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- EMDB-70025: Rhesus Macaque mAb CHM-16 complexed with SARS-CoV-2 spike protein -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-70025
TitleRhesus Macaque mAb CHM-16 complexed with SARS-CoV-2 spike protein
Map datamain map
Sample
  • Complex: Rhesus Macaque mAb CHM-16 complexed with SARS-CoV-2 spike protein
KeywordsCoronavirus / Fab / spike / monoclonal / negative stain EM / VIRAL PROTEIN
Biological speciesMacaca (macaques)
Methodsingle particle reconstruction / negative staining / Resolution: 25.0 Å
AuthorsLin RN / Ward AB
Funding support United States, 1 items
OrganizationGrant numberCountry
Bill & Melinda Gates FoundationINV-004923 United States
CitationJournal: To Be Published
Title: Immunization with heterologous betacoronavirus spike proteins in nonhuman primates to generate cross-reactive antibodies able to neutralize sarbeco- and merbecoviruses
Authors: Dueker K / Capozzola T / Feng Z / Lin RN / Hurtado J / Bangaru S / Yuan M / Beutler N / Garcia E / He W / Callaghan S / Avillion G / Vo L / Li X / Torres JL / Musharrafieh R / Song G / ...Authors: Dueker K / Capozzola T / Feng Z / Lin RN / Hurtado J / Bangaru S / Yuan M / Beutler N / Garcia E / He W / Callaghan S / Avillion G / Vo L / Li X / Torres JL / Musharrafieh R / Song G / Mishra N / Sharma P / Yong P / Anzanello F / Silva M / Melo M / Makhdoomi M / Westfall-Gomez E / Rinaldi W / Ferguson M / Safonova Y / Crotty S / Irvine DJ / Rogers T / Ward AB / Briney B / Wilson IA / Burton DR / Andrabi R
History
DepositionApr 4, 2025-
Header (metadata) releaseApr 8, 2026-
Map releaseApr 8, 2026-
UpdateApr 8, 2026-
Current statusApr 8, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_70025.png

Downloads & links

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Map

FileDownload / File: emd_70025.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmain map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.98 Å/pix.
x 256 pix.
= 506.88 Å		1.98 Å/pix.
x 256 pix.
= 506.88 Å		1.98 Å/pix.
x 256 pix.
= 506.88 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.98 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.014
Minimum - Maximum-0.028013768 - 0.047713608
Average (Standard dev.)-0.0000066828156 (±0.0030580633)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 506.88 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half map B

Fileemd_70025_half_map_1.map
Annotationhalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map A

Fileemd_70025_half_map_2.map
Annotationhalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Rhesus Macaque mAb CHM-16 complexed with SARS-CoV-2 spike protein

EntireName: Rhesus Macaque mAb CHM-16 complexed with SARS-CoV-2 spike protein
Components
  • Complex: Rhesus Macaque mAb CHM-16 complexed with SARS-CoV-2 spike protein

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Supramolecule #1: Rhesus Macaque mAb CHM-16 complexed with SARS-CoV-2 spike protein

SupramoleculeName: Rhesus Macaque mAb CHM-16 complexed with SARS-CoV-2 spike protein
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Macaca (macaques)

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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

BufferpH: 7.4
StainingType: NEGATIVE / Material: Uranyl formate
GridModel: Homemade / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE

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Electron microscopy

MicroscopeTFS TALOS
Image recordingFilm or detector model: FEI CETA (4k x 4k) / Average electron dose: 25.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 1.0 µm
Sample stageCooling holder cryogen: NITROGEN

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Image processing

CTF correctionType: NONE
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6vxx

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 25.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: RELION / Number images used: 1827
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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