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- EMDB-7388: Single Molecule 3D Image of a Hole-Hole Homodimer Species Generat... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-7388 | |||||||||||||||
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Title | Single Molecule 3D Image of a Hole-Hole Homodimer Species Generated in the Production of a Bispecific Recombinant IgG1 (No. 036) | |||||||||||||||
![]() | Single Molecule 3D Image of a Hole-Hole Homodimer Species Generated in the Production of a Bispecific Recombinant IgG1 (No. 036) | |||||||||||||||
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Biological species | unidentified (others) | |||||||||||||||
Method | electron tomography / negative staining / Resolution: 11.95 Å | |||||||||||||||
![]() | Lei D / Liu J / Liu H / Lei M / Ren G | |||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Single-Molecule 3D Images of "Hole-Hole" IgG1 Homodimers by Individual-Particle Electron Tomography. Authors: Dongsheng Lei / Jianfang Liu / Hongbin Liu / Thomas E Cleveland / John P Marino / Ming Lei / Gang Ren / ![]() Abstract: The engineering of immunoglobulin-G molecules (IgGs) is of wide interest for improving therapeutics, for example by modulating the activity or multiplexing the specificity of IgGs to recognize more ...The engineering of immunoglobulin-G molecules (IgGs) is of wide interest for improving therapeutics, for example by modulating the activity or multiplexing the specificity of IgGs to recognize more than one antigen. Optimization of engineered IgG requires knowledge of three-dimensional (3D) structure of synthetic IgG. However, due to flexible nature of the molecules, their structural characterization is challenging. Here, we use our reported individual-particle electron tomography (IPET) method with optimized negative-staining (OpNS) for direct 3D reconstruction of individual IgG hole-hole homodimer molecules. The hole-hole homodimer is an undesired variant generated during the production of a bispecific antibody using the knob-into-hole heterodimer technology. A total of 64 IPET 3D density maps at ~15 Å resolutions were reconstructed from 64 individual molecules, revealing 64 unique conformations. In addition to the known Y-shaped conformation, we also observed an unusual X-shaped conformation. The 3D structure of the X-shaped conformation contributes to our understanding of the structural details of the interaction between two heavy chains in the Fc domain. The IPET approach, as an orthogonal technique to characterize the 3D structure of therapeutic antibodies, provides insight into the 3D structural variety and dynamics of heterogeneous IgG molecules. | |||||||||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 6.9 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 10.3 KB 10.3 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 4.6 KB | Display | ![]() |
Images | ![]() | 11.5 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 78.1 KB | Display | ![]() |
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Full document | ![]() | 77.3 KB | Display | |
Data in XML | ![]() | 494 B | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7353C ![]() 7354C ![]() 7355C ![]() 7356C ![]() 7357C ![]() 7358C ![]() 7359C ![]() 7360C ![]() 7361C ![]() 7362C ![]() 7363C ![]() 7364C ![]() 7365C ![]() 7366C ![]() 7367C ![]() 7368C ![]() 7369C ![]() 7370C ![]() 7371C ![]() 7372C ![]() 7373C ![]() 7374C ![]() 7375C ![]() 7376C ![]() 7377C ![]() 7378C ![]() 7379C ![]() 7380C ![]() 7381C ![]() 7382C ![]() 7383C ![]() 7384C ![]() 7385C ![]() 7386C ![]() 7387C ![]() 7389C ![]() 7390C ![]() 7391C ![]() 7392C ![]() 7393C ![]() 7394C ![]() 7395C ![]() 7396C ![]() 7397C ![]() 7398C ![]() 7399C ![]() 7400C ![]() 7401C ![]() 7402C ![]() 7404C ![]() 7405C ![]() 7406C ![]() 7407C ![]() 7408C ![]() 7409C ![]() 7410C ![]() 7411C ![]() 7412C ![]() 7413C ![]() 7414C ![]() 7415C ![]() 7416C ![]() 7417C ![]() 7418C ![]() 7419C ![]() 7420C ![]() 7421C ![]() 7422C ![]() 7423C ![]() 7424C ![]() 7425C ![]() 7426C ![]() 7427C ![]() 7428C ![]() 7429C ![]() 7430C ![]() 7431C ![]() 7432C ![]() 7433C C: citing same article ( |
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Links
EMDB pages | ![]() ![]() |
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Map
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Annotation | Single Molecule 3D Image of a Hole-Hole Homodimer Species Generated in the Production of a Bispecific Recombinant IgG1 (No. 036) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.96 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : IgG1 hole-hole homodimer
Entire | Name: IgG1 hole-hole homodimer |
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Components |
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-Supramolecule #1: IgG1 hole-hole homodimer
Supramolecule | Name: IgG1 hole-hole homodimer / type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: unidentified (others) |
Recombinant expression | Organism: ![]() ![]() |
-Experimental details
-Structure determination
Method | negative staining |
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![]() | electron tomography |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7 / Details: Dulbecco's phosphate buffered saline (DPBS) |
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Staining | Type: NEGATIVE / Material: Uranyl Formate / Details: The grid was stained with 1% (w/v) uranyl formate |
Grid | Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.039 kPa |
Sectioning | Other: NO SECTIONING |
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Electron microscopy
Microscope | ZEISS LIBRA120PLUS |
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Specialist optics | Energy filter - Name: In-column Omega Filter |
Image recording | Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Average electron dose: 70.48 e/Å2 |
Electron beam | Acceleration voltage: 120 kV / Electron source: LAB6 |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.2 mm / Nominal magnification: 80000 |