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- EMDB-1912: Structure of the Human Myeloma IgG2 Mat. -

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Basic information

Entry
Database: EMDB / ID: EMD-1912
TitleStructure of the Human Myeloma IgG2 Mat.
Map datahuman IgG2 Mat density map
Sample
  • Sample: Human myeloma immunoglobulin class G, subclass 2, MAT hIgG2 Mat
  • Protein or peptide: hIgG2 Mat
KeywordsHuman IgG2 / single particle 3D reconstruction / electron microscopy
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / Resolution: 17.8 Å
AuthorsRyazantsev S / Tischenko V / Nguyen C / Abramov V / Zaviyalov V
CitationJournal: PLoS One / Year: 2013
Title: Three-dimensional structure of the human myeloma IgG2.
Authors: Sergey Ryazantsev / Vladimir Tischenko / Christopher Nguyen / Vyacheslav Abramov / Vladimir Zav'yalov /
Abstract: Human immunoglobulin G, subclass 2 (hIgG2), plays an important role in immunity to bacterial pathogens and in numerous pathological conditions. However, there is a lack of information regarding the ...Human immunoglobulin G, subclass 2 (hIgG2), plays an important role in immunity to bacterial pathogens and in numerous pathological conditions. However, there is a lack of information regarding the three-dimensional (3D) structure of the hIgG2 molecule. We used electron microscopy (EM), differential scanning microcalorimetry (DSC) and fluorescence for structural analysis of the hIgG2. DSC and fluorescence indicated two types of interaction between CH1 domain of Fab (antigen-binding fragment/subunit) and CH2 domain of Fc (complement fixation fragment/subunit) simultaneously present in the sample: close interaction, which increases the thermostability of both, CH1 and CH2 domains, and weak (or no) interaction, which is typical for most IgGs but not hIgG2. Thermodynamics could not determine if both types of interactions are present within a single molecule. To address this question, EM was used. We employed a single-particle reconstruction and negative staining approach to reveal the three-dimensional structure of the hIgG2. A three-dimensional model of hIgG2 was created at 1.78 nm resolution. The hIgG2 is asymmetrical: one Fab subunit is in close proximity to the upper portion of the Fc subunit (CH2 domain) and the other Fab is distant from Fc. The plane of Fab subunits is nearly perpendicular to Fc. EM structure of the hIgG2 is in good agreement with thermodynamic data: a Fab distant from Fc should exhibit a lower melting temperature while a Fab interacting with Fc should exhibit a higher melting temperature. Both types of Fab subunits exist within one molecule resembling an A/B hIgG2 isoform introduced earlier on physicochemical level by Dillon et al. (2008). In such an arrangement, the access to the upper portion of Fc subunit is partially blocked by a Fab subunit. That might explain for instance why hIgG2 mildly activates complement and binds poorly to Fc receptors. Understanding of the three-dimensional structure of the hIgG2 should lead to better design of antibody-based therapeutics.
History
DepositionJun 23, 2011-
Header (metadata) releaseJul 1, 2011-
Map releaseJul 9, 2012-
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: 0.893
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.893
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd-1912.png

Downloads & links

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Map

FileDownload / File: emd_1912.map.gz / Format: CCP4 / Size: 2.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationhuman IgG2 Mat density map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.1 Å/pix.
x 92 pix.
= 193.2 Å		2.1 Å/pix.
x 92 pix.
= 193.2 Å		2.1 Å/pix.
x 92 pix.
= 193.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.893 / Movie #1: 0.893
Minimum - Maximum-0.07153887 - 1.74183214
Average (Standard dev.)0.08099203 (±0.25468364)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-46-46-46
Dimensions929292
Spacing929292
CellA=B=C: 193.2 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.12.12.1
M x/y/z929292
origin x/y/z0.0000.0000.000
length x/y/z193.200193.200193.200
α/β/γ90.00090.00090.000
start NX/NY/NZ-56-56-55
NX/NY/NZ112112112
MAP C/R/S123
start NC/NR/NS-46-46-46
NC/NR/NS929292
D min/max/mean-0.0721.7420.081

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Supplemental data

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Sample components

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Entire : Human myeloma immunoglobulin class G, subclass 2, MAT hIgG2 Mat

EntireName: Human myeloma immunoglobulin class G, subclass 2, MAT hIgG2 Mat
Components
  • Sample: Human myeloma immunoglobulin class G, subclass 2, MAT hIgG2 Mat
  • Protein or peptide: hIgG2 Mat

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Supramolecule #1000: Human myeloma immunoglobulin class G, subclass 2, MAT hIgG2 Mat

SupramoleculeName: Human myeloma immunoglobulin class G, subclass 2, MAT hIgG2 Mat
type: sample / ID: 1000
Details: More than 95 per cent purity. Stored at 4oC for 20 days before usage
Oligomeric state: Monomer / Number unique components: 1
Molecular weightExperimental: 160 KDa / Theoretical: 160 KDa / Method: Gel-electrophoresis, sedimentation

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Macromolecule #1: hIgG2 Mat

MacromoleculeName: hIgG2 Mat / type: protein_or_peptide / ID: 1 / Name.synonym: immunoglobulin G subclass two / Details: highly purified intact human myeloma IgG2 / Number of copies: 1 / Oligomeric state: Monomer / Recombinant expression: No
Source (natural)Organism: Homo sapiens (human) / Strain: hIgG2 Mat / synonym: Human / Tissue: Blood
Molecular weightExperimental: 160 KDa / Theoretical: 160 KDa

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Experimental details

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Structure determination

Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.014 mg/mL
BufferpH: 7.8 / Details: 20 mM ammonium acetate, pH 7.8
GridDetails: 1.4 nm carbon film with carbon holey-film on top of 100 mesh copper hexagonal grid
VitrificationCryogen name: NONE / Instrument: OTHER

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Electron microscopy

MicroscopeJEOL 1200EX
Alignment procedureLegacy - Astigmatism: Corrected at x500,000
Image recordingCategory: CCD / Film or detector model: GENERIC FILM / Number real images: 2 / Details: 2.1 A per pixel / Bits/pixel: 16
Tilt angle min0
Tilt angle max0
Electron beamAcceleration voltage: 80 kV / Electron source: TUNGSTEN HAIRPIN
Electron opticsCalibrated magnification: 60000 / Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 1.4 mm / Nominal defocus max: 0.0 µm / Nominal defocus min: 0.0 µm / Nominal magnification: 60000
Sample stageSpecimen holder: Normal / Specimen holder model: JEOL

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Image processing

DetailsImages were taken at in-focus condition. No CTF correction was performed.
CTF correctionDetails: No correction
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 17.8 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EMAN / Number images used: 3000
Final angle assignmentDetails: Euler space was filled uniformly

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