7XQ8

Structure of human B-cell antigen receptor of the IgM isotype


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Cryo-EM structure of the human IgM B cell receptor.

Su, Q.Chen, M.Shi, Y.Zhang, X.Huang, G.Huang, B.Liu, D.Liu, Z.Shi, Y.

(2022) Science 377: 875-880

  • DOI: https://doi.org/10.1126/science.abo3923
  • Primary Citation of Related Structures:  
    7XQ8

  • PubMed Abstract: 

    The B cell receptor (BCR) initiates immune responses through antigen recognition. We report a 3.3-angstrom cryo-electron microscopy structure of human immunoglobulin M (IgM)-BCR in the resting state. IgM-BCR comprises two heavy chains, two light chains, and the Igα/Igβ heterodimer. The ectodomains of the heavy chains closely stack against those of Igα/Igβ, with one heavy chain locked between Igα and Igβ in the juxtamembrane region. Extracellular interactions may determine isotype specificity of the BCR. The transmembrane helices of IgM-BCR form a four-helix bundle that appears to be conserved among all BCR isotypes. This structure contains 14 glycosylation sites on the IgM-BCR ectodomains and reveals three potential surface binding sites. Our work reveals the organizational principles of the BCR and may facilitate the design of antibody-based therapeutics.


  • Organizational Affiliation

    Research Center for Industries of the Future, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Institute of Biology, Westlake Institute for Advanced Study, Xihu District, Hangzhou 310024, Zhejiang Province, China.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Chimera of Heavy chain of VRC01 antibody Fab and Isoform 2 of Immunoglobulin heavy constant muA [auth C],
C [auth v]
614Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P01871 (Homo sapiens)
Explore P01871 
Go to UniProtKB:  P01871
PHAROS:  P01871
GTEx:  ENSG00000211899 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01871
Glycosylation
Glycosylation Sites: 3Go to GlyGen: P01871-2
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Light chain of Fab fragments of the VRC01 antibody,Immunoglobulin kappa constantB [auth L],
D [auth R]
250Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P01834 (Homo sapiens)
Explore P01834 
Go to UniProtKB:  P01834
PHAROS:  P01834
Entity Groups  
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UniProt GroupP01834
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
B-cell antigen receptor complex-associated protein alpha chainE [auth A]257Homo sapiensMutation(s): 0 
Gene Names: CD79A
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P11912 (Homo sapiens)
Explore P11912 
Go to UniProtKB:  P11912
PHAROS:  P11912
GTEx:  ENSG00000105369 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP11912
Glycosylation
Glycosylation Sites: 6Go to GlyGen: P11912-1
Sequence Annotations
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
B-cell antigen receptor complex-associated protein beta chainF [auth B]260Homo sapiensMutation(s): 0 
Gene Names: CD79B
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P40259 (Homo sapiens)
Explore P40259 
Go to UniProtKB:  P40259
PHAROS:  P40259
GTEx:  ENSG00000007312 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP40259
Glycosylation
Glycosylation Sites: 2Go to GlyGen: P40259-1
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
G [auth C]
H [auth C]
I [auth C]
J [auth v]
K [auth v]
G [auth C],
H [auth C],
I [auth C],
J [auth v],
K [auth v],
L [auth v],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
Q [auth A],
R [auth A],
S [auth B],
T [auth B]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China31930059
National Natural Science Foundation of China (NSFC)China81970633
National Natural Science Foundation of China (NSFC)ChinaU1904146
National Natural Science Foundation of China (NSFC)China81920108015

Revision History  (Full details and data files)

  • Version 1.0: 2022-08-17
    Type: Initial release
  • Version 1.1: 2022-08-31
    Changes: Database references
  • Version 1.2: 2024-10-30
    Changes: Data collection, Structure summary