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- EMDB-53342: Low resolution cryo-EM map of activin A bound to B52 Fabs -

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Basic information

Entry
Database: EMDB / ID: EMD-53342
TitleLow resolution cryo-EM map of activin A bound to B52 Fabs
Map dataLow-resolution map of complex containing two B52 Fabs bound to dimeric growth factor activin A, 2:1 Fab:activin A binding stoichiometry.
Sample
  • Complex: Ternary complex of two B52 Fabs bound to dimeric growth factor activin A.
KeywordsComplex / Fab / Activin A / CYTOKINE
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.43 Å
AuthorsPyeatt GL / Hyvonen M / Maia de Oliveira T / Jin Y / Miller D / Hunt J / Hill CS
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Low resolution cryo-EM map of activin A bound to B52 Fabs
Authors: Pyeatt GL / Hyvonen M / Maia de Oliveira T / Jin Y / Miller D / Hunt J / Hill CS
History
DepositionApr 5, 2025-
Header (metadata) releaseApr 15, 2026-
Map releaseApr 15, 2026-
UpdateApr 15, 2026-
Current statusApr 15, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53342.png

Downloads & links

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Map

FileDownload / File: emd_53342.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationLow-resolution map of complex containing two B52 Fabs bound to dimeric growth factor activin A, 2:1 Fab:activin A binding stoichiometry.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.91 Å/pix.
x 240 pix.
= 458.4 Å		1.91 Å/pix.
x 240 pix.
= 458.4 Å		1.91 Å/pix.
x 240 pix.
= 458.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.91 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.12
Minimum - Maximum-0.31050158 - 0.37979904
Average (Standard dev.)-0.0001366675 (±0.010916348)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 458.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_53342_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_53342_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 : Ternary complex of two B52 Fabs bound to dimeric growth factor ac...

EntireName: Ternary complex of two B52 Fabs bound to dimeric growth factor activin A.
Components
  • Complex: Ternary complex of two B52 Fabs bound to dimeric growth factor activin A.

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Supramolecule #1: Ternary complex of two B52 Fabs bound to dimeric growth factor ac...

SupramoleculeName: Ternary complex of two B52 Fabs bound to dimeric growth factor activin A.
type: complex / ID: 1 / Parent: 0
Details: Fab fragments and activin A generated by insoluble expression in E. coli and protein refolding.
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 146 KDa

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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

Concentration0.21 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
10.0 mMC8H18N2O4SHEPES
200.0 mMNaClsodium chloride
0.5 mM(HO2CCH2)2NCH2CH2N(CH2CO2H)2EDTA

Details: 10 mM HEPES, 200 mM NaCl, 0.5 mM EDTA
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK I
DetailsThe sample was monodisperse and homogenous.

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Number grids imaged: 1 / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 209267
CTF correctionSoftware - Name: cryoSPARC (ver. v4.6.2) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionAlgorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 5.43 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v4.6.2) / Number images used: 329495
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. v4.6.2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. v4.6.2)
FSC plot (resolution estimation)

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