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- PDB-8w5n: Cryo-EM structure of Qb-Ab21 -

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Basic information

Entry
Database: PDB / ID: 8w5n
TitleCryo-EM structure of Qb-Ab21
Components
  • Heavy chain of Ab21
  • Light chain of Ab21
  • Minor capsid protein A1
KeywordsIMMUNE SYSTEM / Qb / Antibody / cryo-EM
Function / homologyRead-through domain / Read-through domain / Levivirus coat protein / Levivirus coat protein / Bacteriophage RNA-type, capsid / viral capsid / structural molecule activity / Minor capsid protein A1
Function and homology information
Biological speciesEscherichia phage Qbeta (virus)
Mus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsBao, K.Y. / Li, R.H. / Hua, Z.L. / Hou, B.D. / Zhu, P.
Funding support China, 4items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)81991495 China
National Natural Science Foundation of China (NSFC)32241029 China
Chinese Academy of SciencesXDB29050600 China
Chinese Academy of SciencesXDB37010100 China
CitationJournal: Cell Rep / Year: 2025
Title: Competition propels, rather than limits, the success of low-affinity B cells in the germinal center response.
Authors: Runhan Li / Keyan Bao / Can Liu / Xuejing Ma / Zhaolin Hua / Ping Zhu / Baidong Hou /
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 ...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.
History
DepositionAug 27, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 26, 2025Provider: repository / Type: Initial release
Revision 1.0Feb 26, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Feb 26, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 26, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 26, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Feb 26, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Minor capsid protein A1
B: Minor capsid protein A1
C: Minor capsid protein A1
H: Heavy chain of Ab21
L: Light chain of Ab21


Theoretical massNumber of molelcules
Total (without water)68,9405
Polymers68,9405
Non-polymers00
Water00
1
A: Minor capsid protein A1
B: Minor capsid protein A1
C: Minor capsid protein A1
H: Heavy chain of Ab21
L: Light chain of Ab21
x 60


Theoretical massNumber of molelcules
Total (without water)4,136,412300
Polymers4,136,412300
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
2


  • Idetical with deposited unit
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Minor capsid protein A1
B: Minor capsid protein A1
C: Minor capsid protein A1
H: Heavy chain of Ab21
L: Light chain of Ab21
x 5


  • icosahedral pentamer
  • 345 kDa, 25 polymers
Theoretical massNumber of molelcules
Total (without water)344,70125
Polymers344,70125
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: Minor capsid protein A1
B: Minor capsid protein A1
C: Minor capsid protein A1
H: Heavy chain of Ab21
L: Light chain of Ab21
x 6


  • icosahedral 23 hexamer
  • 414 kDa, 30 polymers
Theoretical massNumber of molelcules
Total (without water)413,64130
Polymers413,64130
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
5


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))

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Components

#1: Protein Minor capsid protein A1 / Qb coat protein


Mass: 14268.071 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia phage Qbeta (virus) / Production host: Escherichia coli (E. coli) / References: UniProt: Q8LTE1
#2: Antibody Heavy chain of Ab21


Mass: 13729.213 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#3: Antibody Light chain of Ab21


Mass: 12406.779 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Complex of Qb-Ab21 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Mus (mice)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1600 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.13_2998: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 12102 / Symmetry type: POINT

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