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Open data
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Basic information
Entry | ![]() | |||||||||
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Title | IgM BCR fab truncated form | |||||||||
![]() | IgM BCR_Delta_Fab | |||||||||
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![]() | complex / membrane protein / IMMUNE SYSTEM | |||||||||
Function / homology | ![]() CD22 mediated BCR regulation / riboflavin synthase activity / IgM B cell receptor complex / pentameric IgM immunoglobulin complex / pre-B cell allelic exclusion / B cell receptor complex / Cell surface interactions at the vascular wall / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / positive regulation of B cell activation / B cell affinity maturation ...CD22 mediated BCR regulation / riboflavin synthase activity / IgM B cell receptor complex / pentameric IgM immunoglobulin complex / pre-B cell allelic exclusion / B cell receptor complex / Cell surface interactions at the vascular wall / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / positive regulation of B cell activation / B cell affinity maturation / humoral immune response mediated by circulating immunoglobulin / early endosome to late endosome transport / riboflavin biosynthetic process / regulation of cell morphogenesis / regulation of immunoglobulin production / B cell activation / B cell proliferation / positive regulation of endocytosis / antigen processing and presentation / immunoglobulin mediated immune response / immunoglobulin complex, circulating / immunoglobulin receptor binding / positive regulation of B cell proliferation / multivesicular body / bioluminescence / B cell differentiation / complement activation, classical pathway / antigen binding / B cell receptor signaling pathway / response to bacterium / transmembrane signaling receptor activity / positive regulation of peptidyl-tyrosine phosphorylation / positive regulation of immune response / MAPK cascade / antibacterial humoral response / defense response to Gram-negative bacterium / adaptive immune response / positive regulation of MAPK cascade / membrane raft / external side of plasma membrane / perinuclear region of cytoplasm / cell surface / extracellular space / identical protein binding / membrane / plasma membrane / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.0 Å | |||||||||
![]() | Dong Y / Pi X / Wu H / Reth M | |||||||||
Funding support | 1 items
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![]() | ![]() 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
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 129.4 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 17.3 KB 17.3 KB | Display Display | ![]() |
Images | ![]() | 58.9 KB | ||
Filedesc metadata | ![]() | 6.2 KB | ||
Others | ![]() ![]() | 127.1 MB 127.1 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8e4cMC ![]() 8emaC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | IgM BCR_Delta_Fab | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.83 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: IgM BCR Delta Fab
File | emd_27888_half_map_1.map | ||||||||||||
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Annotation | IgM BCR_Delta_Fab | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: IgM BCR Delta Fab
File | emd_27888_half_map_2.map | ||||||||||||
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Annotation | IgM BCR_Delta_Fab | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : BCR complex
Entire | Name: BCR complex |
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Components |
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-Supramolecule #1: BCR complex
Supramolecule | Name: BCR complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 |
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Source (natural) | Organism: ![]() ![]() |
-Macromolecule #1: Isoform 2 of Immunoglobulin heavy constant mu
Macromolecule | Name: Isoform 2 of Immunoglobulin heavy constant mu / type: protein_or_peptide / ID: 1 Details: B1-8 leader sequence: MGWSCIILFLVATATGVHS Strep Tag: WSHPQFEK Rigid linker: AEAAAKEAAAKEAAAKA Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 45.753785 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MGWSCIILFL VATATGVHSG GWSHPQFEKA EAAAKEAAAK EAAAKAAVAE MNPNVNVFVP PRDGFSGPAP RKSKLICEAT NFTPKPITV SWLKDGKLVE SGFTTDPVTI ENKGSTPQTY KVISTLTISE IDWLNLNVYT CRVDHRGLTF LKNVSSTCAA S PSTDILTF ...String: MGWSCIILFL VATATGVHSG GWSHPQFEKA EAAAKEAAAK EAAAKAAVAE MNPNVNVFVP PRDGFSGPAP RKSKLICEAT NFTPKPITV SWLKDGKLVE SGFTTDPVTI ENKGSTPQTY KVISTLTISE IDWLNLNVYT CRVDHRGLTF LKNVSSTCAA S PSTDILTF TIPPSFADIF LSKSANLTCL VSNLATYETL NISWASQSGE PLETKIKIME SHPNGTFSAK GVASVCVEDW NN RKEFVCT VTHRDLPSPQ KKFISKPNEV HKHPPAVYLL PPAREQLNLR ESATVTCLVK GFSPADISVQ WLQRGQLLPQ EKY VTSAPM PEPGAPGFYF THSILTVTEE EWNSGETYTC VVGHEALPHL VTERTVDKST EGEVNAEEEG FENLWTTAST FIVL FLLSL FYSTTVTLFK VK UniProtKB: Immunoglobulin heavy constant mu |
-Macromolecule #2: B-cell antigen receptor complex-associated protein alpha chain,Ye...
