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- EMDB-7471: QA013.2 Fab fragment bound to BG505 T332N SOSIP.664 trimer -

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Basic information

Entry
Database: EMDB / ID: EMD-7471
TitleQA013.2 Fab fragment bound to BG505 T332N SOSIP.664 trimer
Map dataQA013.2-Fab fragment bound to BG505 T332N SOSIP.664 trimer
Sample
  • Complex: Complex of QA013.2 Fab bound to BG505 T332N SOSIP.664 trimer
    • Complex: QA0132 Fab fragment
    • Complex: BG505 T332N SOSIP.664 trimer
Biological speciesHuman immunodeficiency virus / Homo sapiens (human)
Methodsingle particle reconstruction / negative staining / Resolution: 12.5 Å
AuthorsWilliams JA / Lee KK
CitationJournal: Cell Rep / Year: 2018
Title: Superinfection Drives HIV Neutralizing Antibody Responses from Several B Cell Lineages that Contribute to a Polyclonal Repertoire.
Authors: Katherine L Williams / Bingjie Wang / Dana Arenz / James A Williams / Adam S Dingens / Valerie Cortez / Cassandra A Simonich / Stephanie Rainwater / Dara A Lehman / Kelly K Lee / Julie Overbaugh /
Abstract: Eliciting broad and potent HIV-specific neutralizing antibody responses represents the holy grail of HIV vaccine efforts. Data from singly infected individuals with broad and potent plasma ...Eliciting broad and potent HIV-specific neutralizing antibody responses represents the holy grail of HIV vaccine efforts. Data from singly infected individuals with broad and potent plasma neutralizing activity targeting one epitope have guided our understanding of how these responses develop. However, far less is known about responses developed by superinfected individuals who acquire two distinct HIV strains. Here, we isolated HIV-specific mAbs from a superinfected individual with a broad plasma response. In this superinfection case, neutralizing activity resulted from multiple distinct B cell lineages that arose in response to either the initial or the superinfecting virus, including an antibody that targets the N332 supersite. This nAb, QA013.2, was specific to the superinfecting virus and was associated with eventual reemergence of the initial infecting virus. The complex dynamic between viruses in superinfection may drive development of a unique collection of polyclonal nAbs that present a higher barrier to escape than monoclonal responses.
History
DepositionFeb 20, 2018-
Header (metadata) releaseMar 7, 2018-
Map releaseMar 7, 2018-
UpdateMay 15, 2019-
Current statusMay 15, 2019Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.2
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 1.2
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_7471.png

Downloads & links

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Map

FileDownload / File: emd_7471.map.gz / Format: CCP4 / Size: 2.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationQA013.2-Fab fragment bound to BG505 T332N SOSIP.664 trimer
Voxel sizeX=Y=Z: 2.07 Å
Density
Contour LevelBy AUTHOR: 1.0 / Movie #1: 1.2
Minimum - Maximum-7.779764 - 4.9319744
Average (Standard dev.)0.011791622 (±0.31235427)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-41-41-41
Dimensions828282
Spacing828282
CellA=B=C: 169.73999 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.072.072.07
M x/y/z828282
origin x/y/z0.0000.0000.000
length x/y/z169.740169.740169.740
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ208208208
MAP C/R/S123
start NC/NR/NS-41-41-41
NC/NR/NS828282
D min/max/mean-7.7804.9320.012

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Supplemental data

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Sample components

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Entire : Complex of QA013.2 Fab bound to BG505 T332N SOSIP.664 trimer

EntireName: Complex of QA013.2 Fab bound to BG505 T332N SOSIP.664 trimer
Components
  • Complex: Complex of QA013.2 Fab bound to BG505 T332N SOSIP.664 trimer
    • Complex: QA0132 Fab fragment
    • Complex: BG505 T332N SOSIP.664 trimer

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Supramolecule #1: Complex of QA013.2 Fab bound to BG505 T332N SOSIP.664 trimer

SupramoleculeName: Complex of QA013.2 Fab bound to BG505 T332N SOSIP.664 trimer
type: complex / ID: 1 / Parent: 0
Details: Fab fragment generated by papain digestion of IgG antibody. SOSIP.664 Env trimer recombinantly expressed in HEK-293F cells.
Source (natural)Organism: Human immunodeficiency virus
Molecular weightTheoretical: 360 KDa

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Supramolecule #2: QA0132 Fab fragment

SupramoleculeName: QA0132 Fab fragment / type: complex / ID: 2 / Parent: 1 / Details: Fab fragment generated by papain digestion of IgG
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant cell: Human embryonic kidney / Recombinant plasmid: pPPI4

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Supramolecule #3: BG505 T332N SOSIP.664 trimer

SupramoleculeName: BG505 T332N SOSIP.664 trimer / type: complex / ID: 3 / Parent: 1

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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

Concentration.020 mg/mL
BufferpH: 7.5
StainingType: NEGATIVE / Material: Methylamine Tungstate
GridModel: C-flat / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE

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Electron microscopy

MicroscopeFEI TECNAI 12
Image recordingFilm or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Number grids imaged: 1 / Number real images: 146 / Average exposure time: 1.0 sec. / Average electron dose: 27.0 e/Å2
Electron beamAcceleration voltage: 120 kV / Electron source: LAB6
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 2.0 µm / Nominal magnification: 52000
Sample stageSpecimen holder model: SIDE ENTRY, EUCENTRIC

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Image processing

Particle selectionNumber selected: 18000
CTF correctionSoftware - Name: EMAN2 (ver. 2.1)
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5aco

Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 12.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: EMAN2 (ver. 2.1) / Number images used: 12000
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: EMAN2 (ver. 2.1)
FSC plot (resolution estimation)

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