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- EMDB-8125: BG505 SOSIP.664 HIV-1 Env trimer in complex with anti-HIV fusion ... -

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Basic information

Entry
Database: EMDB / ID: EMD-8125
TitleBG505 SOSIP.664 HIV-1 Env trimer in complex with anti-HIV fusion peptide targeting N123-VRC34.01 Fab
Map dataNone
Sample
  • Complex: Complex containing 3 copies of N123-VRC34.01 anti-HIV Fab bound to a trimer of HIV-1 Env B505 SOSIP.664
    • Complex: HIV-1 Env BG505 SOSIP.664
    • Complex: Anti-HIV N123-VRC34.01 antibody fragment antigen binding
Function / homology
Function and homology information


positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane ...positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / identical protein binding / membrane
Similarity search - Function
Envelope glycoprotein Gp160 / Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120
Similarity search - Domain/homology
Envelope glycoprotein gp160
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1 / Homo sapiens (human)
Methodsingle particle reconstruction / negative staining / Resolution: 17.0 Å
AuthorsOzorowski G / Ward AB
CitationJournal: Science / Year: 2016
Title: Fusion peptide of HIV-1 as a site of vulnerability to neutralizing antibody.
Authors: Rui Kong / Kai Xu / Tongqing Zhou / Priyamvada Acharya / Thomas Lemmin / Kevin Liu / Gabriel Ozorowski / Cinque Soto / Justin D Taft / Robert T Bailer / Evan M Cale / Lei Chen / Chang W Choi ...Authors: Rui Kong / Kai Xu / Tongqing Zhou / Priyamvada Acharya / Thomas Lemmin / Kevin Liu / Gabriel Ozorowski / Cinque Soto / Justin D Taft / Robert T Bailer / Evan M Cale / Lei Chen / Chang W Choi / Gwo-Yu Chuang / Nicole A Doria-Rose / Aliaksandr Druz / Ivelin S Georgiev / Jason Gorman / Jinghe Huang / M Gordon Joyce / Mark K Louder / Xiaochu Ma / Krisha McKee / Sijy O'Dell / Marie Pancera / Yongping Yang / Scott C Blanchard / Walther Mothes / Dennis R Burton / Wayne C Koff / Mark Connors / Andrew B Ward / Peter D Kwong / John R Mascola /
Abstract: The HIV-1 fusion peptide, comprising 15 to 20 hydrophobic residues at the N terminus of the Env-gp41 subunit, is a critical component of the virus-cell entry machinery. Here, we report the ...The HIV-1 fusion peptide, comprising 15 to 20 hydrophobic residues at the N terminus of the Env-gp41 subunit, is a critical component of the virus-cell entry machinery. Here, we report the identification of a neutralizing antibody, N123-VRC34.01, which targets the fusion peptide and blocks viral entry by inhibiting conformational changes in gp120 and gp41 subunits of Env required for entry. Crystal structures of N123-VRC34.01 liganded to the fusion peptide, and to the full Env trimer, revealed an epitope consisting of the N-terminal eight residues of the gp41 fusion peptide and glycan N88 of gp120, and molecular dynamics showed that the N-terminal portion of the fusion peptide can be solvent-exposed. These results reveal the fusion peptide to be a neutralizing antibody epitope and thus a target for vaccine design.
History
DepositionMar 17, 2016-
Header (metadata) releaseJun 1, 2016-
Map releaseJun 1, 2016-
UpdateFeb 14, 2018-
Current statusFeb 14, 2018Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 5
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 5
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8125.png

Downloads & links

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Map

FileDownload / File: emd_8125.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNone
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.57 Å/pix.
x 160 pix.
= 251.2 Å		1.57 Å/pix.
x 160 pix.
= 251.2 Å		1.57 Å/pix.
x 160 pix.
= 251.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.57 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 5. / Movie #1: 5
Minimum - Maximum-16.328806 - 39.342570000000002
Average (Standard dev.)0.44375223 (±3.9348037)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions160160160
Spacing160160160
CellA=B=C: 251.20001 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.571.571.57
M x/y/z160160160
origin x/y/z0.0000.0000.000
length x/y/z251.200251.200251.200
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ281156
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS160160160
D min/max/mean-16.32939.3430.444

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Supplemental data

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Sample components

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Entire : Complex containing 3 copies of N123-VRC34.01 anti-HIV Fab bound t...

