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- EMDB-8312: HIV-1 Env BG505 SOSIP.664 trimer in complex with 3 copies of rabb... -

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Basic information

Entry
Database: EMDB / ID: EMD-8312
TitleHIV-1 Env BG505 SOSIP.664 trimer in complex with 3 copies of rabbit antibody 10A fragment antigen binding
Map dataHIV-1 Env BG505 SOSIP.664 trimer in complex with rabbit antibody 10A Fab
Sample
  • Complex: HIV-1 Env BG505 SOSIP.664 in complex with rabbit antibody 10A fragment antigen binding
    • Complex: Rabbit antibody 10A fragment antigen binding
    • Complex: HIV-1 Env BG505 SOSIP.664
Biological speciesOryctolagus cuniculus (rabbit) / Human immunodeficiency virus 1
Methodsingle particle reconstruction / negative staining / Resolution: 20.0 Å
AuthorsOzorowski G / Ward AB
CitationJournal: Cell Rep / Year: 2016
Title: Holes in the Glycan Shield of the Native HIV Envelope Are a Target of Trimer-Elicited Neutralizing Antibodies.
Authors: Laura E McCoy / Marit J van Gils / Gabriel Ozorowski / Terrence Messmer / Bryan Briney / James E Voss / Daniel W Kulp / Matthew S Macauley / Devin Sok / Matthias Pauthner / Sergey Menis / ...Authors: Laura E McCoy / Marit J van Gils / Gabriel Ozorowski / Terrence Messmer / Bryan Briney / James E Voss / Daniel W Kulp / Matthew S Macauley / Devin Sok / Matthias Pauthner / Sergey Menis / Christopher A Cottrell / Jonathan L Torres / Jessica Hsueh / William R Schief / Ian A Wilson / Andrew B Ward / Rogier W Sanders / Dennis R Burton /
Abstract: A major advance in the search for an HIV vaccine has been the development of a near-native Envelope trimer (BG505 SOSIP.664) that can induce robust autologous Tier 2 neutralization. Here, potently ...A major advance in the search for an HIV vaccine has been the development of a near-native Envelope trimer (BG505 SOSIP.664) that can induce robust autologous Tier 2 neutralization. Here, potently neutralizing monoclonal antibodies (nAbs) from rabbits immunized with BG505 SOSIP.664 are shown to recognize an immunodominant region of gp120 centered on residue 241. Residue 241 occupies a hole in the glycan defenses of the BG505 isolate, with fewer than 3% of global isolates lacking a glycan site at this position. However, at least one conserved glycan site is missing in 89% of viruses, suggesting the presence of glycan holes in most HIV isolates. Serum evidence is consistent with targeting of holes in natural infection. The immunogenic nature of breaches in the glycan shield has been under-appreciated in previous attempts to understand autologous neutralizing antibody responses and has important potential consequences for HIV vaccine design.
History
DepositionAug 4, 2016-
Header (metadata) releaseSep 7, 2016-
Map releaseSep 7, 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: 0.07
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.07
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8312.png

Downloads & links

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Map

FileDownload / File: emd_8312.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHIV-1 Env BG505 SOSIP.664 trimer in complex with rabbit antibody 10A Fab
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: 0.07 / Movie #1: 0.07
Minimum - Maximum-0.01615489 - 0.14911528
Average (Standard dev.)0.005205078 (±0.020296734)
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-0.0160.1490.005

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Supplemental data

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Sample components

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Entire : HIV-1 Env BG505 SOSIP.664 in complex with rabbit antibody 10A fra...

EntireName: HIV-1 Env BG505 SOSIP.664 in complex with rabbit antibody 10A fragment antigen binding
Components
  • Complex: HIV-1 Env BG505 SOSIP.664 in complex with rabbit antibody 10A fragment antigen binding
    • Complex: Rabbit antibody 10A fragment antigen binding
    • Complex: HIV-1 Env BG505 SOSIP.664

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Supramolecule #1: HIV-1 Env BG505 SOSIP.664 in complex with rabbit antibody 10A fra...

SupramoleculeName: HIV-1 Env BG505 SOSIP.664 in complex with rabbit antibody 10A fragment antigen binding
type: complex / ID: 1 / Parent: 0
Molecular weightTheoretical: 570 KDa

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Supramolecule #2: Rabbit antibody 10A fragment antigen binding

SupramoleculeName: Rabbit antibody 10A fragment antigen binding / type: complex / ID: 2 / Parent: 1
Details: Fab generated by proteolytic cleavage of IgG antibody
Source (natural)Organism: Oryctolagus cuniculus (rabbit)
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant strain: HEK293F / Recombinant plasmid: pCMV3
Molecular weightTheoretical: 50 KDa

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Supramolecule #3: HIV-1 Env BG505 SOSIP.664

SupramoleculeName: HIV-1 Env BG505 SOSIP.664 / type: complex / ID: 3 / Parent: 1
Source (natural)Organism: Human immunodeficiency virus 1
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant strain: HEK293F / Recombinant plasmid: pPPI4
Molecular weightTheoretical: 420 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 / Details: 50 mM Tris-HCl, pH 7.4, 150 mM NaCl
StainingType: NEGATIVE / Material: uranyl formate
Details: 2% uranyl formate used to stain sample for 60 seconds.
GridModel: EMS Cu400 / Material: COPPER / Support film - Material: PARLODION / Support film - topology: CONTINUOUS / Pretreatment - Type: PLASMA CLEANING
DetailsComplex formed by overnight incubation of Fab with Env at a 6x molar excess of Fab to Env and dilution to 0.03 mg/mL prior to grid adsorption.

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: FEI CETA (4k x 4k) / Average electron dose: 25.0 e/Å2
Details: Stage tilts of -50, -40, -30, -20, -10, and 0 degrees were performed to increase orientation sampling.
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination 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
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Details: Initial model created using representative 2D class averages
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 20.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: SPARX / Number images used: 7050
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: EMAN2 / Software - details: e2initialmodel
Final angle assignmentType: PROJECTION MATCHING

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