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- EMDB-45943: Ab1271 Fab-bound 6535.3 SOSIP.664 trimer -

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Basic information

Entry
Database: EMDB / ID: EMD-45943
TitleAb1271 Fab-bound 6535.3 SOSIP.664 trimer
Map dataSharpened EM map
Sample
  • Complex: HIV-1 6535.3 SOSIP.664 in complex with a single copy of Ab1271 Fab
    • Complex: Ab1271 Fab
    • Complex: HIV-1 6535.3 SOSIP.664
KeywordsHIV-1 / SOSIP / VIRAL PROTEIN
Biological speciesHomo sapiens (human) / Human immunodeficiency virus 1
Methodsingle particle reconstruction / cryo EM / Resolution: 6.3 Å
AuthorsDeLaitsch AT / Bjorkman PJ
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)P01 AI100148 United States
Bill & Melinda Gates FoundationINV-002143 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)P50 1U54AI170856 United States
CitationJournal: NPJ Vaccines / Year: 2024
Title: Neutralizing antibodies elicited in macaques recognize V3 residues on altered conformations of HIV-1 Env trimer.
Authors: Andrew T DeLaitsch / Jennifer R Keeffe / Harry B Gristick / Juliet A Lee / Wenge Ding / Weimin Liu / Ashwin N Skelly / George M Shaw / Beatrice H Hahn / Pamela J Björkman /
Abstract: Eliciting broadly neutralizing antibodies that protect against diverse HIV-1 strains is a primary goal of AIDS vaccine research. We characterized Ab1456 and Ab1271, two heterologously-neutralizing ...Eliciting broadly neutralizing antibodies that protect against diverse HIV-1 strains is a primary goal of AIDS vaccine research. We characterized Ab1456 and Ab1271, two heterologously-neutralizing antibodies elicited in non-human primates by priming with an engineered V3-targeting SOSIP Env immunogen and boosting with increasingly native-like SOSIP Envs derived from different strain backgrounds. Structures of Env trimers in complex with these antibodies revealed V3 targeting, but on conformational states of Env distinct from the typical closed, prefusion trimeric SOSIP structure. Env trimers bound by Ab1456 adopted conformations resembling CD4-bound open Env states in the absence of soluble CD4, whereas trimers bound by Ab1271 exhibited a trimer apex-altered conformation to accommodate antibody binding. The finding that elicited antibodies cross-neutralized by targeting altered, non-closed, prefusion Env trimer conformations provides important information about Env dynamics that is relevant for HIV-1 vaccine design aimed at raising antibodies to desired epitopes on closed pre-fusion Env trimers.
History
DepositionJul 26, 2024-
Header (metadata) releaseDec 11, 2024-
Map releaseDec 11, 2024-
UpdateDec 18, 2024-
Current statusDec 18, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_45943.png

Downloads & links

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Map

FileDownload / File: emd_45943.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened EM map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 360 pix.
= 299.52 Å		0.83 Å/pix.
x 360 pix.
= 299.52 Å		0.83 Å/pix.
x 360 pix.
= 299.52 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.832 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.075
Minimum - Maximum-0.13675761 - 0.3339777
Average (Standard dev.)0.0014167734 (±0.011341239)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 299.52002 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half map A

Fileemd_45943_half_map_1.map
Annotationhalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map B

Fileemd_45943_half_map_2.map
Annotationhalf map B
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-1 6535.3 SOSIP.664 in complex with a single copy of Ab1271 Fab

EntireName: HIV-1 6535.3 SOSIP.664 in complex with a single copy of Ab1271 Fab
Components
  • Complex: HIV-1 6535.3 SOSIP.664 in complex with a single copy of Ab1271 Fab
    • Complex: Ab1271 Fab
    • Complex: HIV-1 6535.3 SOSIP.664

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Supramolecule #1: HIV-1 6535.3 SOSIP.664 in complex with a single copy of Ab1271 Fab

SupramoleculeName: HIV-1 6535.3 SOSIP.664 in complex with a single copy of Ab1271 Fab
type: complex / ID: 1 / Parent: 0

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Supramolecule #2: Ab1271 Fab

SupramoleculeName: Ab1271 Fab / type: complex / ID: 2 / Parent: 1
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: HIV-1 6535.3 SOSIP.664

SupramoleculeName: HIV-1 6535.3 SOSIP.664 / type: complex / ID: 3 / Parent: 1
Source (natural)Organism: Human immunodeficiency virus 1

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1.1 mg/mL
BufferpH: 8
Component:
ConcentrationNameFormula
0.02 MTris
0.15 MSodium ChlorideNaCl
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK IV / Details: 3s blot, 0 blot force.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 2898 / Average exposure time: 1.6 sec. / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 134369
Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 6.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 38818
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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