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- EMDB-9003: CP506 Fab/BG505 SOSIP.664 complexe -

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Basic information

Entry
Database: EMDB / ID: EMD-9003
TitleCP506 Fab/BG505 SOSIP.664 complexe
Map data
SampleCP506 Fab/BG505 SOSIP.664 complex:
BG505 SOSIP.664 Env trimer / guinea pig CP506 Fab
Biological speciesCavia porcellus (domestic guinea pig) / Human immunodeficiency virus 1
Methodsingle particle reconstruction / Resolution: 26.5 Å
AuthorsYang YY / Ward AB
CitationJournal: Cell Rep / Year: 2019
Title: The HIV-1 Envelope Glycoprotein C3/V4 Region Defines a Prevalent Neutralization Epitope following Immunization.
Authors: Lin Lei / Yuhe R Yang / Karen Tran / Yimeng Wang / Chi-I Chiang / Gabriel Ozorowski / Yongli Xiao / Andrew B Ward / Richard T Wyatt / Yuxing Li /
Abstract: Despite recent progress in engineering native trimeric HIV-1 envelope glycoprotein (Env) mimics as vaccine candidates, Env trimers often induce vaccine-matched neutralizing antibody (NAb) responses. ...Despite recent progress in engineering native trimeric HIV-1 envelope glycoprotein (Env) mimics as vaccine candidates, Env trimers often induce vaccine-matched neutralizing antibody (NAb) responses. Understanding the specificities of autologous NAb responses and the underlying molecular mechanisms restricting the neutralization breadth is therefore informative to improve vaccine efficacy. Here, we delineate the response specificity by single B cell sorting and serum analysis of guinea pigs immunized with BG505 SOSIP.664 Env trimers. Our results reveal a prominent immune target containing both conserved and strain-specific residues in the C3/V4 region of Env in trimer-vaccinated animals. The defined NAb response shares a high degree of similarity with the early NAb response developed by a naturally infected infant from whom the HIV virus strain BG505 was isolated and later developed a broadly NAb response. Our study describes strain-specific responses and their possible evolution pathways, thereby highlighting the potential to broaden NAb responses by immunogen re-design.
History
DepositionJul 27, 2018-
Header (metadata) releaseOct 31, 2018-
Map releaseMay 8, 2019-
UpdateMay 8, 2019-
Current statusMay 8, 2019Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.01
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.01
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9003.png

Downloads & links

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Map

FileDownload / File: emd_9003.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.05 Å/pix.
x 192 pix.
= 393.6 Å		2.05 Å/pix.
x 192 pix.
= 393.6 Å		2.05 Å/pix.
x 192 pix.
= 393.6 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: 0.01 / Movie #1: 0.01
Minimum - Maximum-0.027688198 - 0.058422524
Average (Standard dev.)-0.00009826251 (±0.003022909)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions192192192
Spacing192192192
CellA=B=C: 393.59998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.052.052.05
M x/y/z192192192
origin x/y/z0.0000.0000.000
length x/y/z393.600393.600393.600
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS192192192
D min/max/mean-0.0280.058-0.000

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Supplemental data

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Sample components

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Entire CP506 Fab/BG505 SOSIP.664 complex

EntireName: CP506 Fab/BG505 SOSIP.664 complex / Number of components: 3

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Component #1: protein, CP506 Fab/BG505 SOSIP.664 complex

ProteinName: CP506 Fab/BG505 SOSIP.664 complex / Recombinant expression: No
SourceSpecies: Cavia porcellus (domestic guinea pig)
Source (engineered)Expression System: Homo sapiens (human)

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Component #2: protein, BG505 SOSIP.664 Env trimer

ProteinName: BG505 SOSIP.664 Env trimer / Recombinant expression: No
SourceSpecies: Human immunodeficiency virus 1
Source (engineered)Expression System: Homo sapiens (human)

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Component #3: protein, guinea pig CP506 Fab

ProteinName: guinea pig CP506 Fab / Recombinant expression: No
SourceSpecies: Cavia porcellus (domestic guinea pig)
Source (engineered)Expression System: Homo sapiens (human)

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle
Sample solutionSpecimen conc.: 0.03 mg/mL / pH: 7.4
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
LensMagnification: 52000.0 X (nominal) / Cs: 2.2 mm / Imaging mode: BRIGHT FIELD / Defocus: 1500.0 - nm
Specimen HolderModel: SIDE ENTRY, EUCENTRIC
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: 12100
3D reconstructionSoftware: RELION / Resolution: 26.5 Å / Resolution method: FSC 0.5 CUT-OFF
FSC plot (resolution estimation)

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