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- EMDB-7863: HIV-1 Envelope Glycoprotein clone PC64M4C054.SOSIP.664 in complex... -

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Basic information

Entry
Database: EMDB / ID: 7863
TitleHIV-1 Envelope Glycoprotein clone PC64M4C054.SOSIP.664 in complex with PCT64_13C Fab
Map dataHIV-1 Envelope Glycoprotein clone PC64M4C054.SOSIP.664 in complex with PCT64_13C Fab, primary map
SampleHIV-1 Envelope glycoprotein clone PC64M4C054.SOSIP.664 in complex with PCT64_13C Fab
  • HIV-1 Envelope Glycoprotein clone PC64M4C054.SOSIP.664
  • (Immunoglobulin G PCT64-13C Fab, ...) x 2
SourceHuman immunodeficiency virus 1 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / 5.1 Å resolution
AuthorsBerndsens ZB / Rantalainen KR / Ward AB
CitationJournal: Cell Rep / Year: 2018
Title: Co-evolution of HIV Envelope and Apex-Targeting Neutralizing Antibody Lineage Provides Benchmarks for Vaccine Design.
Authors: Kimmo Rantalainen / Zachary T Berndsen / Sasha Murrell / Liwei Cao / Oluwarotimi Omorodion / Jonathan L Torres / Mengyu Wu / Jeffrey Umotoy / Jeffrey Copps / Pascal Poignard / Elise Landais / James C Paulson / Ian A Wilson / Andrew B Ward
Abstract: Broadly neutralizing antibodies (bnAbs) targeting the HIV envelope glycoprotein (Env) typically take years to develop. Longitudinal analyses of both neutralizing antibody lineages and viruses at ...Broadly neutralizing antibodies (bnAbs) targeting the HIV envelope glycoprotein (Env) typically take years to develop. Longitudinal analyses of both neutralizing antibody lineages and viruses at serial time points during infection provide a basis for understanding the co-evolutionary contest between HIV and the humoral immune system. Here, we describe the structural characterization of an apex-targeting antibody lineage and autologous clade A viral Env from a donor in the Protocol C cohort. Comparison of Ab-Env complexes at early and late time points reveals that, within the antibody lineage, the CDRH3 loop rigidifies, the bnAb angle of approach steepens, and surface charges are mutated to accommodate glycan changes. Additionally, we observed differences in site-specific glycosylation between soluble and full-length Env constructs, which may be important for tuning optimal immunogenicity in soluble Env trimers. These studies therefore provide important guideposts for design of immunogens that prime and mature nAb responses to the Env V2-apex.
DateDeposition: May 9, 2018 / Header (metadata) release: May 30, 2018 / Map release: Jun 27, 2018 / Last update: Jun 27, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.04
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.04
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_7863.map.gz (map file in CCP4 format, 131073 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
320 pix
1.03 Å/pix.
= 329.6 Å
320 pix
1.03 Å/pix.
= 329.6 Å
320 pix
1.03 Å/pix.
= 329.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.03 Å
Density
Contour Level:0.04 (by author), 0.04 (movie #1):
Minimum - Maximum-0.056611713 - 0.12975307
Average (Standard dev.)0.00026299935 (0.0055751163)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions320320320
Origin0.0.0.
Limit319.319.319.
Spacing320320320
CellA=B=C: 329.59998 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.031.031.03
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z329.600329.600329.600
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ384384384
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-0.0570.1300.000

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Supplemental data

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Mask #1

Fileemd_7863_msk_1.map
Projections & Slices
AxesZYX
Projections
Slices (1/2)
Density Histograms

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Sample components

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Entire HIV-1 Envelope glycoprotein clone PC64M4C054.SOSIP.664 in complex...

EntireName: HIV-1 Envelope glycoprotein clone PC64M4C054.SOSIP.664 in complex with PCT64_13C Fab
Number of components: 4

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Component #1: protein, HIV-1 Envelope glycoprotein clone PC64M4C054.SOSIP.664 i...

ProteinName: HIV-1 Envelope glycoprotein clone PC64M4C054.SOSIP.664 in complex with PCT64_13C Fab
Recombinant expression: No
SourceSpecies: Human immunodeficiency virus 1

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Component #2: protein, HIV-1 Envelope Glycoprotein clone PC64M4C054.SOSIP.664

ProteinName: HIV-1 Envelope Glycoprotein clone PC64M4C054.SOSIP.664
Recombinant expression: No
SourceSpecies: Human immunodeficiency virus 1
Source (engineered)Expression System: Homo sapiens (human)

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Component #3: protein, Immunoglobulin G PCT64-13C Fab, Heavy chain

ProteinName: Immunoglobulin G PCT64-13C Fab, Heavy chain / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #4: protein, Immunoglobulin G PCT64-13C Fab, Light chain

ProteinName: Immunoglobulin G PCT64-13C Fab, Light chain / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionpH: 7.4
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 277.15 K / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 81.1 e/Å2 / Illumination mode: FLOOD BEAM
LensCs: 2.7 mm / Imaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 2006

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 45661
3D reconstructionResolution: 5.1 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot
(resolution estimation)

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