+Open data
-Basic information
Entry | Database: PDB / ID: 8ema | ||||||
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Title | mouse full length B cell receptor | ||||||
Components |
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Keywords | IMMUNE SYSTEM / COMPLEX / MEMBRANE PROTEIN | ||||||
Function / homology | Function and homology information CD22 mediated BCR regulation / riboflavin synthase activity / IgM B cell receptor complex / B cell receptor complex / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / riboflavin biosynthetic process / immunoglobulin complex / B cell activation / B cell proliferation / bioluminescence ...CD22 mediated BCR regulation / riboflavin synthase activity / IgM B cell receptor complex / B cell receptor complex / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / riboflavin biosynthetic process / immunoglobulin complex / B cell activation / B cell proliferation / bioluminescence / immunoglobulin mediated immune response / multivesicular body / B cell differentiation / antigen binding / B cell receptor signaling pathway / response to bacterium / transmembrane signaling receptor activity / adaptive immune response / membrane raft / external side of plasma membrane / extracellular region / identical protein binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) Aliivibrio fischeri (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 8.2 Å | ||||||
Authors | Ying, D. / Xiong, P. / Michael, R. | ||||||
Funding support | 1items
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Citation | Journal: Nature / Year: 2022 Title: Structural principles of B cell antigen receptor assembly. Authors: Ying Dong / Xiong Pi / Frauke Bartels-Burgahn / Deniz Saltukoglu / Zhuoyi Liang / Jianying Yang / Frederick W Alt / Michael Reth / Hao Wu / Abstract: The B cell antigen receptor (BCR) is composed of a membrane-bound class M, D, G, E or A immunoglobulin for antigen recognition and a disulfide-linked Igα (also known as CD79A) and Igβ (also known ...The B cell antigen receptor (BCR) is composed of a membrane-bound class M, D, G, E or A immunoglobulin for antigen recognition and a disulfide-linked Igα (also known as CD79A) and Igβ (also known as CD79B) heterodimer (Igα/β) that functions as the signalling entity through intracellular immunoreceptor tyrosine-based activation motifs (ITAMs). The organizing principle of the BCR remains unknown. Here we report cryo-electron microscopy structures of mouse full-length IgM BCR and its Fab-deleted form. At the ectodomain (ECD), the Igα/β heterodimer mainly uses Igα to associate with Cµ3 and Cµ4 domains of one heavy chain (µHC) while leaving the other heavy chain (µHC') unbound. The transmembrane domain (TMD) helices of µHC and µHC' interact with those of the Igα/β heterodimer to form a tight four-helix bundle. The asymmetry at the TMD prevents the recruitment of two Igα/β heterodimers. Notably, the connecting peptide between the ECD and TMD of µHC intervenes in between those of Igα and Igβ to guide TMD assembly through charge complementarity. Weaker but distinct density for the Igβ ITAM nestles next to the TMD, suggesting potential autoinhibition of ITAM phosphorylation. Interfacial analyses suggest that all BCR classes utilize a general organizational architecture. Our studies provide a structural platform for understanding B cell signalling and designing rational therapies against BCR-mediated diseases. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8ema.cif.gz | 351 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ema.ent.gz | 286.7 KB | Display | PDB format |
PDBx/mmJSON format | 8ema.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8ema_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 8ema_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 8ema_validation.xml.gz | 60.1 KB | Display | |
Data in CIF | 8ema_validation.cif.gz | 89.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/em/8ema ftp://data.pdbj.org/pub/pdb/validation_reports/em/8ema | HTTPS FTP |
-Related structure data
Related structure data | 27848MC 8e4cC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Antibody | Mass: 68133.039 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ighv1-72, Ighm, Igh-6 / Production host: Mus musculus (house mouse) / References: UniProt: P06328, UniProt: P01872-2 #2: Antibody | Mass: 25057.957 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse) / References: UniProt: G0YP42 #3: Protein | | Mass: 42837.230 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Flag-DYKDDDDK Linker: RSIATRS YFP: ...Details: Flag-DYKDDDDK Linker: RSIATRS YFP:MFKGIVEGIGIIEKIDIYTDLDKYAIRFPENMLNGIKKESSIMFNGCFLTVTSVNSNIVWFDIFEKEARKLDTFREYKVGDRVNLGTFPKFGAASGGHILSARISCVASIIEIIENEDYQQMWIQIPENFTEFLIDKDYIAVDGISLTIDTIKNNQFFISLPLKIAQNTNMKWRKKGDKVNVELSNKINANQCW,Flag-DYKDDDDK Linker: RSIATRS YFP:MFKGIVEGIGIIEKIDIYTDLDKYAIRFPENMLNGIKKESSIMFNGCFLTVTSVNSNIVWFDIFEKEARKLDTFREYKVGDRVNLGTFPKFGAASGGHILSARISCVASIIEIIENEDYQQMWIQIPENFTEFLIDKDYIAVDGISLTIDTIKNNQFFISLPLKIAQNTNMKWRKKGDKVNVELSNKINANQCW Source: (gene. exp.) Mus musculus (house mouse), (gene. exp.) Aliivibrio fischeri (bacteria) Gene: Cd79a, Iga, Mb-1, luxY / Production host: Mus musculus (house mouse) / References: UniProt: P11911, UniProt: P21578 #4: Protein | | Mass: 25752.375 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cd79b, Igb / Production host: Mus musculus (house mouse) / References: UniProt: P15530 |
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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: B cell receptor / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Source (natural) | Organism: Mus musculus (house mouse) |
Source (recombinant) | Organism: Mus musculus (house mouse) |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-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: OTHER |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm |
Image recording | Electron dose: 1.6 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
CTF correction | Type: NONE |
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3D reconstruction | Resolution: 8.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 30218 / Symmetry type: POINT |