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- EMDB-44670: HIV Env BG505.SOSIP N332-GT5 protein complexed by mEM with polycl... -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-44670
TitleHIV Env BG505.SOSIP N332-GT5 protein complexed by mEM with polyclonal Fab representative of Group 2
Map dataPolyclonal Antibody Epitope: V1/V3
Sample
  • Complex: HIV Env N332-GT5 in complex with polyclonal antibodies from mouse sera using mEM
KeywordsHIV / Envelope / N332-GT5 / polyclonal antibody / complex / microfluidics / VIRAL PROTEIN
Biological speciesHuman immunodeficiency virus 1
Methodsingle particle reconstruction / negative staining / Resolution: 20.0 Å
AuthorsSewall LM / Ward AB / Torrents de la Pena A
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI136621 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)UM1 AI144462 United States
Bill & Melinda Gates FoundationINV-002916 United States
CitationJournal: Nat Biomed Eng / Year: 2025
Title: Rapid and High-Throughput Imaging of Immune Complexes Using Microfluidics and Single Particle Electron Microscopy
Authors: Sewall LM / de Paiva Froes Rocha R / Gibson G / Louie M / Xie Z / Bangaru S / Tran AS / Ozorowski G / Mohanty S / Beutler N / Burton DR / Shaw AC / Batista FD / Chocarro Ruiz B / Torrents de la Pena A / Ward AB
History
DepositionApr 30, 2024-
Header (metadata) releaseApr 23, 2025-
Map releaseApr 23, 2025-
UpdateApr 23, 2025-
Current statusApr 23, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_44670.png

Downloads & links

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Map

FileDownload / File: emd_44670.map.gz / Format: CCP4 / Size: 3.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPolyclonal Antibody Epitope: V1/V3
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.87 Å/pix.
x 96 pix.
= 179.52 Å		1.87 Å/pix.
x 96 pix.
= 179.52 Å		1.87 Å/pix.
x 96 pix.
= 179.52 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.87 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.01
Minimum - Maximum-0.04139742 - 0.08385091
Average (Standard dev.)0.00011150106 (±0.0039891917)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions969696
Spacing969696
CellA=B=C: 179.52 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Polyclonal Antibody Epitope: Base

Fileemd_44670_additional_1.map
AnnotationPolyclonal Antibody Epitope: Base
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map 1 Polyclonal Antibody Epitope: V1/V3

Fileemd_44670_half_map_1.map
AnnotationHalf Map 1 Polyclonal Antibody Epitope: V1/V3
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map 2 Polyclonal Antibody Epitope: V1/V3

Fileemd_44670_half_map_2.map
AnnotationHalf Map 2 Polyclonal Antibody Epitope: V1/V3
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : HIV Env N332-GT5 in complex with polyclonal antibodies from mouse...

EntireName: HIV Env N332-GT5 in complex with polyclonal antibodies from mouse sera using mEM
Components
  • Complex: HIV Env N332-GT5 in complex with polyclonal antibodies from mouse sera using mEM

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Supramolecule #1: HIV Env N332-GT5 in complex with polyclonal antibodies from mouse...

SupramoleculeName: HIV Env N332-GT5 in complex with polyclonal antibodies from mouse sera using mEM
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Human immunodeficiency virus 1

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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 / Details: 10 mM Tris, 150 mM NaCl
StainingType: NEGATIVE / Material: Uranyl Formate

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Average electron dose: 6.6 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 73000
Sample stageSpecimen holder model: OTHER / Cooling holder cryogen: NITROGEN

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6ohw

Final reconstructionResolution.type: BY AUTHOR / Resolution: 20.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 12000
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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