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- PDB-8w5g: Cryo-EM structure of Qb-Ab7 -

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Basic information

Entry
Database: PDB / ID: 8w5g
TitleCryo-EM structure of Qb-Ab7
Components
  • Heavy chain of Ab7
  • Light chain of Ab7
  • 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: 4 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 26, 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
L: Light chain of Ab7
H: Heavy chain of Ab7
C: Minor capsid protein A1


Theoretical massNumber of molelcules
Total (without water)63,5675
Polymers63,5675
Non-polymers00
Water00
1
A: Minor capsid protein A1
B: Minor capsid protein A1
L: Light chain of Ab7
H: Heavy chain of Ab7
C: Minor capsid protein A1
x 60


Theoretical massNumber of molelcules
Total (without water)3,814,015300
Polymers3,814,015300
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
L: Light chain of Ab7
H: Heavy chain of Ab7
C: Minor capsid protein A1
x 5


  • icosahedral pentamer
  • 318 kDa, 25 polymers
Theoretical massNumber of molelcules
Total (without water)317,83525
Polymers317,83525
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: Minor capsid protein A1
B: Minor capsid protein A1
L: Light chain of Ab7
H: Heavy chain of Ab7
C: Minor capsid protein A1
x 6


  • icosahedral 23 hexamer
  • 381 kDa, 30 polymers
Theoretical massNumber of molelcules
Total (without water)381,40230
Polymers381,40230
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 / A1 read-through protein


Mass: 14136.874 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 Light chain of Ab7


Mass: 10956.034 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 Heavy chain of Ab7


Mass: 10200.267 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-Ab7 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Mus musculus (house mouse)
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: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 1300 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.19.2_4158: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 15049 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0034362
ELECTRON MICROSCOPYf_angle_d0.585925
ELECTRON MICROSCOPYf_dihedral_angle_d4.968610
ELECTRON MICROSCOPYf_chiral_restr0.044694
ELECTRON MICROSCOPYf_plane_restr0.005771

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