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- EMDB-44738: HIV Envelope BG505 SOSIP.664 in complex with one Fab of CH103 E75... -

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Basic information

Entry
Database: EMDB / ID: EMD-44738
TitleHIV Envelope BG505 SOSIP.664 in complex with one Fab of CH103 E75K/D76N mutant
Map dataHIV Envelope BG505 SOSIP.664 in complex with one Fab of CH103 E75K/D76N mutant
Sample
  • Complex: Complex of BG505 SOSIP.664 with two CH103 wildtype Fabs
    • Complex: BG505 SOSIP Trimer
    • Complex: CH103 E75K/D76N mutant Fab
KeywordsHIV Envelope Antibody Complex / VIRAL PROTEIN
Biological speciesHuman immunodeficiency virus 2 / Homo sapiens (human)
Methodsingle particle reconstruction / negative staining / Resolution: 10.0 Å
AuthorsEdwards RJ / Mansouri K
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)UM1 AI144371 United States
CitationJournal: To Be Published
Title: Acquisition of Quaternary Interaction during Lineage Maturation Increases the Potency of an HIV-1 Broadly Neutralizing Antibody
Authors: Liu Q / Parsons R / Wiehe K / Edwards RJ / Saunders KO / Zhang P / Miao H / Williams W / Huang X / Janowska K / Mansouri K / Acharya P / Haynes BF / Lusso P
History
DepositionMay 3, 2024-
Header (metadata) releaseMay 15, 2024-
Map releaseMay 15, 2024-
UpdateMay 15, 2024-
Current statusMay 15, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_44738.png

Downloads & links

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Map

FileDownload / File: emd_44738.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHIV Envelope BG505 SOSIP.664 in complex with one Fab of CH103 E75K/D76N mutant
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.16 Å/pix.
x 160 pix.
= 345.6 Å		2.16 Å/pix.
x 160 pix.
= 345.6 Å		2.16 Å/pix.
x 160 pix.
= 345.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.16 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0431
Minimum - Maximum-0.05536712 - 0.10675142
Average (Standard dev.)0.0006623454 (±0.008575518)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions160160160
Spacing160160160
CellA=B=C: 345.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: BG505-CH103 KN mutant half map

Fileemd_44738_half_map_1.map
AnnotationBG505-CH103 KN mutant half map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: BG505-CH103 KN mutant half map

Fileemd_44738_half_map_2.map
AnnotationBG505-CH103 KN mutant half 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 : Complex of BG505 SOSIP.664 with two CH103 wildtype Fabs

EntireName: Complex of BG505 SOSIP.664 with two CH103 wildtype Fabs
Components
  • Complex: Complex of BG505 SOSIP.664 with two CH103 wildtype Fabs
    • Complex: BG505 SOSIP Trimer
    • Complex: CH103 E75K/D76N mutant Fab

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Supramolecule #1: Complex of BG505 SOSIP.664 with two CH103 wildtype Fabs

SupramoleculeName: Complex of BG505 SOSIP.664 with two CH103 wildtype Fabs
type: complex / ID: 1 / Parent: 0
Molecular weightTheoretical: 46 KDa

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Supramolecule #2: BG505 SOSIP Trimer

SupramoleculeName: BG505 SOSIP Trimer / type: complex / ID: 2 / Parent: 1
Source (natural)Organism: Human immunodeficiency virus 2 / Strain: BG505

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Supramolecule #3: CH103 E75K/D76N mutant Fab

SupramoleculeName: CH103 E75K/D76N mutant Fab / type: complex / ID: 3 / Parent: 1
Source (natural)Organism: Homo sapiens (human) / Strain: BG505

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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

Concentration0.3 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
150.0 mMNaClsodium chloride
20.0 mMHEPESHEPES buffer
5.0 mMNaN3sodium azide
StainingType: NEGATIVE / Material: uranyl formate
Details: Quenched sample was applied to a glow-discharged carbon-coated 300 mesh EM grid for 10 seconds, blotted and stained with 2 g/dL uranyl formate for 1 minute, blotted and air dried.
GridModel: Homemade / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 4 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 20 sec.
DetailsComplex formed by incubating 20 micrograms trimer with 36 micrograms Fab overnight at 4 degrees C, followed by SEC purification over a Superose 6 Increase 10 300 column. Purified complex was concentrated to 1-2 mg/ml with a 100 kDA spin concentrator, then diluted with buffer containing 8 mM glutaraldehyde and incubated for 5 minutes. Excess glutaraldehyde was quenched by adding 1 M Tris buffer to a final Tris concentration of 80 mM.

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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: 130 / Average exposure time: 0.25 sec. / Average electron dose: 32.0 e/Å2
Electron beamAcceleration voltage: 120 kV / Electron source: LAB6
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.2 µm / Nominal magnification: 49000
Sample stageSpecimen holder model: SIDE ENTRY, EUCENTRIC

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Image processing

Particle selectionNumber selected: 211354
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6uda


Details: Low-pass filtered at 60 angstroms
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: EXACT BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 10.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 64403
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final 3D classificationNumber classes: 9 / Avg.num./class: 11363 / Software - Name: RELION (ver. 3.0)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: RIGID BODY FIT

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