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- EMDB-27888: IgM BCR fab truncated form -

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Basic information

Entry
Database: EMDB / ID: EMD-27888
TitleIgM BCR fab truncated form
Map dataIgM BCR_Delta_Fab
Sample
  • Complex: BCR complex
    • Protein or peptide: Isoform 2 of Immunoglobulin heavy constant mu
    • Protein or peptide: B-cell antigen receptor complex-associated protein alpha chain,Yellow fluorescent protein
    • Protein or peptide: B-cell antigen receptor complex-associated protein beta chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Keywordscomplex / membrane protein / IMMUNE SYSTEM
Function / homology
Function and homology information


CD22 mediated BCR regulation / riboflavin synthase activity / IgM B cell receptor complex / pentameric IgM immunoglobulin complex / B cell receptor complex / Cell surface interactions at the vascular wall / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / pre-B cell allelic exclusion / 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 / B cell receptor complex / Cell surface interactions at the vascular wall / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / pre-B cell allelic exclusion / 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 / immunoglobulin complex, circulating / immunoglobulin receptor binding / B cell proliferation / B cell activation / antigen processing and presentation / positive regulation of endocytosis / immunoglobulin mediated immune response / complement activation, classical pathway / positive regulation of B cell proliferation / antigen binding / multivesicular body / B cell differentiation / bioluminescence / response to bacterium / B cell receptor signaling pathway / positive regulation of peptidyl-tyrosine phosphorylation / positive regulation of immune response / MAPK cascade / transmembrane signaling receptor activity / 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
Lumazine-binding protein / Lumazine-binding domain / Lumazine binding domain / Riboflavin synthase alpha chain lumazine-binding repeat profile. / B-cell antigen receptor complex-associated protein alpha/beta chain / Immunoreceptor tyrosine-based activation motif / Phosphorylated immunoreceptor signalling ITAM / ITAM motif mammalian type profile. / Immunoreceptor tyrosine-based activation motif / Immunoglobulin ...Lumazine-binding protein / Lumazine-binding domain / Lumazine binding domain / Riboflavin synthase alpha chain lumazine-binding repeat profile. / B-cell antigen receptor complex-associated protein alpha/beta chain / Immunoreceptor tyrosine-based activation motif / Phosphorylated immunoreceptor signalling ITAM / ITAM motif mammalian type profile. / Immunoreceptor tyrosine-based activation motif / Immunoglobulin / Immunoglobulin domain / ATP synthase subunit alpha, N-terminal domain-like superfamily / : / Riboflavin synthase-like beta-barrel / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Immunoglobulin heavy constant mu / B-cell antigen receptor complex-associated protein alpha chain / B-cell antigen receptor complex-associated protein beta chain / Yellow fluorescent protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.0 Å
AuthorsDong Y / Pi X / Wu H / Reth M
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: 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
DepositionAug 18, 2022-
Header (metadata) releaseNov 16, 2022-
Map releaseNov 16, 2022-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_27888.png

Downloads & links

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Map

FileDownload / File: emd_27888.map.gz / Format: CCP4 / Size: 137.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationIgM BCR_Delta_Fab
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 330 pix.
= 273.9 Å		0.83 Å/pix.
x 330 pix.
= 273.9 Å		0.83 Å/pix.
x 330 pix.
= 273.9 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.18
Minimum - Maximum-3.2019117 - 4.8990765
Average (Standard dev.)0.0010471328 (±0.040835362)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions330330330
Spacing330330330
CellA=B=C: 273.9 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: IgM BCR Delta Fab

Fileemd_27888_half_map_1.map
AnnotationIgM BCR_Delta_Fab
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: IgM BCR Delta Fab

Fileemd_27888_half_map_2.map
AnnotationIgM BCR_Delta_Fab
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : BCR complex

EntireName: BCR complex
Components
  • Complex: BCR complex
    • Protein or peptide: Isoform 2 of Immunoglobulin heavy constant mu
    • Protein or peptide: B-cell antigen receptor complex-associated protein alpha chain,Yellow fluorescent protein
    • Protein or peptide: B-cell antigen receptor complex-associated protein beta chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: BCR complex

SupramoleculeName: BCR complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Mus musculus (house mouse)

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Macromolecule #1: Isoform 2 of Immunoglobulin heavy constant mu

MacromoleculeName: 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
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 45.753785 KDa
Recombinant expressionOrganism: Mus musculus (house mouse)
SequenceString: 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

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Macromolecule #2: B-cell antigen receptor complex-associated protein alpha chain,Ye...

MacromoleculeName: 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
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 42.83723 KDa
Recombinant expressionOrganism: Mus musculus (house mouse)
SequenceString: 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

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Macromolecule #3: B-cell antigen receptor complex-associated protein beta chain

MacromoleculeName: 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
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 25.752375 KDa
Recombinant expressionOrganism: Mus musculus (house mouse)
SequenceString: 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

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Macromolecule #4: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / Details: full length cd79b / Number of copies: 5 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.9 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 1.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination 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 modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 282429
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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