7YSG

Cryo-EM structure of human FcmR bound to sIgM


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.18 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Immunoglobulin M perception by Fc mu R.

Li, Y.Shen, H.Zhang, R.Ji, C.Wang, Y.Su, C.Xiao, J.

(2023) Nature 615: 907-912

  • DOI: https://doi.org/10.1038/s41586-023-05835-w
  • Primary Citation of Related Structures:  
    7YSG, 7YTC, 7YTD, 7YTE

  • PubMed Abstract: 

    Immunoglobulin M (IgM) is the first antibody to emerge during embryonic development and the humoral immune response 1 . IgM can exist in several distinct forms, including monomeric, membrane-bound IgM within the B cell receptor (BCR) complex, pentameric and hexameric IgM in serum and secretory IgM on the mucosal surface. FcμR, the only IgM-specific receptor in mammals, recognizes different forms of IgM to regulate diverse immune responses 2-5 . However, the underlying molecular mechanisms remain unknown. Here we delineate the structural basis of the FcμR-IgM interaction by crystallography and cryo-electron microscopy. We show that two FcμR molecules interact with a Fcμ-Cμ4 dimer, suggesting that FcμR can bind to membrane-bound IgM with a 2:1 stoichiometry. Further analyses reveal that FcμR-binding sites are accessible in the context of IgM BCR. By contrast, pentameric IgM can recruit four FcμR molecules to bind on the same side and thereby facilitate the formation of an FcμR oligomer. One of these FcμR molecules occupies the binding site of the secretory component. Nevertheless, four FcμR molecules bind to the other side of secretory component-containing secretory IgM, consistent with the function of FcμR in the retrotransport of secretory IgM. These results reveal intricate mechanisms of IgM perception by FcμR.


  • Organizational Affiliation

    State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, P. R. China.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Immunoglobulin heavy constant mu232Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
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PHAROS:  P01871
GTEx:  ENSG00000211899 
Entity Groups  
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UniProt GroupP01871
Glycosylation
Glycosylation Sites: 1Go to GlyGen: P01871-2
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Immunoglobulin J chainI [auth J]136Homo sapiensMutation(s): 0 
Gene Names: JCHAINIGCJIGJ
UniProt & NIH Common Fund Data Resources
Find proteins for P01591 (Homo sapiens)
Explore P01591 
Go to UniProtKB:  P01591
PHAROS:  P01591
GTEx:  ENSG00000132465 
Entity Groups  
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UniProt GroupP01591
Glycosylation
Glycosylation Sites: 1Go to GlyGen: P01591-1
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Secretory componentL [auth P]541Homo sapiensMutation(s): 0 
Gene Names: PIGR
UniProt & NIH Common Fund Data Resources
Find proteins for P01833 (Homo sapiens)
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Go to UniProtKB:  P01833
PHAROS:  P01833
GTEx:  ENSG00000162896 
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UniProt GroupP01833
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Fas apoptotic inhibitory molecule 3M [auth R],
N [auth S],
O [auth U],
P [auth V]
107Homo sapiensMutation(s): 0 
Gene Names: FCMRFAIM3TOSO
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Find proteins for O60667 (Homo sapiens)
Explore O60667 
Go to UniProtKB:  O60667
PHAROS:  O60667
GTEx:  ENSG00000162894 
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UniProt GroupO60667
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 5
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseQ [auth I]2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG (Subject of Investigation/LOI)
Query on NAG

Download Ideal Coordinates CCD File 
AA [auth L]
R [auth A]
S [auth B]
T [auth C]
U [auth D]
AA [auth L],
R [auth A],
S [auth B],
T [auth C],
U [auth D],
V [auth E],
W [auth F],
X [auth G],
Y [auth H],
Z [auth K]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.18 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, China)China--

Revision History  (Full details and data files)

  • Version 1.0: 2023-02-01
    Type: Initial release
  • Version 1.1: 2023-04-12
    Changes: Database references
  • Version 1.2: 2023-05-03
    Changes: Database references
  • Version 1.3: 2024-11-20
    Changes: Data collection, Structure summary