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- EMDB-46672: Cryo-EM structure of partially open HIV-1 BG505 SOSIP.664 Env bou... -

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Basic information

Entry
Database: EMDB / ID: EMD-46672
TitleCryo-EM structure of partially open HIV-1 BG505 SOSIP.664 Env bound to 3-sCD4, 3-17b Fab and 1-VRC34.01 Fab, Population 3
Map dataHIV-1 BG505 SOSIP Env bound to 3-sCD4, 317 fab and 1-VRC34.01
Sample
  • Complex: A Complex of ectodomain of HIV-1 BG505 SOSIP.664 Env with sCD4, 17b Fab and VRC34.01 Fab
    • Complex: HIV-1 BG505 SOSIP.664 Env
    • Complex: sCD4
    • Complex: 17b Fab
    • Complex: VRC34.01 Fab
KeywordsRecombinantly purified HIV-1 Env / sCD4 / 17b Fab and VRC34.01 Fab / viral Env / vaccine / VIRAL PROTEIN
Biological speciesHuman immunodeficiency virus 1 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.4 Å
AuthorsThakur B / Acharya P
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI145687 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)U54 AI170752 United States
CitationJournal: Nat Commun / Year: 2025
Title: Conformational trajectory of the HIV-1 fusion peptide during CD4-induced envelope opening.
Authors: Bhishem Thakur / Revansiddha H Katte / Wang Xu / Katarzyna Janowska / Salam Sammour / Rory Henderson / Maolin Lu / Peter D Kwong / Priyamvada Acharya /
Abstract: The hydrophobic fusion peptide (FP), a critical component of the HIV-1 entry machinery, is located at the N terminus of the envelope (Env) gp41 subunit. The receptor-binding gp120 subunit of Env ...The hydrophobic fusion peptide (FP), a critical component of the HIV-1 entry machinery, is located at the N terminus of the envelope (Env) gp41 subunit. The receptor-binding gp120 subunit of Env forms a heterodimer with gp41. The gp120/gp41 heterodimer assembles into a homotrimer, in which FP is accessible for antibody binding. Env conformational changes or "opening" that follow receptor binding result in FP relocating to a newly formed interprotomer pocket at the gp41-gp120 interface where it is sterically inaccessible to antibodies. The mechanistic steps connecting the entry-related transition of antibody accessible-to-inaccessible FP configurations remain unresolved. Here, using SOSIP-stabilized Env ectodomains, we visualize that the FP remains accessible for antibody binding despite substantial receptor-induced Env opening. We delineate stepwise Env opening from its closed state to a functional CD4-bound symmetrically open Env in which we show that FP was accessible for antibody binding. We define downstream re-organizations that lead to the formation of a gp120/gp41 cavity into which the FP buries to become inaccessible for antibody binding. These findings improve our understanding of HIV-1 entry and delineate the entry-related conformational trajectory of a key site of HIV vulnerability to neutralizing antibody.
History
DepositionAug 21, 2024-
Header (metadata) releaseApr 30, 2025-
Map releaseApr 30, 2025-
UpdateOct 1, 2025-
Current statusOct 1, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_46672.png

Downloads & links

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Map

FileDownload / File: emd_46672.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHIV-1 BG505 SOSIP Env bound to 3-sCD4, 317 fab and 1-VRC34.01
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 320 pix.
= 345.6 Å		1.08 Å/pix.
x 320 pix.
= 345.6 Å		1.08 Å/pix.
x 320 pix.
= 345.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.08 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0983
Minimum - Maximum-0.2137235 - 0.478178
Average (Standard dev.)0.0006593323 (±0.018579349)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 345.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_46672_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_46672_half_map_2.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 : A Complex of ectodomain of HIV-1 BG505 SOSIP.664 Env with sCD4, 1...

EntireName: A Complex of ectodomain of HIV-1 BG505 SOSIP.664 Env with sCD4, 17b Fab and VRC34.01 Fab
Components
  • Complex: A Complex of ectodomain of HIV-1 BG505 SOSIP.664 Env with sCD4, 17b Fab and VRC34.01 Fab
    • Complex: HIV-1 BG505 SOSIP.664 Env
    • Complex: sCD4
    • Complex: 17b Fab
    • Complex: VRC34.01 Fab

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Supramolecule #1: A Complex of ectodomain of HIV-1 BG505 SOSIP.664 Env with sCD4, 1...

SupramoleculeName: A Complex of ectodomain of HIV-1 BG505 SOSIP.664 Env with sCD4, 17b Fab and VRC34.01 Fab
type: complex / ID: 1 / Parent: 0
Molecular weightTheoretical: 300 KDa

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Supramolecule #2: HIV-1 BG505 SOSIP.664 Env

SupramoleculeName: HIV-1 BG505 SOSIP.664 Env / type: complex / ID: 2 / Parent: 1
Source (natural)Organism: Human immunodeficiency virus 1

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Supramolecule #3: sCD4

SupramoleculeName: sCD4 / type: complex / ID: 3 / Parent: 1
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #4: 17b Fab

SupramoleculeName: 17b Fab / type: complex / ID: 4 / Parent: 1
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #5: VRC34.01 Fab

SupramoleculeName: VRC34.01 Fab / type: complex / ID: 5 / Parent: 1
Source (natural)Organism: Homo sapiens (human)

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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

Concentration1.3 mg/mL
BufferpH: 8
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 298 K / Instrument: LEICA EM CPC

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 58.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.8 µm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1105644
CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 6.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 25613
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationSoftware - Name: cryoSPARC
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL

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