Macromolecule | Name: B-cell antigen receptor complex-associated protein alpha chain,Yellow fluorescent protein type: protein_or_peptide / ID: 2 Details: Flag tag:DYKDDDDK Linker: RSIATRS,Flag tag:DYKDDDDK Linker: RSIATRS YFP: ...Details: Flag tag:DYKDDDDK Linker: RSIATRS,Flag tag:DYKDDDDK Linker: RSIATRS YFP:MFKGIVEGIGIIEKIDIYTDLDKYAIRFPENMLNGIKKESSIMFNGCFLTVTSVNSNIVWFDIFEKEARKLDTFREYKVGDRVNLGTFPKFGAASGGHILSARISCVASIIEIIENEDYQQMWIQIPENFTEFLIDKDYIAVDGISLTIDTIKNNQFFISLPLKIAQNTNMKWRKKGDKVNVELSNKINANQCW,Flag Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 42.83723 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: DYKDDDDKMP GGLEALRALP LLLFLSYACL GPGCQALRVE GGPPSLTVNL GEEARLTCEN NGRNPNITWW FSLQSNITWP PVPLGPGQG TTGQLFFPEV NKNHRGLYWC QVIENNILKR SCGTYLRVRN PVPRPFLDMG EGTKNRIITA EGIILLFCAV V PGTLLLFR ...String: DYKDDDDKMP GGLEALRALP LLLFLSYACL GPGCQALRVE GGPPSLTVNL GEEARLTCEN NGRNPNITWW FSLQSNITWP PVPLGPGQG TTGQLFFPEV NKNHRGLYWC QVIENNILKR SCGTYLRVRN PVPRPFLDMG EGTKNRIITA EGIILLFCAV V PGTLLLFR KRWQNEKFGR SIATRSMFKG IVEGIGIIEK IDIYTDLDKY AIRFPENMLN GIKKESSIMF NGCFLTVTSV NS NIVWFDI FEKEARKLDT FREYKVGDRV NLGTFPKFGA ASGGHILSAR ISCVASIIEI IENEDYQQMW IQIPENFTEF LID KDYIAV DGISLTIDTI KNNQFFISLP LKIAQNTNMK WRKKGDKVNV ELSNKINANQ CW UniProtKB: B-cell antigen receptor complex-associated protein alpha chain, Yellow fluorescent protein |
-Macromolecule #3: B-cell antigen receptor complex-associated protein beta chain
Macromolecule | Name: B-cell antigen receptor complex-associated protein beta chain type: protein_or_peptide / ID: 3 / Details: full length cd79b / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 25.752375 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MATLVLSSMP CHWLLFLLLL FSGEPVPAMT SSDLPLNFQG SPCSQIWQHP RFAAKKRSSM VKFHCYTNHS GALTWFRKRG SQQPQELVS EEGRIVQTQN GSVYTLTIQN IQYEDNGIYF CKQKCDSANH NVTDSCGTEL LVLGFSTLDQ LKRRNTLKDG I ILIQTLLI ...String: MATLVLSSMP CHWLLFLLLL FSGEPVPAMT SSDLPLNFQG SPCSQIWQHP RFAAKKRSSM VKFHCYTNHS GALTWFRKRG SQQPQELVS EEGRIVQTQN GSVYTLTIQN IQYEDNGIYF CKQKCDSANH NVTDSCGTEL LVLGFSTLDQ LKRRNTLKDG I ILIQTLLI ILFIIVPIFL LLDKDDGKAG MEEDHTYEGL NIDQTATYED IVTLRTGEVK WSVGEHPGQE UniProtKB: B-cell antigen receptor complex-associated protein beta chain |
-Macromolecule #4: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / Details: full length cd79b / Number of copies: 5 / Formula: NAG |
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Molecular weight | Theoretical: 221.208 Da |
Chemical component information | ![]() ChemComp-NAG: |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 0.9 mg/mL |
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Buffer | pH: 7.5 |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 1.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Startup model | Type of model: NONE |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 282429 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |