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- EMDB-16150: 8:1 binding of FcMR on IgM pentameric core -

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Basic information

Entry
Database: EMDB / ID: EMD-16150
Title8:1 binding of FcMR on IgM pentameric core
Map data
Sample
  • Complex: human FcMR/IgM-Fc complex
    • Protein or peptide: Immunoglobulin heavy constant mu
    • Protein or peptide: Fas apoptotic inhibitory molecule 3
    • Protein or peptide: Immunoglobulin J chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsIgM Fc receptor / IMMUNE SYSTEM
Function / homology
Function and homology information


high-affinity IgM receptor activity / immunoglobulin transcytosis in epithelial cells / IgM binding / regulation of B cell receptor signaling pathway / polymeric immunoglobulin binding / Fc receptor-mediated immune complex endocytosis / humoral immune response mediated by circulating immunoglobulin / cellular defense response / trans-Golgi network membrane / early endosome membrane ...high-affinity IgM receptor activity / immunoglobulin transcytosis in epithelial cells / IgM binding / regulation of B cell receptor signaling pathway / polymeric immunoglobulin binding / Fc receptor-mediated immune complex endocytosis / humoral immune response mediated by circulating immunoglobulin / cellular defense response / trans-Golgi network membrane / early endosome membrane / lysosomal membrane / negative regulation of apoptotic process / extracellular region / plasma membrane
Similarity search - Function
: / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Immunoglobulin mu Fc receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.63 Å
AuthorsChen Q / Rosenthal P / Tolar P
Funding support United Kingdom, 6 items
OrganizationGrant numberCountry
Cancer Research UKFC001143 United Kingdom
Medical Research Council (MRC, United Kingdom)FC001143 United Kingdom
Wellcome TrustFC001143 United Kingdom
Cancer Research UKFC001185 United Kingdom
Medical Research Council (MRC, United Kingdom)FC001185 United Kingdom
Wellcome TrustFC001185 United Kingdom
CitationJournal: Nat Struct Mol Biol / Year: 2023
Title: Structural basis for Fc receptor recognition of immunoglobulin M.
Authors: Qu Chen / Rajesh P Menon / Laura Masino / Pavel Tolar / Peter B Rosenthal /
Abstract: Immunoglobulin Fc receptors are cell surface transmembrane proteins that bind to the Fc constant region of antibodies and play critical roles in regulating immune responses by activation of immune ...Immunoglobulin Fc receptors are cell surface transmembrane proteins that bind to the Fc constant region of antibodies and play critical roles in regulating immune responses by activation of immune cells, clearance of immune complexes and regulation of antibody production. FcμR is the immunoglobulin M (IgM) antibody isotype-specific Fc receptor involved in the survival and activation of B cells. Here we reveal eight binding sites for the human FcμR immunoglobulin domain on the IgM pentamer by cryogenic electron microscopy. One of the sites overlaps with the binding site for the polymeric immunoglobulin receptor (pIgR), but a different mode of FcμR binding explains its antibody isotype specificity. Variation in FcμR binding sites and their occupancy reflects the asymmetry of the IgM pentameric core and the versatility of FcμR binding. The complex explains engagement with polymeric serum IgM and the monomeric IgM B-cell receptor (BCR).
History
DepositionNov 16, 2022-
Header (metadata) releaseApr 12, 2023-
Map releaseApr 12, 2023-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_16150.png

Downloads & links

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Map

FileDownload / File: emd_16150.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 400 pix.
= 432. Å		1.08 Å/pix.
x 400 pix.
= 432. Å		1.08 Å/pix.
x 400 pix.
= 432. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.08 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.06
Minimum - Maximum-0.278489 - 0.84429437
Average (Standard dev.)0.0008920603 (±0.012633708)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 432.00003 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_16150_msk_1.map
Projections & Slices
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Half map: #2

Fileemd_16150_half_map_1.map
Projections & Slices
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Half map: #1

Fileemd_16150_half_map_2.map
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Sample components

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Entire : human FcMR/IgM-Fc complex

