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- EMDB-8168: BF520.1 Fab fragment bound to BG505 T332N SOSIP.664 trimer -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-8168
TitleBF520.1 Fab fragment bound to BG505 T332N SOSIP.664 trimer
Map dataBF520.1 Fab fragment bound to BG505 T332N SOSIP.664 trimer
Sample
  • Complex: BF520.1 Fab complexed with BG505.C2 T332N SOSIP.664 trimer
    • Complex: BF520.1 Fab
    • Complex: BG505.C2 T332N SOSIP.664 trimer
Function / homology
Function and homology information


positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / virus-mediated perturbation of host defense response / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope ...positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / virus-mediated perturbation of host defense response / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / structural molecule activity / virion attachment to host cell / host cell plasma membrane / virion membrane / identical protein binding / plasma membrane
Similarity search - Function
Envelope glycoprotein Gp160 / Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120
Similarity search - Domain/homology
Envelope glycoprotein gp160
Similarity search - Component
Biological speciesHomo sapiens (human) / Human immunodeficiency virus 1
Methodsingle particle reconstruction / negative staining / Resolution: 10.9 Å
AuthorsWilliams JA / Lee KK
CitationJournal: Cell / Year: 2016
Title: HIV-1 Neutralizing Antibodies with Limited Hypermutation from an Infant.
Authors: Cassandra A Simonich / Katherine L Williams / Hans P Verkerke / James A Williams / Ruth Nduati / Kelly K Lee / Julie Overbaugh /
Abstract: HIV-1 broadly neutralizing antibodies (bnAbs) develop in a subset of infected adults and exhibit high levels of somatic hypermutation (SHM) due to years of affinity maturation. There is no precedent ...HIV-1 broadly neutralizing antibodies (bnAbs) develop in a subset of infected adults and exhibit high levels of somatic hypermutation (SHM) due to years of affinity maturation. There is no precedent for eliciting highly mutated antibodies by vaccination, nor is it practical to wait years for a desired response. Infants develop broad responses early, which may suggest a more direct path to generating bnAbs. Here, we isolated ten neutralizing antibodies (nAbs) contributing to plasma breadth of an infant at ∼1 year post-infection, including one with cross-clade breadth. The nAbs bind to envelope trimer from the transmitted virus, suggesting that this interaction may have initiated development of the infant nAbs. The infant cross-clade bnAb targets the N332 supersite on envelope but, unlike adult bnAbs targeting this site, lacks indels and has low SHM. The identification of this infant bnAb illustrates that HIV-1-specific neutralization breadth can develop without prolonged affinity maturation and extensive SHM.
History
DepositionApr 29, 2016-
Header (metadata) releaseJul 13, 2016-
Map releaseJul 13, 2016-
UpdateFeb 14, 2018-
Current statusFeb 14, 2018Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.5
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 1.5
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8168.png

Downloads & links

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Map

FileDownload / File: emd_8168.map.gz / Format: CCP4 / Size: 2.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationBF520.1 Fab fragment bound to BG505 T332N SOSIP.664 trimer
Voxel sizeX=Y=Z: 4.14 Å
Density
Contour LevelBy AUTHOR: 1.56 / Movie #1: 1.5
Minimum - Maximum-10.246309 - 5.69479
Average (Standard dev.)0.01362123 (±0.3383385)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-42-42-42
Dimensions848484
Spacing848484
CellA=B=C: 347.75998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.144.144.14
M x/y/z848484
origin x/y/z0.0000.0000.000
length x/y/z347.760347.760347.760
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ281156
MAP C/R/S123
start NC/NR/NS-42-42-42
NC/NR/NS848484
D min/max/mean-10.2465.6950.014

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Supplemental data

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Half map: BF520.1 Fab fragment bound to BG505 T332N SOSIP.664...

Fileemd_8168_half_map_1.map
AnnotationBF520.1 Fab fragment bound to BG505 T332N SOSIP.664 trimer, half map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: BF520.1 Fab fragment bound to BG505 T332N SOSIP.664...

Fileemd_8168_half_map_2.map
AnnotationBF520.1 Fab fragment bound to BG505 T332N SOSIP.664 trimer, half map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : BF520.1 Fab complexed with BG505.C2 T332N SOSIP.664 trimer

EntireName: BF520.1 Fab complexed with BG505.C2 T332N SOSIP.664 trimer
Components
  • Complex: BF520.1 Fab complexed with BG505.C2 T332N SOSIP.664 trimer
    • Complex: BF520.1 Fab
    • Complex: BG505.C2 T332N SOSIP.664 trimer

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Supramolecule #1: BF520.1 Fab complexed with BG505.C2 T332N SOSIP.664 trimer

SupramoleculeName: BF520.1 Fab complexed with BG505.C2 T332N SOSIP.664 trimer
type: complex / ID: 1 / Parent: 0

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Supramolecule #2: BF520.1 Fab

SupramoleculeName: BF520.1 Fab / type: complex / ID: 2 / Parent: 1
Details: Fab domains generated by papain digestion of BF520.1 IgG
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: BG505.C2 T332N SOSIP.664 trimer

SupramoleculeName: BG505.C2 T332N SOSIP.664 trimer / type: complex / ID: 3 / Parent: 1
Source (natural)Organism: Human immunodeficiency virus 1 / Strain: BG505.C2 T332N
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant cell: HEK 293F / Recombinant plasmid: pPPI4

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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

Concentration0.020 mg/mL
BufferpH: 7.5
StainingType: NEGATIVE / Material: methylamine tungstate
GridMaterial: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE

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Electron microscopy

MicroscopeFEI TECNAI SPIRIT
Electron beamAcceleration voltage: 120 kV / Electron source: LAB6
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 52000
Sample stageSpecimen holder model: SIDE ENTRY, EUCENTRIC / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Average electron dose: 24.0 e/Å2
Experimental equipment
Model: Tecnai Spirit / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: EMAN (ver. 2.1)
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5aco


Details: PDB entry 5ACO was filtered to 60 Angstrom resolution and used as an initial model.
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: EMAN (ver. 2.1)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: EMAN (ver. 2.1)
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 10.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: EMAN (ver. 2.1) / Number images used: 18325
FSC plot (resolution estimation)

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