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- EMDB-7859: Full Length HIV-1 Envelope Glycoprotein clone PC64M18C043 in comp... -

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Basic information

Entry
Database: EMDB / ID: 7859
TitleFull Length HIV-1 Envelope Glycoprotein clone PC64M18C043 in complex with PGT151 Fab and PCT64-35S Fab
Map dataFull Length HIV-1 Envelope Glycoprotein clone PC64M18C043 in complex with PGT151 Fab and PCT64-35S Fab, primary map
SampleFull Length HIV-1 Envelope Glycoprotein clone PC64M18C043 in complex with PCT64-35S Fab and PGT151 Fab
  • Full Length HIV-1 Envelope Glycoprotein clone PC64M18C043
  • (Immunoglobulin G ...) x 4
SourceHuman immunodeficiency virus 1 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / 6.8 Å resolution
AuthorsBerndsen ZT / Rantalainen K / 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_7859.map.gz (map file in CCP4 format, 67109 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
256 pix
1.46 Å/pix.
= 373.76 Å
256 pix
1.46 Å/pix.
= 373.76 Å
256 pix
1.46 Å/pix.
= 373.76 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.46 Å
Density
Contour Level:0.04 (by author), 0.04 (movie #1):
Minimum - Maximum-0.05317737 - 0.1651219
Average (Standard dev.)-0.0001583287 (0.0070029404)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions256256256
Origin0.0.0.
Limit255.255.255.
Spacing256256256
CellA=B=C: 373.76 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.461.461.46
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z373.760373.760373.760
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ384384384
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.0530.165-0.000

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Supplemental data

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Sample components

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Entire Full Length HIV-1 Envelope Glycoprotein clone PC64M18C043 in comp...

EntireName: Full Length HIV-1 Envelope Glycoprotein clone PC64M18C043 in complex with PCT64-35S Fab and PGT151 Fab
Number of components: 6

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Component #1: protein, Full Length HIV-1 Envelope Glycoprotein clone PC64M18C04...

ProteinName: Full Length HIV-1 Envelope Glycoprotein clone PC64M18C043 in complex with PCT64-35S Fab and PGT151 Fab
Recombinant expression: No
SourceSpecies: Human immunodeficiency virus 1
Source (engineered)Expression System: Homo sapiens (human) / Cell of expression system: HEK293F

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Component #2: protein, Full Length HIV-1 Envelope Glycoprotein clone PC64M18C043

ProteinName: Full Length HIV-1 Envelope Glycoprotein clone PC64M18C043
Recombinant expression: No
SourceSpecies: Human immunodeficiency virus 1
Source (engineered)Expression System: Homo sapiens (human)

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Component #3: protein, Immunoglobulin G PGT151 Fab, Heavy chain

ProteinName: Immunoglobulin G PGT151 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 PGT151, Light chain

ProteinName: Immunoglobulin G PGT151, Light chain / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #5: protein, Immunoglobulin G PCT64_35S Fab, Heavy chain

ProteinName: Immunoglobulin G PCT64_35S Fab, Heavy chain / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #6: protein, Immunoglobulin G PCT64_35S, Light chain

ProteinName: Immunoglobulin G PCT64_35S, 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: 7.5
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Temperature: 277.15 K / Details: Specimen was manually frozen.

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
ImagingMicroscope: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 37.5 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 980

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 60093
3D reconstructionResolution: 6.8 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot
(resolution estimation)

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