+Open data
-Basic information
Entry | Database: PDB / ID: 8ghz | ||||||
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Title | Cryo-EM structure of fish immunogloblin M-Fc | ||||||
Components | Teleost immunoglobulin M protein | ||||||
Keywords | IMMUNE SYSTEM / Immunoglobulin M / IgM | ||||||
Biological species | Oncorhynchus mykiss (rainbow trout) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.78 Å | ||||||
Authors | Lyu, M. / Stadtmueller, B.M. / Malyutin, A.G. | ||||||
Funding support | United States, 1items
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Citation | Journal: Nat Commun / Year: 2023 Title: The structure of the teleost Immunoglobulin M core provides insights on polymeric antibody evolution, assembly, and function. Authors: Mengfan Lyu / Andrey G Malyutin / Beth M Stadtmueller / Abstract: Polymeric (p) immunoglobulins (Igs) serve broad functions during vertebrate immune responses. Typically, pIgs contain between two and six Ig monomers, each with two antigen binding fragments and one ...Polymeric (p) immunoglobulins (Igs) serve broad functions during vertebrate immune responses. Typically, pIgs contain between two and six Ig monomers, each with two antigen binding fragments and one fragment crystallization (Fc). In addition, many pIgs assemble with a joining-chain (JC); however, the number of monomers and potential to include JC vary with species and heavy chain class. Here, we report the cryo-electron microscopy structure of IgM from a teleost (t) species, which does not encode JC. The structure reveals four tIgM Fcs linked through eight C-terminal tailpieces (Tps), which adopt a single β-sandwich-like domain (Tp assembly) located between two Fcs. Specifically, two of eight heavy chains fold uniquely, resulting in a structure distinct from mammalian IgM, which typically contains five IgM monomers, one JC and a centrally-located Tp assembly. Together with mutational analysis, structural data indicate that pIgs have evolved a range of assembly mechanisms and structures, each likely to support unique antibody effector functions. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8ghz.cif.gz | 663.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ghz.ent.gz | 565.5 KB | Display | PDB format |
PDBx/mmJSON format | 8ghz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8ghz_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 8ghz_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 8ghz_validation.xml.gz | 63.9 KB | Display | |
Data in CIF | 8ghz_validation.cif.gz | 93.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gh/8ghz ftp://data.pdbj.org/pub/pdb/validation_reports/gh/8ghz | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 26998.514 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Oncorhynchus mykiss (rainbow trout) / Plasmid: pD2610-v1 / Cell line (production host): HEK293F / Production host: Homo sapiens (human) #2: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: rainbow trout (Oncorhynchus mykiss) immunoglobulin M Fc Type: COMPLEX Details: Heavy chain constant domains 3 and 4 including C-terminal tailpiece Entity ID: #1 / Source: RECOMBINANT | |||||||||||||||
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Source (natural) | Organism: Oncorhynchus mykiss (rainbow trout) | |||||||||||||||
Source (recombinant) | Organism: Homo sapiens (human) | |||||||||||||||
Buffer solution | pH: 7.8 | |||||||||||||||
Buffer component |
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Specimen | Conc.: 0.1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||
Specimen support | Details: Pelco easiGlow at 25 mA / Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 | |||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 600 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 3618 Details: Images were collected with SerialEM using beam image-shift in a 3x3x3 pattern. A total of ~60 e/A2 was fractionated into 40 frames movies. |
EM imaging optics | Energyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV |
Image scans | Width: 5760 / Height: 4092 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 1300000 | ||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C2 (2 fold cyclic) | ||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.78 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 61000 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 169.44 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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