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- EMDB-72671: CD4 binding site mouse polyclonal antibodies in complex with BG50... -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-72671
TitleCD4 binding site mouse polyclonal antibodies in complex with BG505 GT1.1 SOSIP following saRNA construct GR14 immunization
Map datamain map
Sample
  • Complex: CD4 binding site and gp41-base mouse polyclonal antibodies in complex with BG505 GT1.1 SOSIP following saRNA construct GR14 immunization
    • Complex: BG505 GT1.1 SOSIP
KeywordsEMPEM / VRC01 / HIV / vaccine design / germline targeting / VIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex
Biological speciesMus musculus (house mouse) / Human immunodeficiency virus 1
Methodsingle particle reconstruction / negative staining / Resolution: 22.0 Å
AuthorsOzorowski G / Gibson G / Ward AB
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)P01 AI110657 United States
CitationJournal: To Be Published
Title: Membrane-associated RNA HIV Immunogen Induces Robust Germinal Center Responses by VRC01 Precursors
Authors: Koo J-H / Sanchez I
History
DepositionSep 11, 2025-
Header (metadata) releaseSep 23, 2026-
Map releaseSep 23, 2026-
UpdateSep 23, 2026-
Current statusSep 23, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_72671.png

Downloads & links

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Map

FileDownload / File: emd_72671.map.gz / Format: CCP4 / Size: 3.4 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.)
3.96 Å/pix.
x 96 pix.
= 380.352 Å		3.96 Å/pix.
x 96 pix.
= 380.352 Å		3.96 Å/pix.
x 96 pix.
= 380.352 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.962 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02
Minimum - Maximum-0.072128125 - 0.1369682
Average (Standard dev.)0.00016604322 (±0.005994838)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions969696
Spacing969696
CellA=B=C: 380.352 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half map B

Fileemd_72671_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_72671_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 : CD4 binding site and gp41-base mouse polyclonal antibodies in com...

EntireName: CD4 binding site and gp41-base mouse polyclonal antibodies in complex with BG505 GT1.1 SOSIP following saRNA construct GR14 immunization
Components
  • Complex: CD4 binding site and gp41-base mouse polyclonal antibodies in complex with BG505 GT1.1 SOSIP following saRNA construct GR14 immunization
    • Complex: BG505 GT1.1 SOSIP

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Supramolecule #1: CD4 binding site and gp41-base mouse polyclonal antibodies in com...

SupramoleculeName: CD4 binding site and gp41-base mouse polyclonal antibodies in complex with BG505 GT1.1 SOSIP following saRNA construct GR14 immunization
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Mus musculus (house mouse)

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Supramolecule #2: BG505 GT1.1 SOSIP

SupramoleculeName: BG505 GT1.1 SOSIP / type: complex / ID: 2 / Parent: 1
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

Concentration0.03 mg/mL
BufferpH: 7.4
StainingType: NEGATIVE / Material: uranyl formate
GridModel: Homemade / Material: COPPER / Mesh: 400 / Support film - Material: PARLODION / Support film - topology: CONTINUOUS

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (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: 2.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 73000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER

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Image processing

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

6v0r


Details: coordinates converted to map using UCSF Chimera molmap and low pass filtered to 40A
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 22.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: RELION (ver. 4.0) / Number images used: 110457
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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