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- EMDB-8078: BG505 SOSIP.664 HIV-1 Env trimer in complex with anti-HIV CH235.1... -

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Basic information

Entry
Database: EMDB / ID: EMD-8078
TitleBG505 SOSIP.664 HIV-1 Env trimer in complex with anti-HIV CH235.12 wk323 Fab
Map dataNone
Sample
  • Complex: Complex containing 3 copies of CH235.12 wk323 anti-HIV Fab bound to a trimer of HIV-1 Env BG505 SOSIP.664
    • Complex: HIV-1 Env BG505 SOSIP.664
    • Complex: Anti-HIV CH235.12 wk323 antibody fragment antigen binding
Biological speciesHuman immunodeficiency virus 1 / Homo sapiens (human)
Methodsingle particle reconstruction / negative staining / Resolution: 17.0 Å
AuthorsOzorowski G / Ward AB
CitationJournal: Cell / Year: 2016
Title: Maturation Pathway from Germline to Broad HIV-1 Neutralizer of a CD4-Mimic Antibody.
Authors: Mattia Bonsignori / Tongqing Zhou / Zizhang Sheng / Lei Chen / Feng Gao / M Gordon Joyce / Gabriel Ozorowski / Gwo-Yu Chuang / Chaim A Schramm / Kevin Wiehe / S Munir Alam / Todd Bradley / ...Authors: Mattia Bonsignori / Tongqing Zhou / Zizhang Sheng / Lei Chen / Feng Gao / M Gordon Joyce / Gabriel Ozorowski / Gwo-Yu Chuang / Chaim A Schramm / Kevin Wiehe / S Munir Alam / Todd Bradley / Morgan A Gladden / Kwan-Ki Hwang / Sheelah Iyengar / Amit Kumar / Xiaozhi Lu / Kan Luo / Michael C Mangiapani / Robert J Parks / Hongshuo Song / Priyamvada Acharya / Robert T Bailer / Allen Cao / Aliaksandr Druz / Ivelin S Georgiev / Young D Kwon / Mark K Louder / Baoshan Zhang / Anqi Zheng / Brenna J Hill / Rui Kong / Cinque Soto / / James C Mullikin / Daniel C Douek / David C Montefiori / Michael A Moody / George M Shaw / Beatrice H Hahn / Garnett Kelsoe / Peter T Hraber / Bette T Korber / Scott D Boyd / Andrew Z Fire / Thomas B Kepler / Lawrence Shapiro / Andrew B Ward / John R Mascola / Hua-Xin Liao / Peter D Kwong / Barton F Haynes /
Abstract: Antibodies with ontogenies from VH1-2 or VH1-46-germline genes dominate the broadly neutralizing response against the CD4-binding site (CD4bs) on HIV-1. Here, we define with longitudinal sampling ...Antibodies with ontogenies from VH1-2 or VH1-46-germline genes dominate the broadly neutralizing response against the CD4-binding site (CD4bs) on HIV-1. Here, we define with longitudinal sampling from time-of-infection the development of a VH1-46-derived antibody lineage that matured to neutralize 90% of HIV-1 isolates. Structures of lineage antibodies CH235 (week 41 from time-of-infection, 18% breadth), CH235.9 (week 152, 77%), and CH235.12 (week 323, 90%) demonstrated the maturing epitope to focus on the conformationally invariant portion of the CD4bs. Similarities between CH235 lineage and five unrelated CD4bs lineages in epitope focusing, length-of-time to develop breadth, and extraordinary level of somatic hypermutation suggested commonalities in maturation among all CD4bs antibodies. Fortunately, the required CH235-lineage hypermutation appeared substantially guided by the intrinsic mutability of the VH1-46 gene, which closely resembled VH1-2. We integrated our CH235-lineage findings with a second broadly neutralizing lineage and HIV-1 co-evolution to suggest a vaccination strategy for inducing both lineages.
History
DepositionFeb 20, 2016-
Header (metadata) releaseMar 23, 2016-
Map releaseMar 23, 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: 0.08
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.08
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8078.png

Downloads & links

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Map

FileDownload / File: emd_8078.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.)
2.05 Å/pix.
x 160 pix.
= 328. Å		2.05 Å/pix.
x 160 pix.
= 328. Å		2.05 Å/pix.
x 160 pix.
= 328. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.05 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.08 / Movie #1: 0.08
Minimum - Maximum-0.015095317 - 0.15566593
Average (Standard dev.)0.0027085745 (±0.016653256)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions160160160
Spacing160160160
CellA=B=C: 328.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.052.052.05
M x/y/z160160160
origin x/y/z0.0000.0000.000
length x/y/z328.000328.000328.000
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-0.0150.1560.003

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Supplemental data

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Sample components

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Entire : Complex containing 3 copies of CH235.12 wk323 anti-HIV Fab bound ...

EntireName: Complex containing 3 copies of CH235.12 wk323 anti-HIV Fab bound to a trimer of HIV-1 Env BG505 SOSIP.664
Components
  • Complex: Complex containing 3 copies of CH235.12 wk323 anti-HIV Fab bound to a trimer of HIV-1 Env BG505 SOSIP.664
    • Complex: HIV-1 Env BG505 SOSIP.664
    • Complex: Anti-HIV CH235.12 wk323 antibody fragment antigen binding

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Supramolecule #1: Complex containing 3 copies of CH235.12 wk323 anti-HIV Fab bound ...

SupramoleculeName: Complex containing 3 copies of CH235.12 wk323 anti-HIV Fab bound to a trimer of HIV-1 Env BG505 SOSIP.664
type: complex / ID: 1 / Parent: 0
Molecular weightTheoretical: 420 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: Solubilized and stabilized HIV-1 Env trimer from strain BG505. Engineered disulfide between A501C and T605C. I559P mutation to stabilize in pre-fusion state. Truncation after D664 to ...Details: Solubilized and stabilized HIV-1 Env trimer from strain BG505. Engineered disulfide between A501C and T605C. I559P mutation to stabilize in pre-fusion state. Truncation after D664 to increase solubility. Formed with three gp140 subunits.
Source (natural)Organism: Human immunodeficiency virus 1 / Strain: B41
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant cell: HEK293F / Recombinant plasmid: pPPI4

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Supramolecule #3: Anti-HIV CH235.12 wk323 antibody fragment antigen binding

SupramoleculeName: Anti-HIV CH235.12 wk323 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
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 60 seconds, and blotting again.
GridModel: EMS / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Pretreatment - Type: PLASMA CLEANING

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Electron microscopy

MicroscopeFEI TECNAI F20
DetailsCollected a tilt series of -50, -40, -30, -20, -10, and 0 degrees.
Image recordingFilm or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Digitization - Sampling interval: 15.6 µm / Average electron dose: 25.0 e/Å2
Electron beamAcceleration voltage: 120 kV / Electron source: LAB6
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus min: 1.5 µm / Nominal magnification: 52000
Sample stageSpecimen holder model: SIDE ENTRY, EUCENTRIC
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: CTFind3
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

4zmj


Details: Coordinates of ligand-free BG505 SOSIP.664 were converted to an EM volume and low-pass filtered to 60 Angstrom.
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: RELION (ver. 1.4) / Number images used: 15565
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 1.4)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 1.4)
Final 3D classificationSoftware - Name: RELION (ver. 1.4)

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