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Yorodumi- PDB-8adz: Cryo-EM structure of full-length human immunoglobulin M - F(ab')2... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8adz | |||||||||||||||||||||
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Title | Cryo-EM structure of full-length human immunoglobulin M - F(ab')2 conformation 2 | |||||||||||||||||||||
Components |
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Keywords | IMMUNE SYSTEM / full-length human immunoglobulin M | |||||||||||||||||||||
Biological species | Homo sapiens (human) | |||||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6.7 Å | |||||||||||||||||||||
Authors | Chen, Q. / Rosenthal, P. / Tolar, P. | |||||||||||||||||||||
Funding support | United Kingdom, 6items
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Citation | Journal: Nat Commun / Year: 2022 Title: Cryomicroscopy reveals the structural basis for a flexible hinge motion in the immunoglobulin M pentamer. Authors: Qu Chen / Rajesh Menon / Lesley J Calder / Pavel Tolar / Peter B Rosenthal / Abstract: Immunoglobulin M (IgM) is the most ancient of the five isotypes of immunoglobulin (Ig) molecules and serves as the first line of defence against pathogens. Here, we use cryo-EM to image the structure ...Immunoglobulin M (IgM) is the most ancient of the five isotypes of immunoglobulin (Ig) molecules and serves as the first line of defence against pathogens. Here, we use cryo-EM to image the structure of the human full-length IgM pentamer, revealing antigen binding domains flexibly attached to the asymmetric and rigid core formed by the Cμ4 and Cμ3 constant regions and the J-chain. A hinge is located at the Cμ3/Cμ2 domain interface, allowing Fabs and Cμ2 to pivot as a unit both in-plane and out-of-plane. This motion is different from that observed in IgG and IgA, where the two Fab arms are able to swing independently. A biased orientation of one pair of Fab arms results from asymmetry in the constant domain (Cμ3) at the IgM subunit interacting most extensively with the J-chain. This may influence the multi-valent binding to surface-associated antigens and complement pathway activation. By comparison, the structure of the Fc fragment in the IgM monomer is similar to that of the pentamer, but is more dynamic in the Cμ4 domain. | |||||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8adz.cif.gz | 657.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8adz.ent.gz | 542.8 KB | Display | PDB format |
PDBx/mmJSON format | 8adz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8adz_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 8adz_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 8adz_validation.xml.gz | 97.8 KB | Display | |
Data in CIF | 8adz_validation.cif.gz | 149.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ad/8adz ftp://data.pdbj.org/pub/pdb/validation_reports/ad/8adz | HTTPS FTP |
-Related structure data
Related structure data | 15376MC 7qdoC 8adyC 8ae0C 8ae2C 8ae3C M: map data used to model this data C: citing same article (ref.) |
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-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Protein , 1 types, 2 molecules IB
#3: Protein | Mass: 12769.625 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) |
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-Immunoglobulin ... , 2 types, 11 molecules MNOQEFGRKSJ
#4: Protein | Mass: 41875.766 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) #5: Protein | | Mass: 15483.329 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) |
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-Antibody , 2 types, 4 molecules LVHU
#1: Antibody | Mass: 23367.873 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) #2: Antibody | Mass: 24574.730 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) |
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-Sugars , 2 types, 13 molecules
#6: Polysaccharide | Source method: isolated from a genetically manipulated source #7: Sugar | ChemComp-NAG / |
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-Details
Has ligand of interest | N |
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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: Full-length human IgM pentamer / Type: COMPLEX / Entity ID: #1-#5 / Source: NATURAL |
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Source (natural) | Organism: Homo sapiens (human) |
Buffer solution | pH: 8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 277 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: 75000 X / Calibrated magnification: 128440 X / Nominal defocus max: 5000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 34.2 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 6.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 50904 / Symmetry type: POINT |