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- EMDB-37304: Cryo-EM structure of QbN10F-Ab40 -

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Basic information

Entry
Database: EMDB / ID: EMD-37304
TitleCryo-EM structure of QbN10F-Ab40
Map data
Sample
  • Complex: Complex of QbN10F-Ab40
    • Protein or peptide: Light chain of Ab40
    • Protein or peptide: Heavy chain of Ab40
    • Protein or peptide: Minor capsid protein A1
KeywordsQb / Antibody / cryo-EM / IMMUNE SYSTEM
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 speciesMus (mice) / Mus musculus (house mouse) / Escherichia phage Qbeta (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsBao KY / Li RH / Hou BD / Zhu P
Funding support China, 4 items
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, 2023-
Header (metadata) releaseFeb 26, 2025-
Map releaseFeb 26, 2025-
UpdateFeb 26, 2025-
Current statusFeb 26, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_37304.png

Downloads & links

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Map

FileDownload / File: emd_37304.map.gz / Format: CCP4 / Size: 22.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.32 Å/pix.
x 180 pix.
= 237.6 Å		1.32 Å/pix.
x 180 pix.
= 237.6 Å		1.32 Å/pix.
x 180 pix.
= 237.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.32 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.4
Minimum - Maximum-0.8851646 - 1.5671102
Average (Standard dev.)0.010131491 (±0.08713434)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions180180180
Spacing180180180
CellA=B=C: 237.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_37304_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_37304_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Complex of QbN10F-Ab40

EntireName: Complex of QbN10F-Ab40
Components
  • Complex: Complex of QbN10F-Ab40
    • Protein or peptide: Light chain of Ab40
    • Protein or peptide: Heavy chain of Ab40
    • Protein or peptide: Minor capsid protein A1

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Supramolecule #1: Complex of QbN10F-Ab40

SupramoleculeName: Complex of QbN10F-Ab40 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Mus (mice)

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Macromolecule #1: Light chain of Ab40

MacromoleculeName: Light chain of Ab40 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 12.671184 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
VHSDIVMSQS PSSLAVSIGE KVTLTCKSSQ SLLFSSNQKN YLAWYQQNPG QSPKLLIYWA STRESGVPDR FTGSGSGTDF TLTISSVKA EDLAIYYCQQ YFRYPAFGGG TKLEIK

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Macromolecule #2: Heavy chain of Ab40

MacromoleculeName: Heavy chain of Ab40 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 13.22445 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
VHSEVQLQQS GPELVKSGTS VKLSCKASGY SFTDHSLHWV KQSHGESLEW IGYFSPNNGG TIYNQKFMGK ATLTVDRSSS TAYMDLHNL TSADSAVYFC STGWDYGPFD SWGQGTTLTV SS

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Macromolecule #3: Minor capsid protein A1

MacromoleculeName: Minor capsid protein A1 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage Qbeta (virus)
Molecular weightTheoretical: 14.301144 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MAKLETVTLG FIGKDGKQTL VLNPRGVNPT NGVASLSQAG AVPALEKRVT VSVSQPSRNR KNYKVQVKIQ NPTACTANGS CDPSVTRQA YADVTFSFTQ YSTDEERAFV RTELAALLAS PLLIDAIDQL NPAY

UniProtKB: Minor capsid protein A1

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.6 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 371069
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: RANDOM ASSIGNMENT

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