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- EMDB-8299: AMC011 HIV-1 Env SOSIP trimer in complex with autologous anti-HIV... -

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Basic information

Entry
Database: EMDB / ID: EMD-8299
TitleAMC011 HIV-1 Env SOSIP trimer in complex with autologous anti-HIV antibody ACS202
Map dataAMC011 HIV-1 Env SOSIP trimer in complex with anti-HIV antibody ACS202
Sample
  • Complex: AMC011 HIV-1 Env trimer in complex with three copies of anti-HIV antibody ACS202 fragment antigen binding
Biological speciesHuman immunodeficiency virus 1
Methodsingle particle reconstruction / negative staining / Resolution: 21.0 Å
AuthorsOzorowski G / Ward AB
CitationJournal: Nat Microbiol / Year: 2016
Title: An HIV-1 antibody from an elite neutralizer implicates the fusion peptide as a site of vulnerability.
Authors: Marit J van Gils / Tom L G M van den Kerkhof / Gabriel Ozorowski / Christopher A Cottrell / Devin Sok / Matthias Pauthner / Jesper Pallesen / Natalia de Val / Anila Yasmeen / Steven W de ...Authors: Marit J van Gils / Tom L G M van den Kerkhof / Gabriel Ozorowski / Christopher A Cottrell / Devin Sok / Matthias Pauthner / Jesper Pallesen / Natalia de Val / Anila Yasmeen / Steven W de Taeye / Anna Schorcht / Stephanie Gumbs / Inez Johanna / Karen Saye-Francisco / Chi-Hui Liang / Elise Landais / Xiaoyan Nie / Laura K Pritchard / Max Crispin / Garnett Kelsoe / Ian A Wilson / Hanneke Schuitemaker / Per Johan Klasse / John P Moore / Dennis R Burton / Andrew B Ward / Rogier W Sanders /
Abstract: The induction by vaccination of broadly neutralizing antibodies (bNAbs) capable of neutralizing various HIV-1 viral strains is challenging, but understanding how a subset of HIV-infected individuals ...The induction by vaccination of broadly neutralizing antibodies (bNAbs) capable of neutralizing various HIV-1 viral strains is challenging, but understanding how a subset of HIV-infected individuals develops bNAbs may guide immunization strategies. Here, we describe the isolation and characterization of the bNAb ACS202 from an elite neutralizer that recognizes a new, trimer-specific and cleavage-dependent epitope at the gp120-gp41 interface of the envelope glycoprotein (Env), involving the glycan N88 and the gp41 fusion peptide. In addition, an Env trimer, AMC011 SOSIP.v4.2, based on early virus isolates from the same elite neutralizer, was constructed, and its structure by cryo-electron microscopy at 6.2 Å resolution reveals a closed, pre-fusion conformation similar to that of the BG505 SOSIP.664 trimer. The availability of a native-like Env trimer and a bNAb from the same elite neutralizer provides the opportunity to design vaccination strategies aimed at generating similar bNAbs against a key functional site on HIV-1.
History
DepositionJul 21, 2016-
Header (metadata) releaseSep 21, 2016-
Map releaseSep 21, 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: 0.11
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.11
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8299.png

Downloads & links

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Map

FileDownload / File: emd_8299.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationAMC011 HIV-1 Env SOSIP trimer in complex with anti-HIV antibody ACS202
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.98 Å/pix.
x 160 pix.
= 316.8 Å		1.98 Å/pix.
x 160 pix.
= 316.8 Å		1.98 Å/pix.
x 160 pix.
= 316.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.98 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.11 / Movie #1: 0.11
Minimum - Maximum-0.029346144 - 0.30702263
Average (Standard dev.)0.0022693234 (±0.031627107)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions160160160
Spacing160160160
CellA=B=C: 316.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.981.981.98
M x/y/z160160160
origin x/y/z0.0000.0000.000
length x/y/z316.800316.800316.800
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-0.0290.3070.002

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Supplemental data

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Sample components

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Entire : AMC011 HIV-1 Env trimer in complex with three copies of anti-HIV ...

EntireName: AMC011 HIV-1 Env trimer in complex with three copies of anti-HIV antibody ACS202 fragment antigen binding
Components
  • Complex: AMC011 HIV-1 Env trimer in complex with three copies of anti-HIV antibody ACS202 fragment antigen binding

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Supramolecule #1: AMC011 HIV-1 Env trimer in complex with three copies of anti-HIV ...

SupramoleculeName: AMC011 HIV-1 Env trimer in complex with three copies of anti-HIV antibody ACS202 fragment antigen binding
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Human immunodeficiency virus 1 / Strain: AMC011
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant cell: HEK293F / Recombinant plasmid: pPPI4
Molecular weightTheoretical: 570 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

Concentration0.01 mg/mL
BufferpH: 7.4 / Details: Tris-buffered saline
StainingType: NEGATIVE / Material: uranyl formate
Details: Negatively stained with 2% w/v uranyl formate for 60 seconds.
GridModel: EMS Cu400 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Atmosphere: OTHER
DetailsThe two components of the complex were incubated overnight at room temperature (molar excess of Fab) and diluted prior to grid preparation.

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
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
Details: Stage tilt of -50, -40, -30, -20, -10, 0 degrees to increase orientation sampling
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: 73000
Sample stageSpecimen holder model: SIDE ENTRY, EUCENTRIC
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: RELION (ver. 1.4)
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

4zmj


Details: Simulated electron density map from PDB coordinates, low pass-filtered to 60 Angstrom resolution
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 21.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: RELION (ver. 1.4) / Number images used: 11913
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 1.4)
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION
Final 3D classificationSoftware - Name: RELION (ver. 1.4)

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