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- EMDB-7107: HIV-1 Envelope Glycoprotein clone PC64M4c054 SOSIP in complex wit... -

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Basic information

Entry
Database: EMDB / ID: 7107
TitleHIV-1 Envelope Glycoprotein clone PC64M4c054 SOSIP in complex with PGV04 Fab
Map dataprimary map
SampleHIV-1 Envelope Glycoprotein clone PC64M4c054 SOSIP.664 in complex with PGV04 Fab
  • HIV-1 Envelope Glycoprotein clone PC64M4c054 SOSIP.664
  • (Human IgG Fab PGV04 Heavy ...) x 2
SourceHuman immunodeficiency virus 1
Methodsingle particle reconstruction / 27 Å resolution
AuthorsBerndsen ZT / Rantalainen K / Ward AB
CitationJournal: Immunity / Year: 2017
Title: HIV Envelope Glycoform Heterogeneity and Localized Diversity Govern the Initiation and Maturation of a V2 Apex Broadly Neutralizing Antibody Lineage.
Authors: Elise Landais / Ben Murrell / Bryan Briney / Sasha Murrell / Kimmo Rantalainen / Zachary T Berndsen / Alejandra Ramos / Lalinda Wickramasinghe / Melissa Laird Smith / Kemal Eren / Natalia de Val / Mengyu Wu / Audrey Cappelletti / Jeffrey Umotoy / Yolanda Lie / Terri Wrin / Paul Algate / Po-Ying Chan-Hui / Etienne Karita / / / Andrew B Ward / Ian A Wilson / Dennis R Burton / Davey Smith / Sergei L Kosakovsky Pond / Pascal Poignard
Abstract: Understanding how broadly neutralizing antibodies (bnAbs) to HIV envelope (Env) develop during natural infection can help guide the rational design of an HIV vaccine. Here, we described a bnAb ...Understanding how broadly neutralizing antibodies (bnAbs) to HIV envelope (Env) develop during natural infection can help guide the rational design of an HIV vaccine. Here, we described a bnAb lineage targeting the Env V2 apex and the Ab-Env co-evolution that led to development of neutralization breadth. The lineage Abs bore an anionic heavy chain complementarity-determining region 3 (CDRH3) of 25 amino acids, among the shortest known for this class of Abs, and achieved breadth with only 10% nucleotide somatic hypermutation and no insertions or deletions. The data suggested a role for Env glycoform heterogeneity in the activation of the lineage germline B cell. Finally, we showed that localized diversity at key V2 epitope residues drove bnAb maturation toward breadth, mirroring the Env evolution pattern described for another donor who developed V2-apex targeting bnAbs. Overall, these findings suggest potential strategies for vaccine approaches based on germline-targeting and serial immunogen design.
DateDeposition: Nov 7, 2017 / Header (metadata) release: Dec 6, 2017 / Map release: Dec 6, 2017 / Last update: Dec 6, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.03
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_7107.map.gz (map file in CCP4 format, 1049 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
64 pix
4.1 Å/pix.
= 262.4 Å
64 pix
4.1 Å/pix.
= 262.4 Å
64 pix
4.1 Å/pix.
= 262.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 4.1 Å
Density
Contour Level:0.03 (by author), 0.03 (movie #1):
Minimum - Maximum-0.045905747 - 0.17662056
Average (Standard dev.)0.0010671521 (0.017476585)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions646464
Origin000
Limit636363
Spacing646464
CellA=B=C: 262.4 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.14.14.1
M x/y/z646464
origin x/y/z0.0000.0000.000
length x/y/z262.400262.400262.400
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS646464
D min/max/mean-0.0460.1770.001

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Supplemental data

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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 PGV04 Fab
Number of components: 4
MassTheoretical: 225 kDa

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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 PGV04 Fab
Recombinant expression: No
MassTheoretical: 225 kDa
SourceSpecies: Human immunodeficiency virus 1
Source (engineered)Expression System: Homo sapiens (human)

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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
Source (engineered)Expression System: Human immunodeficiency virus 1

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Component #3: protein, Human IgG Fab PGV04 Heavy Chain

ProteinName: Human IgG Fab PGV04 Heavy Chain / Recombinant expression: No
Source (engineered)Expression System: Homo sapiens (human)

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Component #4: protein, Human IgG Fab PGV04 Heavy Chain

ProteinName: Human IgG Fab PGV04 Heavy Chain / Recombinant expression: No
Source (engineered)Expression System: Homo sapiens (human)

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle
Sample solutionpH: 7.4
Support filmunspecified
VitrificationCryogen name: NONE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Spirit / Image courtesy: FEI Company
ImagingMicroscope: FEI TECNAI SPIRIT
Electron gunElectron source: LAB6 / Accelerating voltage: 120 kV / Electron dose: 25 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: TVIPS TEMCAM-F416 (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C3 (3 fold cyclic) / Number of projections: 11429
3D reconstructionSoftware: RELION / Resolution: 27 Å / Resolution method: FSC 0.5 CUT-OFF
FSC plot
(resolution estimation)

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