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Title:3D map of a peptide conjugated antibody particle by individual-particle electron tomography (IPET) and optimized negative-staining.
Authors:Tong H, Zhang L, Kaspar A, Rames M, Huang L, Woodnutt G, Ren G
Sample:Peptide-conjugated Human IgG1 Antibody
Method:Tomography (16.5 angstroms resolution)
Red flagLatest update:2013-02-13
Sample
Sample name: Peptide-conjugated Human IgG1 Antibody
Oligomeric state: Monomer
Theoretical molecular weight of the sample: 0.16
Components:
ID Type Name Exp. MW (MDa) Oligomeric details Recombinant expression Synthetic Organism UniProt identifier GO identifier InterPro identifier Virus identifier Details
1proteinIgG Antibody0.16MonomerfalseHomo sapiens
Experiment
Specimen state: Particle
Specimen preparation:
pHSpecimen conc.DetailsStainingSpecimen support details
7.40.01 mg/mL1X Dulbeccos phosphate-buffered saline (Invitrogen, La Jolla, CA), 2.7 mM KCl, 1.46 mM KH2PO4, 136.9 mM NaCl, and 8.1 mM Na2HPO4EM Specimens were prepared by optimized negative-staining EM specimen preparation protocol as described Zhang L. and Ren G, Journal of Lipid Research, (2010) 51, 1228-1236; (2011) 52, 175-84 and BBA (2013) 1830, 2150-9. In brief, antibody was diluted to 0.01 mg/ml with deionized water. Aliquots (about 3ul) were applied to the 200 mesh glow-discharged thin carbon-coated EM grids (Cu-200CN, Pacific Grid-Tech, USA). The grid was washed by deionized water for three times, and then washed by 1% uranyl formate for three times before blotting to drying.200 mesh glow-discharged thin carbon-coated EM grids (Cu-200CN, Pacific Grid-Tech, USA)
Vitrification:
Cryogen nameHumidityTemp.Instr.MethodTime resolvedDetails
NONE% KNONE ms
Imaging:
MicroscopeVoltageIllumination modeImaging modeCsDefocus min.Defocus max.Nominal mag.Calibrated mag.Electron sourceDetectorDetector distanceAstigmatism
OTHER120 kVFLOOD BEAMBRIGHT FIELD2.2 mm1000 nm2000 nm80000LAB6Ultra scan 4K mm
FEI TECNAI 20200 kVFLOOD BEAMBRIGHT FIELD2.0 mm1000 nm2000 nm80000LAB6Ultra scan 4K mm

Specimen holderHolder modelTilt min.Tilt max.Energy filterEnergy windowTemp.Temp. min.Temp. max.Beam tiltElectron doseOther detailsDate
GatanOTHER-70.5°70.5° eV K K K mrad250 e/Å2tilt step is 1.5 degree01-MAY-2012
GatanOTHER-70.5°70.5° eV K K K mrad250 e/Å2tilt step is 1.5 degree01-OCT-2009
Processing
Protocol:Focused ET reconstruction (FETR) algorithms
Software:Individual-partcile, electron, tomogrphy, (IPET), and, FETR
CTF correction:TOMOCTF
Number of tilts:95
Tilt angle increment:1.5°
Imposed symmetry:C1
Resolution by author:16.5 Å
Resolution method:Intra-FSC.
Processing details:Map was reconstructed by individual-particle electron tomography (IPET)and Focus ET Reconstruction Algorithm. Reconstruction was done by Individual-Particle Tomography Reconstruction (IPET) method.
Scanned images:
Num. imagesSampling sizeOD rangeQuant. bit numberOther detailsScanner
951.406 μm/pixel16
Fitting:
PDBProtocolTarget crit.SoftwareB valueFitting spacePDB chainDetails
1IGT rigid bodyManualREALManually fit each domain into the density map in order to compare the conformational different between the peptide-conjugated antibody structure and PDB structure in term of domain size and shape.