EntireName: human FcMR/IgM-Fc complex
Components
  • Complex: human FcMR/IgM-Fc complex
    • Protein or peptide: Immunoglobulin heavy constant mu
    • Protein or peptide: Fas apoptotic inhibitory molecule 3
    • Protein or peptide: Immunoglobulin J chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: human FcMR/IgM-Fc complex

SupramoleculeName: human FcMR/IgM-Fc complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Immunoglobulin heavy constant mu

MacromoleculeName: Immunoglobulin heavy constant mu / type: protein_or_peptide / ID: 1 / Number of copies: 10 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 38.343086 KDa
SequenceString: IAELPPKVSV FVPPRDGFFG NPRKSKLICQ ATGFSPRQIQ VSWLREGKQV GSGVTTDQVQ AEAKESGPTT YKVTSTLTIK ESDWLGQSM FTCRVDHRGL TFQQNASSMC VPDQDTAIRV FAIPPSFASI FLTKSTKLTC LVTDLTTYDS VTISWTRQNG E AVKTHTNI ...String:
IAELPPKVSV FVPPRDGFFG NPRKSKLICQ ATGFSPRQIQ VSWLREGKQV GSGVTTDQVQ AEAKESGPTT YKVTSTLTIK ESDWLGQSM FTCRVDHRGL TFQQNASSMC VPDQDTAIRV FAIPPSFASI FLTKSTKLTC LVTDLTTYDS VTISWTRQNG E AVKTHTNI SESHPNATFS AVGEASICED DWNSGERFTC TVTHTDLPSP LKQTISRPKG VALHRPDVYL LPPAREQLNL RE SATITCL VTGFSPADVF VQWMQRGQPL SPEKYVTSAP MPEPQAPGRY FAHSILTVSE EEWNTGETYT CVVAHEALPN RVT ERTVDK STGKPTLYNV SLVMSDTAGT CY

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Macromolecule #2: Fas apoptotic inhibitory molecule 3

MacromoleculeName: Fas apoptotic inhibitory molecule 3 / type: protein_or_peptide / ID: 2 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 26.020617 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: RILPEVKVEG ELGGSVTIKC PLPEMHVRIY LCREMAGSGT CGTVVSTTNF IKAEYKGRVT LKQYPRKNLF LVEVTQLTES DSGVYACGA GMNTDRGKTQ KVTLNVHSEY EPSWEEQPMP ETPKWFHLPY LFQMPAYASS SKFVTRVTTP AQRGKVPPVH H SSPTTQIT ...String:
RILPEVKVEG ELGGSVTIKC PLPEMHVRIY LCREMAGSGT CGTVVSTTNF IKAEYKGRVT LKQYPRKNLF LVEVTQLTES DSGVYACGA GMNTDRGKTQ KVTLNVHSEY EPSWEEQPMP ETPKWFHLPY LFQMPAYASS SKFVTRVTTP AQRGKVPPVH H SSPTTQIT HRPRVSRASS VAGDKPRTFL PSTTASKISA LEGLLKPQTP SYNHHTRLHR QRALDYGSQS GREGQG

UniProtKB: Immunoglobulin mu Fc receptor

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Macromolecule #3: Immunoglobulin J chain

MacromoleculeName: Immunoglobulin J chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 18.120586 KDa
SequenceString:
MKNHLLFWGV LAVFIKAVHV KAQEDERIVL VDNKCKCARI TSRIIRSSED PNEDIVERNI RIIVPLNNRE NISDPTSPLR TRFVYHLSD LCKKCDPTEV ELDNQIVTAT QSNICDEDSA TETCYTYDRN KCYTAVVPLV YGGETKMVET ALTPDACYPD

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Macromolecule #5: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 5 / Number of copies: 8 / 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

Concentration0.1 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Average electron dose: 50.6 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Calibrated defocus max: 4.0 µm / Calibrated defocus min: 1.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.2 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6kxs

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.63 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 516875
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL
Output model

PDB-8bpe:
8:1 binding of FcMR on IgM pentameric core

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