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- EMDB-2554: electron tomography average of an IgG hexamer -

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Basic information

Entry
Database: EMDB / ID: EMD-2554
Titleelectron tomography average of an IgG hexamer
Map datareconstruction of IgG1-005-RGY hexamer
Sample
  • Sample: IgG1-005-RGY monoclonal antibody
  • Protein or peptide: IgG1-005-E345R-E430G-S440Y
KeywordsIgG hexamer / IgG / classical complement activation
Biological speciesHomo sapiens (human)
Methodsubtomogram averaging / negative staining / Resolution: 22.0 Å
AuthorsDiebolder CA / Beurskens FJ / de Jong RN / Koning RI / Strumane K / Lindorfer MA / Voorhorst M / Ugurlar D / Rosati S / Heck AJR ...Diebolder CA / Beurskens FJ / de Jong RN / Koning RI / Strumane K / Lindorfer MA / Voorhorst M / Ugurlar D / Rosati S / Heck AJR / van de Winkel JGJ / Wilson IA / Koster AJ / Taylor RP / Ollmann-Saphire E / Burton DR / Schuurman J / Gros P / Parren PWHI
CitationJournal: Science / Year: 2014
Title: Complement is activated by IgG hexamers assembled at the cell surface.
Authors: Christoph A Diebolder / Frank J Beurskens / Rob N de Jong / Roman I Koning / Kristin Strumane / Margaret A Lindorfer / Marleen Voorhorst / Deniz Ugurlar / Sara Rosati / Albert J R Heck / Jan ...Authors: Christoph A Diebolder / Frank J Beurskens / Rob N de Jong / Roman I Koning / Kristin Strumane / Margaret A Lindorfer / Marleen Voorhorst / Deniz Ugurlar / Sara Rosati / Albert J R Heck / Jan G J van de Winkel / Ian A Wilson / Abraham J Koster / Ronald P Taylor / Erica Ollmann Saphire / Dennis R Burton / Janine Schuurman / Piet Gros / Paul W H I Parren /
Abstract: Complement activation by antibodies bound to pathogens, tumors, and self antigens is a critical feature of natural immune defense, a number of disease processes, and immunotherapies. How antibodies ...Complement activation by antibodies bound to pathogens, tumors, and self antigens is a critical feature of natural immune defense, a number of disease processes, and immunotherapies. How antibodies activate the complement cascade, however, is poorly understood. We found that specific noncovalent interactions between Fc segments of immunoglobulin G (IgG) antibodies resulted in the formation of ordered antibody hexamers after antigen binding on cells. These hexamers recruited and activated C1, the first component of complement, thereby triggering the complement cascade. The interactions between neighboring Fc segments could be manipulated to block, reconstitute, and enhance complement activation and killing of target cells, using all four human IgG subclasses. We offer a general model for understanding antibody-mediated complement activation and the design of antibody therapeutics with enhanced efficacy.
History
DepositionJan 15, 2014-
Header (metadata) releaseJan 29, 2014-
Map releaseMar 26, 2014-
UpdateMar 26, 2014-
Current statusMar 26, 2014Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 125
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 125
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_2554.png

Downloads & links

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Map

FileDownload / File: emd_2554.map.gz / Format: CCP4 / Size: 19.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationreconstruction of IgG1-005-RGY hexamer
Voxel sizeX=Y=Z: 4.4 Å
Density
Contour LevelBy AUTHOR: 125.0 / Movie #1: 125
Minimum - Maximum41.395481109999999 - 166.617950439999987
Average (Standard dev.)119.885620119999999 (±2.07971597)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions174174174
Spacing174174174
CellA=B=C: 765.60004 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.44.44.4
M x/y/z174174174
origin x/y/z0.0000.0000.000
length x/y/z765.600765.600765.600
α/β/γ90.00090.00090.000
start NX/NY/NZ-207-207-206
NX/NY/NZ414414414
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS174174174
D min/max/mean41.395166.618119.886

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Supplemental data

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Segmentation: this mask represents the FC hexamer

Annotationthis mask represents the FC hexamer
Fileemd_2554_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : IgG1-005-RGY monoclonal antibody

EntireName: IgG1-005-RGY monoclonal antibody
Components
  • Sample: IgG1-005-RGY monoclonal antibody
  • Protein or peptide: IgG1-005-E345R-E430G-S440Y

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Supramolecule #1000: IgG1-005-RGY monoclonal antibody

SupramoleculeName: IgG1-005-RGY monoclonal antibody / type: sample / ID: 1000 / Details: sample is a mix of monomers and hexamers / Oligomeric state: one homohexamer / Number unique components: 1
Molecular weightExperimental: 890 KDa / Method: native mass spectrometry

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Macromolecule #1: IgG1-005-E345R-E430G-S440Y

MacromoleculeName: IgG1-005-E345R-E430G-S440Y / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Oligomeric state: Hexamer / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human) / synonym: Human
Molecular weightExperimental: 148.5 KDa / Theoretical: 145.4 KDa
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant cell: Freestyle 293-F / Recombinant plasmid: pcDNA3.3

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Experimental details

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Structure determination

Methodnegative staining
Processingsubtomogram averaging
Aggregation stateparticle

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Sample preparation

Concentration0.03 mg/mL
StainingType: NEGATIVE / Details: negative staining with 3% uranyl acetate
GridDetails: 400 mesh copper grids with carbon support
VitrificationCryogen name: NONE / Instrument: OTHER

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Electron microscopy

MicroscopeFEI TECNAI F20
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 50000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2 mm / Nominal defocus max: 1.035 µm / Nominal defocus min: 1.01 µm / Nominal magnification: 50000
Sample stageSpecimen holder model: SIDE ENTRY, EUCENTRIC / Tilt series - Axis1 - Min angle: -66 ° / Tilt series - Axis1 - Max angle: 66 °
Alignment procedureLegacy - Astigmatism: Objective lens astigmatism was corrected at 50,000 times magnification
DateSep 3, 2013
Image recordingCategory: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k)
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 22.0 Å / Resolution method: OTHER / Software - Name: IMOD, PEET, TOMOCTF / Details: final map was calculated from 200 sub tomograms / Number subtomograms used: 200
Detailsmanual picking of 237 particles from two tomograms (PEET stalkInit), random particle as initial reference, iterative refinement in PEET

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Atomic model buiding 1

Initial modelPDB ID:

1hzh

SoftwareName: Chimera
Detailsmanual docking
RefinementSpace: REAL / Protocol: RIGID BODY FIT

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