A / Complement C1q subcomponent subunit B / Complement C1q subcomponent subunit C / Immunoglobulin gamma-1 heavy chain
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsubtomogram averaging / cryo EM / Resolution: 25.0 Å
AuthorsHowes SC / Koning RI / de Jong RN / Beurskens FJ / Koster AJ / Sharp TH
Funding support Netherlands, 6 items
OrganizationGrant numberCountry
Netherlands Organisation for Scientific ResearchCW 714.013.002 Netherlands
Netherlands Organisation for Scientific ResearchSTW 13711 Netherlands
Netherlands Organisation for Scientific Research700.57.010 Netherlands
European Research Council233229 Netherlands
Institute of Chemical ImmunologyNWO 024.002.009 Netherlands
Netherlands Centre for Electron NanoscopyNWO 175.010.2009.001 Netherlands
CitationJournal: Science / Year: 2018
Title: Structures of C1-IgG1 provide insights into how danger pattern recognition activates complement.
Authors: Deniz Ugurlar / Stuart C Howes / Bart-Jan de Kreuk / Roman I Koning / Rob N de Jong / Frank J Beurskens / Janine Schuurman / Abraham J Koster / Thomas H Sharp / Paul W H I Parren / Piet Gros /
Abstract: Danger patterns on microbes or damaged host cells bind and activate C1, inducing innate immune responses and clearance through the complement cascade. How these patterns trigger complement initiation ...Danger patterns on microbes or damaged host cells bind and activate C1, inducing innate immune responses and clearance through the complement cascade. How these patterns trigger complement initiation remains elusive. Here, we present cryo-electron microscopy analyses of C1 bound to monoclonal antibodies in which we observed heterogeneous structures of single and clustered C1-immunoglobulin G1 (IgG1) hexamer complexes. Distinct C1q binding sites are observed on the two Fc-CH2 domains of each IgG molecule. These are consistent with known interactions and also reveal additional interactions, which are supported by functional IgG1-mutant analysis. Upon antibody binding, the C1q arms condense, inducing rearrangements of the C1rs proteases and tilting C1q's cone-shaped stalk. The data suggest that C1r may activate C1s within single, strained C1 complexes or between neighboring C1 complexes on surfaces.
History
DepositionDec 20, 2017-
Header (metadata) releaseDec 27, 2017-
Map releaseFeb 28, 2018-
UpdateSep 30, 2020-
Current statusSep 30, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.5
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 1.5
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4231.png

Downloads & links

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Map

FileDownload / File: emd_4231.map.gz / Format: CCP4 / Size: 2.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationC1-IgG1 complex observed on liposomes
Voxel sizeX=Y=Z: 5.38 Å
Density
Contour LevelBy AUTHOR: 1.5 / Movie #1: 1.5
Minimum - Maximum-4.5099797 - 8.18637
Average (Standard dev.)0.637008600 (±0.9999992)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-42-42-42
Dimensions848484
Spacing848484
CellA=B=C: 451.92 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z5.385.385.38
M x/y/z848484
origin x/y/z0.0000.0000.000
length x/y/z451.920451.920451.920
α/β/γ90.00090.00090.000
start NX/NY/NZ212211153
NX/NY/NZ80102186
MAP C/R/S123
start NC/NR/NS-42-42-42
NC/NR/NS848484
D min/max/mean-4.5108.1860.000

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Supplemental data

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Additional map: Class 1 of neighboring C1-IgG1 complexes

Fileemd_4231_additional_1.map
AnnotationClass 1 of neighboring C1-IgG1 complexes
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: C1-IgG1 complex observed on liposomes refined using mask...

Fileemd_4231_additional_2.map
AnnotationC1-IgG1 complex observed on liposomes refined using mask that excluded the membrane and Fab regions
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Class 2 of neighboring C1-IgG1 complexes

Fileemd_4231_additional_3.map
AnnotationClass 2 of neighboring C1-IgG1 complexes
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Class 3 of neighboring C1-IgG1 complexes

Fileemd_4231_additional_4.map
AnnotationClass 3 of neighboring C1-IgG1 complexes
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map of C1-IgG1 complex observed on liposomes

Fileemd_4231_half_map_1.map
AnnotationHalf map of C1-IgG1 complex observed on liposomes
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map of C1-IgG1 complex observed on liposomes

Fileemd_4231_half_map_2.map
AnnotationHalf map of C1-IgG1 complex observed on liposomes
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : C1-IgG1 complex on liposomes

EntireName: C1-IgG1 complex on liposomes
Components
  • Complex: C1-IgG1 complex on liposomes
    • Complex: IgG1 antibodies
    • Complex: C1 complex

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Supramolecule #1: C1-IgG1 complex on liposomes

SupramoleculeName: C1-IgG1 complex on liposomes / type: complex / ID: 1 / Parent: 0
Details: Liposomes containing di-nitrophenyl haptens were incubated with monoclonal antibodies and C1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 700 KDa

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Supramolecule #2: IgG1 antibodies

SupramoleculeName: IgG1 antibodies / type: complex / ID: 2 / Parent: 1
Details: Monoclonal IgG1 recombinantly expressed in HEK293 FreeStyle cells, purified and bound to liposomes.
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant cell: HEK293

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Supramolecule #3: C1 complex

SupramoleculeName: C1 complex / type: complex / ID: 3 / Parent: 1
Details: C1 complex purified from human serum containing C1q, C1r, and C1s. Map from focused alignment and classification.
Source (natural)Organism: Homo sapiens (human)

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation stateparticle

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Sample preparation

Concentration1.3 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
50.0 mMC8H18N2O4SHEPES
145.0 mMNaClSodium chloridesodium chloride
3.0 mMCaCl2calcium chloride
GridModel: Quantifoil R2/1 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 96 % / Chamber temperature: 294 K / Instrument: LEICA EM GP
Details: 3 microlitres applied and incubated for 30 seconds, blot for 1 second before plunging.
DetailsExtruded liposomes were incubated with IgG1 and C1. Gold fiducials were added just before applying to grids.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus min: 0.3 µm / Nominal magnification: 53000
Specialist opticsPhase plate: VOLTA PHASE PLATE / Energy filter - Name: GIF Quantum LS
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3710 pixel / Digitization - Dimensions - Height: 3838 pixel / Digitization - Sampling interval: 5.0 µm / Digitization - Frames/image: 1-6 / Average electron dose: 1.2 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

ExtractionNumber tomograms: 34 / Number images used: 51274 / Method: Manually annotate liposome surfaces / Software - Name: Dynamo (ver. 1.1.291)
Details: Equally spaced sub-volumes were extracted from the surfaces of liposomes
Final 3D classificationSoftware - Name: Dynamo (ver. 1.1.291)
Final angle assignmentType: OTHER / Software - Name: Dynamo (ver. 1.1.291)
Details: Volume matching after filtering reference volume to angular range present in sub-volume
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 25.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: Dynamo / Number subtomograms used: 1660
FSC plot (resolution estimation)

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