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- EMDB-72184: Negative Stain Electron Microscopy map of the Measles Virus Fusio... -

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Basic information

Entry
Database: EMDB / ID: EMD-72184
TitleNegative Stain Electron Microscopy map of the Measles Virus Fusion Glycoprotein Ectodomain in Complex with the Neutralizing Antibody 4F09
Map data
Sample
  • Complex: Negative Stain Electron Microscopy map of the Measles Virus Fusion Glycoprotein Ectodomain in Complex with the Neutralizing Antibody 4F09
    • Complex: Measles Virus Fusion Glycoprotein Ectodomain
    • Complex: Antibody 4F09
KeywordsVIRAL PROTEIN / glycoprotein / immune system / measles / high-resolution / ectodomain / fusion / antibody / complex
Biological speciesMeasles morbillivirus / Homo sapiens (human)
Methodsingle particle reconstruction / negative staining / Resolution: 11.0 Å
AuthorsZyla D / Acciani M / Niemeyer G / Saphire EO
Funding support Switzerland, United States, 7 items
OrganizationGrant numberCountry
Swiss National Science FoundationP2EZP3_195680 Switzerland
Swiss National Science FoundationP500PB_210992 Switzerland
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)NS105699 United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)NS091263 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI176833 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1R56AI183536-01A1 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)5R21AI180456-02 United States
CitationJournal: To Be Published
Title: Negative Stain Electron Microscopy map of the Measles Virus Fusion Glycoprotein Ectodomain in Complex with the Neutralizing Antibody 3A12
Authors: Acciani M / Zyla D / Niemeyer G / Saphire EO
History
DepositionAug 15, 2025-
Header (metadata) releaseApr 22, 2026-
Map releaseApr 22, 2026-
UpdateApr 22, 2026-
Current statusApr 22, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_72184.png

Downloads & links

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Map

FileDownload / File: emd_72184.map.gz / Format: CCP4 / Size: 3.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
5.1 Å/pix.
x 100 pix.
= 510. Å		5.1 Å/pix.
x 100 pix.
= 510. Å		5.1 Å/pix.
x 100 pix.
= 510. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 5.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.01
Minimum - Maximum-0.86274886 - 2.9097247
Average (Standard dev.)0.0025402072 (±0.10550164)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions100100100
Spacing100100100
CellA=B=C: 510.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_72184_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_72184_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 : Negative Stain Electron Microscopy map of the Measles Virus Fusio...

EntireName: Negative Stain Electron Microscopy map of the Measles Virus Fusion Glycoprotein Ectodomain in Complex with the Neutralizing Antibody 4F09
Components
  • Complex: Negative Stain Electron Microscopy map of the Measles Virus Fusion Glycoprotein Ectodomain in Complex with the Neutralizing Antibody 4F09
    • Complex: Measles Virus Fusion Glycoprotein Ectodomain
    • Complex: Antibody 4F09

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Supramolecule #1: Negative Stain Electron Microscopy map of the Measles Virus Fusio...

SupramoleculeName: Negative Stain Electron Microscopy map of the Measles Virus Fusion Glycoprotein Ectodomain in Complex with the Neutralizing Antibody 4F09
type: complex / ID: 1 / Parent: 0
Molecular weightTheoretical: 450 KDa

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Supramolecule #2: Measles Virus Fusion Glycoprotein Ectodomain

SupramoleculeName: Measles Virus Fusion Glycoprotein Ectodomain / type: complex / ID: 2 / Parent: 1
Source (natural)Organism: Measles morbillivirus / Strain: Ichinose-B95a

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Supramolecule #3: Antibody 4F09

SupramoleculeName: Antibody 4F09 / type: complex / ID: 3 / Parent: 1
Source (natural)Organism: Homo sapiens (human)

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Experimental details

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Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.02 mg/mL
BufferpH: 8 / Details: HEPES 50 mM, pH 8.0, NaCl 150 mM
StainingType: NEGATIVE / Material: Uranyl Acetate
GridModel: C-flat / Material: COPPER / Support film - Material: GRAPHENE OXIDE / Support film - topology: CONTINUOUS

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Electron microscopy

MicroscopeTFS KRIOS
SoftwareName: SerialEM
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number real images: 216 / Average exposure time: 2.0 sec. / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 2.0 µm / Nominal magnification: 18000
Sample stageSpecimen holder model: SIDE ENTRY, EUCENTRIC / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 226000
CTF correctionSoftware - Name: cryoSPARC (ver. 4.5) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionNumber classes used: 1 / Resolution.type: BY AUTHOR / Resolution: 11.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.5) / Number images used: 226000
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.5)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.5)
Final 3D classificationNumber classes: 3 / Software - Name: cryoSPARC (ver. 4.5)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

8uut

source_name: PDB, initial_model_type: experimental model
source_name: AlphaFold, initial_model_type: in silico model
SoftwareName: UCSF ChimeraX
RefinementSpace: REAL / Protocol: RIGID BODY FIT

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