8W5F | pdb_00008w5f

Cryo-EM structure of Qb-Ab6


Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report

Validation slider image for 8W5F

This is version 1.1 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 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.

Macromolecule Content 

  • Total Structure Weight: 54.63 kDa 
  • Atom Count: 3,700 
  • Modeled Residue Count: 485 
  • Deposited Residue Count: 502 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Light chain of Ab6A [auth L]110Mus musculusMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Heavy chain of Ab6B [auth H]126Mus musculusMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Minor capsid protein A1C [auth c],
D [auth C]
133Escherichia phage QbetaMutation(s): 0 
UniProt
Find proteins for P03615 (Escherichia virus Qbeta)
Explore P03615 
Go to UniProtKB:  P03615
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03615
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



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
  • Version 1.1: 2025-06-25
    Changes: Data collection