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- EMDB-7427: Single-Molecule 3D Image of Half IgG1 (No. 010) -

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Basic information

Entry
Database: EMDB / ID: EMD-7427
TitleSingle-Molecule 3D Image of Half IgG1 (No. 010)
Map dataSingle-Molecule 3D Image of Half IgG1 (No. 010)
Sample
  • Complex: Half IgG1
Biological speciesunidentified (others)
Methodelectron tomography / negative staining / Resolution: 14.07 Å
AuthorsLei D / Liu J / Liu H / Lei M / Ren G
Funding support United States, 4 items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)DMR-1344290 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM104427 United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)R01HL115153 United States
Department of Energy (DOE, United States)DE-AC02-05CH11231 United States
CitationJournal: Sci Rep / Year: 2019
Title: Single-Molecule 3D Images of "Hole-Hole" IgG1 Homodimers by Individual-Particle Electron Tomography.
Authors: Lei D / Liu J / Liu H / Marino JP / Lei M / Ren G
History
DepositionJan 25, 2018-
Header (metadata) releaseFeb 21, 2018-
Map releaseJan 30, 2019-
UpdateDec 25, 2019-
Current statusDec 25, 2019Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.2
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.2
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol

Downloads & links

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Map

FileDownload / File: emd_7427.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSingle-Molecule 3D Image of Half IgG1 (No. 010)
Voxel sizeX=Y=Z: 2.96 Å
Density
Contour LevelMovie #1: 0.2
Minimum - Maximum-0.28655916 - 2.230659
Average (Standard dev.)0.0015741149 (±0.04546764)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin0430
Dimensions128128128
Spacing128128128
CellA=B=C: 378.88 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.962.962.96
M x/y/z128128128
origin x/y/z0.0000.0000.000
length x/y/z378.880378.880378.880
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ281156
MAP C/R/S123
start NC/NR/NS4300
NC/NR/NS128128128
D min/max/mean-0.2872.2310.002

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Supplemental data

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Sample components

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Entire : Half IgG1

EntireName: Half IgG1
Components
  • Complex: Half IgG1

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Supramolecule #1: Half IgG1

SupramoleculeName: Half IgG1 / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: unidentified (others)
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster) / Recombinant cell: ovary

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Experimental details

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Structure determination

Methodnegative staining
Processingelectron tomography
Aggregation stateparticle

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Sample preparation

BufferpH: 7 / Details: Dulbecco's phosphate buffered saline (DPBS)
StainingType: NEGATIVE / Material: Uranyl Formate / Details: The grid was stained with 1% (w/v) uranyl formate
GridMaterial: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.039 kPa
SectioningOther: NO SECTIONING

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Electron microscopy

MicroscopeZEISS LIBRA120PLUS
Specialist opticsEnergy filter - Name: In-column Omega Filter
Image recordingFilm or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Average electron dose: 71.21 e/Å2
Electron beamAcceleration voltage: 120 kV / Electron source: LAB6
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.2 mm / Nominal magnification: 80000

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Image processing

DetailsX-ray speckles in images were removed before CTF correction.
Final reconstructionAlgorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 14.07 Å / Resolution method: FSC 0.5 CUT-OFF
Details: The 3D reconstruction was performed by using Individual-Particle Electron Tomography (IPET). The obtained 3D map was Gaussian low-pass filtered to 2 nm. Image of the 3D map was taken in ...Details: The 3D reconstruction was performed by using Individual-Particle Electron Tomography (IPET). The obtained 3D map was Gaussian low-pass filtered to 2 nm. Image of the 3D map was taken in Chimera with the 'hide dust' function activated.
Number images used: 61

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