8W5E

Cryo-EM structure of Qb-Ab4


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Competition propels, rather than limits, the success of low-affinity B cells in the germinal center response.

Li, R.Bao, K.Liu, C.Ma, X.Hua, Z.Zhu, P.Hou, B.

(2025) Cell Rep 44: 115334-115334

  • DOI: https://doi.org/10.1016/j.celrep.2025.115334
  • Primary Citation of Related Structures:  
    8W5D, 8W5E, 8W5F, 8W5G, 8W5H, 8W5I, 8W5L, 8W5M, 8W5N, 8W5O, 8W5P, 8W5Q, 8W5R, 8W5T, 8W5U, 8W5V, 8W5W

  • PubMed Abstract: 

    The germinal center (GC) sets an environment where antigen-specific B cells are compelled to continuously increase their affinity to compete for the antigen and obtain Tfh help for survival and propagation. Previous studies indicated that low-affinity B cells are disadvantaged in the presence of high-affinity ones, suggesting that competition may lead to the elimination of low-affinity B cells and their descendants. However, using a multivalent virus-mimicking antigen, our study demonstrates that low-affinity B cells not only successfully participate in GC responses alongside high-affinity B cells but also undergo accelerated affinity maturation under the more stringent competition. Furthermore, our cryo-electron-microscopy-based structural analysis reveals that both low-affinity and high-affinity B cells compete for the same antigenic epitope. Although the applicability of this idealized GC competition to true pathogen-induced responses remains uncertain, this change in perspective on the role of competition in low-affinity B cell evolution provides valuable insights for vaccine development.


  • Organizational Affiliation

    State Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Heavy chain of Ab4A [auth H]124Mus musculusMutation(s): 0 
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Minor capsid protein A1B [auth c],
C
133Escherichia phage QbetaMutation(s): 0 
UniProt
Find proteins for Q8LTE1 (Escherichia virus Qbeta)
Explore Q8LTE1 
Go to UniProtKB:  Q8LTE1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8LTE1
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Light chain of Ab4D [auth L]110Mus musculusMutation(s): 0 
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Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
SEP
Query on SEP
A [auth H]L-PEPTIDE LINKINGC3 H8 N O6 PSER
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.13_2998:

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China81991495
National Natural Science Foundation of China (NSFC)China32241029
Chinese Academy of SciencesChinaXDB29050600
Chinese Academy of SciencesChinaXDB37010100

Revision History  (Full details and data files)

  • Version 1.0: 2025-02-26
    Type: Initial release