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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 dataCP506 Fab/BG505 SOSIP.664 complexes
Sample
  • Complex: CP506 Fab/BG505 SOSIP.664 complex
    • Complex: BG505 SOSIP.664 Env trimer
      • Complex: guinea pig CP506 Fab
Biological speciesCavia porcellus (domestic guinea pig) / Human immunodeficiency virus 1
Methodsingle particle reconstruction / negative staining / 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
  • Download
  • 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)
AnnotationCP506 Fab/BG505 SOSIP.664 complexes
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
Components
  • Complex: CP506 Fab/BG505 SOSIP.664 complex
    • Complex: BG505 SOSIP.664 Env trimer
      • Complex: guinea pig CP506 Fab

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Supramolecule #1: CP506 Fab/BG505 SOSIP.664 complex

SupramoleculeName: CP506 Fab/BG505 SOSIP.664 complex / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Cavia porcellus (domestic guinea pig)
Recombinant expressionOrganism: Homo sapiens (human)

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Supramolecule #2: BG505 SOSIP.664 Env trimer

SupramoleculeName: BG505 SOSIP.664 Env trimer / type: complex / ID: 2 / Parent: 1
Source (natural)Organism: Human immunodeficiency virus 1
Recombinant expressionOrganism: Homo sapiens (human)

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Supramolecule #3: guinea pig CP506 Fab

SupramoleculeName: guinea pig CP506 Fab / type: complex / ID: 3 / Parent: 2
Source (natural)Organism: Cavia porcellus (domestic guinea pig)
Recombinant expressionOrganism: Homo sapiens (human)

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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
StainingType: NEGATIVE / Material: 2% Uranyl Formate
GridModel: Homemade / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Pretreatment - Type: GLOW DISCHARGE

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Electron microscopy

MicroscopeFEI TECNAI SPIRIT
Image recordingFilm or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Average exposure time: 0.5 sec. / Average electron dose: 25.0 e/Å2
Electron beamAcceleration voltage: 120 kV / Electron source: LAB6
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.2 mm / Nominal defocus min: 1.5 µm / Nominal magnification: 52000
Sample stageSpecimen holder model: SIDE ENTRY, EUCENTRIC
Experimental equipment
Model: Tecnai Spirit / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

4zmj

Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 26.5 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: RELION (ver. 2.1) / Number images used: 12100
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 2.1)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 2.1)
Final 3D classificationNumber classes: 4 / Software - Name: RELION (ver. 2.1)
FSC plot (resolution estimation)

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