EntireName: Complex containing 3 copies of N123-VRC34.01 anti-HIV Fab bound to a trimer of HIV-1 Env B505 SOSIP.664
Components
  • Complex: Complex containing 3 copies of N123-VRC34.01 anti-HIV Fab bound to a trimer of HIV-1 Env B505 SOSIP.664
    • Complex: HIV-1 Env BG505 SOSIP.664
    • Complex: Anti-HIV N123-VRC34.01 antibody fragment antigen binding

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Supramolecule #1: Complex containing 3 copies of N123-VRC34.01 anti-HIV Fab bound t...

SupramoleculeName: Complex containing 3 copies of N123-VRC34.01 anti-HIV Fab bound to a trimer of HIV-1 Env B505 SOSIP.664
type: complex / ID: 1 / Parent: 0
Molecular weightTheoretical: 570 KDa

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

SupramoleculeName: HIV-1 Env BG505 SOSIP.664 / type: complex / ID: 2 / Parent: 1
Details: Soluble and stabilized HIV-1 Env trimer from strain BG505. Engineered disulfide between A501C and T605C. I559P mutation to stabilize in pre-fusion state. Addition of N332 to restore ...Details: Soluble and stabilized HIV-1 Env trimer from strain BG505. Engineered disulfide between A501C and T605C. I559P mutation to stabilize in pre-fusion state. Addition of N332 to restore glycosylation site for purification and antigenic properties. Truncation after D664 to increase solubility. Formed with three gp140 subunits.
Source (natural)Organism: Human immunodeficiency virus 1 / Strain: BG505
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant cell: HEK293F / Recombinant plasmid: pPPI4

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Supramolecule #3: Anti-HIV N123-VRC34.01 antibody fragment antigen binding

SupramoleculeName: Anti-HIV N123-VRC34.01 antibody fragment antigen binding
type: complex / ID: 3 / Parent: 1
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant cell: Expi 293 / Recombinant plasmid: pcDNA3.1
Molecular weightTheoretical: 50 KDa

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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
Component:
ConcentrationNameFormula
50.0 mMTris
150.0 mMSodium chlorideNaCl

Details: Sterile filtered buffer
StainingType: NEGATIVE / Material: 2% w/v uranyl formate
Details: Negatively stained EM samples were prepared on carbon-coated Cu400 grids by applying sample for 10 seconds, blotting, applying 2% w/v uranyl formate for 45 seconds, and blotting again.
GridModel: EMS / Material: COPPER / Support film - Material: CARBON / Pretreatment - Type: PLASMA CLEANING
DetailsTrimers were incubated with a 6-molar excess of Fab overnight at room temperature.

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Electron microscopy

MicroscopeFEI TECNAI 20
DetailsCollected a tilt series of -50, -40, -30, -20, -10, and 0 degrees.
Image recordingFilm or detector model: FEI CETA (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Digitization - Sampling interval: 14.0 µm / Average electron dose: 25.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 92000
Sample stageSpecimen holder model: SIDE ENTRY, EUCENTRIC

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Image processing

DetailsDark and light camera corrections were performed prior to data acquisition.
Startup modelType of model: NONE
Details: EMAN2 e2initialmodel.py was used to generate an initial model from 2D class averages.
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 17.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: SPARX / Software - details: sxali3d.py / Number images used: 9261
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: EMAN2 / Software - details: e2initialmodel.py
Final angle assignmentType: PROJECTION MATCHING / Software - Name: SPARX / Software - details: sxali3d.py
Details: Sparx sxali3d.py was used to refine particles against an initial model generated by EMAN2.

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