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- EMDB-77690: Antibody 44715-B.01 bound to HIV Env 25710 SOSIP trimer -

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Basic information

Entry
Database: EMDB / ID: EMD-77690
TitleAntibody 44715-B.01 bound to HIV Env 25710 SOSIP trimer
Map dataNegative stain electron microscopy reconstruction of antibody 44715-B.01 bound to HIV Env 25710 SOSIP trimer
Sample
  • Complex: Complex of antibody 44715-B.01 bound to HIV Env 25710 SOSIP trimer
    • Complex: Antibody 44715-B.01
    • Complex: HIV Env 25710 SOSIP trimer
KeywordsRhesus antibody HIV Env / IMMUNE SYSTEM
Biological speciesMacaca mulatta (Rhesus monkey) / Homo sapiens (human)
Methodsingle particle reconstruction / negative staining / Resolution: 13.3 Å
AuthorsEdwards RJ / Hogarty MP
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)P01-AI131251 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01-AI197997 United States
CitationJournal: To Be Published
Title: Shortening variable region 1 of the HIV envelope accelerates V3-glycan bNAb induction in SHIV-infected rhesus macaques
Authors: Hogarty MP / Li H / Zhao C / Martella CL / Skelly AN / Habib R / Connell AJ / Bibollet-Ruche F / Liu W / Carey JW / Ayyanathan K / Ding W / Lora J / Park Y / Lewis E / Rando J / Chohan N / ...Authors: Hogarty MP / Li H / Zhao C / Martella CL / Skelly AN / Habib R / Connell AJ / Bibollet-Ruche F / Liu W / Carey JW / Ayyanathan K / Ding W / Lora J / Park Y / Lewis E / Rando J / Chohan N / Singh A / Murphe A / Mansouri K / Spence TN / Wiehe KJ / Williams WB / Saunders KO / Wagh K / Seaman MS / Edwards RJ / Haynes BF / Hahn BH / Shaw GM
History
DepositionJun 19, 2026-
Header (metadata) releaseJul 1, 2026-
Map releaseJul 1, 2026-
UpdateJul 1, 2026-
Current statusJul 1, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_77690.png

Downloads & links

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Map

FileDownload / File: emd_77690.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNegative stain electron microscopy reconstruction of antibody 44715-B.01 bound to HIV Env 25710 SOSIP trimer
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.08 Å/pix.
x 160 pix.
= 332.8 Å		2.08 Å/pix.
x 160 pix.
= 332.8 Å		2.08 Å/pix.
x 160 pix.
= 332.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.08 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0267
Minimum - Maximum-0.04438992 - 0.07433182
Average (Standard dev.)0.00048439688 (±0.005393898)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions160160160
Spacing160160160
CellA=B=C: 332.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Unsharpened negative stain electron microscopy reconstruction of antibody...

Fileemd_77690_additional_1.map
AnnotationUnsharpened negative stain electron microscopy reconstruction of antibody 44715-B.01 bound to HIV Env 25710 SOSIP trimer
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map 2 of negative stain electron microscopy reconstruction...

Fileemd_77690_half_map_1.map
AnnotationHalf-map 2 of negative stain electron microscopy reconstruction of antibody 44715-B.01 bound to HIV Env 25710 SOSIP trimer
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map 1 of negative stain electron microscopy reconstruction...

Fileemd_77690_half_map_2.map
AnnotationHalf-map 1 of negative stain electron microscopy reconstruction of antibody 44715-B.01 bound to HIV Env 25710 SOSIP trimer
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Complex of antibody 44715-B.01 bound to HIV Env 25710 SOSIP trimer

EntireName: Complex of antibody 44715-B.01 bound to HIV Env 25710 SOSIP trimer
Components
  • Complex: Complex of antibody 44715-B.01 bound to HIV Env 25710 SOSIP trimer
    • Complex: Antibody 44715-B.01
    • Complex: HIV Env 25710 SOSIP trimer

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Supramolecule #1: Complex of antibody 44715-B.01 bound to HIV Env 25710 SOSIP trimer

SupramoleculeName: Complex of antibody 44715-B.01 bound to HIV Env 25710 SOSIP trimer
type: complex / ID: 1 / Parent: 0
Molecular weightTheoretical: 480 KDa

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Supramolecule #2: Antibody 44715-B.01

SupramoleculeName: Antibody 44715-B.01 / type: complex / ID: 2 / Parent: 1
Source (natural)Organism: Macaca mulatta (Rhesus monkey)

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Supramolecule #3: HIV Env 25710 SOSIP trimer

SupramoleculeName: HIV Env 25710 SOSIP trimer / 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

Concentration0.1 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
150.0 mMNa2SO4sodium sulfate
2.5 mMNaClsodium chloride
2.8 mMNaN3sodium azide
20.0 mMHEPESHEPES buffer
StainingType: NEGATIVE / Material: Uranyl Formate
Details: Five mircoliters of sample was applied to a glow-discharged carbon film-covered EM grid, blotted, and stained with 2 g/dL uranyl formate for 1 minute, then blotted and air dried.
GridModel: EMS Formvar Carbon / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 0.4 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec.
DetailsComplex was formed by mixing full-length IgG with Env SOSIP trimer at a 1.5:1 ratio (IgG:Env), at a nominal Env concentration of 0.4 mg/ml, for 1 hour at room temperature. A portion of the was then diluted 1:1 with buffer containing 16 mM glutaraldehyde and fixed for 5 minutes, then sufficient 1 M tris stock was added for a final concentration of 80 mM Tris to quench excess glutaraldehyde. Quenched sample was then diluted 1:1 with buffer and used for negtative staining.

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Electron microscopy

MicroscopeFEI/PHILIPS EM420
Image recordingFilm or detector model: OTHER / Digitization - Dimensions - Width: 8736 pixel / Digitization - Dimensions - Height: 8740 pixel / Number grids imaged: 1 / Number real images: 102 / Average exposure time: 0.25 sec. / Average electron dose: 30.0 e/Å2
Electron beamAcceleration voltage: 120 kV / Electron source: LAB6
Electron opticsC2 aperture diameter: 150.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 5.0 µm / Nominal defocus min: 0.2 µm / Nominal magnification: 49000
Sample stageSpecimen holder model: SIDE ENTRY, EUCENTRIC / Cooling holder cryogen: NITROGEN

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Image processing

Particle selectionNumber selected: 692280
CTF correctionType: NONE
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5fyk


Details: Coordinates from 5FYK for the trimer only were used to generate a map at 20 angstrom resolution and 2.4 angstroms per pixel using UCSF Chimera's molmap function
Final reconstructionNumber classes used: 1 / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 13.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0.8) / Number images used: 10713
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0.8)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0.8)
Final 3D classificationNumber classes: 9 / Avg.num./class: 9604 / Software - Name: RELION (ver. 3.0.8)
FSC plot (resolution estimation)

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