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- EMDB-20101: B41 SOSIP.664 trimer in complex with two Fab fragments of the sil... -

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Basic information

Entry
Database: EMDB / ID: EMD-20101
TitleB41 SOSIP.664 trimer in complex with two Fab fragments of the silent-face targeting bNAb SF12, and one Fab fragment of the V3-targeting bNAb 10-1074
Map data
SampleComplex of B41 SOSIP.664 trimer with three SF12 Fabs and one 10-1074 Fab.:
B41 SOSIP.664 trimer / 10-1074 Fab / SF12 Fab
Biological speciesHuman immunodeficiency virus 1 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.36 Å
AuthorsBarnes CO / Bjorkman PJ
CitationJournal: Immunity / Year: 2019
Title: Broad and Potent Neutralizing Antibodies Recognize the Silent Face of the HIV Envelope.
Authors: Till Schoofs / Christopher O Barnes / Nina Suh-Toma / Jovana Golijanin / Philipp Schommers / Henning Gruell / Anthony P West / Franziska Bach / Yu Erica Lee / Lilian Nogueira / Ivelin S Georgiev / Robert T Bailer / Julie Czartoski / John R Mascola / Michael S Seaman / M Juliana McElrath / Nicole A Doria-Rose / Florian Klein / Michel C Nussenzweig / Pamela J Bjorkman /
Abstract: Broadly neutralizing antibodies (bNAbs) against HIV-1 envelope (Env) inform vaccine design and are potential therapeutic agents. We identified SF12 and related bNAbs with up to 62% neutralization ...Broadly neutralizing antibodies (bNAbs) against HIV-1 envelope (Env) inform vaccine design and are potential therapeutic agents. We identified SF12 and related bNAbs with up to 62% neutralization breadth from an HIV-infected donor. SF12 recognized a glycan-dominated epitope on Env's silent face and was potent against clade AE viruses, which are poorly covered by V3-glycan bNAbs. A 3.3Å cryo-EM structure of a SF12-Env trimer complex showed additional contacts to Env protein residues by SF12 compared with VRC-PG05, the only other known donor-derived silentface antibody, explaining SF12's increased neutralization breadth, potency, and resistance to Env mutation routes. Asymmetric binding of SF12 was associated with distinct N-glycan conformations across Env protomers, demonstrating intra-Env glycan heterogeneity. Administrating SF12 to HIV-1-infected humanized mice suppressed viremia and selected for viruses lacking the N448 glycan. Effective bNAbs can therefore be raised against HIV-1 Env's silent face, suggesting their potential for HIV-1 prevention, therapy, and vaccine development.
DateDeposition: Apr 14, 2019 / Header (metadata) release: May 8, 2019 / Map release: Jun 5, 2019 / Update: Jun 5, 2019

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.016
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.016
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_20101.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.09 Å/pix.
x 256 pix.
= 279.04 Å
1.09 Å/pix.
x 256 pix.
= 279.04 Å
1.09 Å/pix.
x 256 pix.
= 279.04 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.09 Å
Density
Contour LevelBy AUTHOR: 0.016 / Movie #1: 0.016
Minimum - Maximum-0.03687159 - 0.067034245
Average (Standard dev.)0.00036268955 (±0.0027245393)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 279.04 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.091.091.09
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z279.040279.040279.040
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.0370.0670.000

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Supplemental data

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Sample components

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Entire Complex of B41 SOSIP.664 trimer with three SF12 Fabs and one 10-1...

EntireName: Complex of B41 SOSIP.664 trimer with three SF12 Fabs and one 10-1074 Fab.
Details: Fab fragment generated by recombinant expression and complexed with the B41 SOSIP.664 trimer
Number of components: 4

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Component #1: protein, Complex of B41 SOSIP.664 trimer with three SF12 Fabs and...

ProteinName: Complex of B41 SOSIP.664 trimer with three SF12 Fabs and one 10-1074 Fab.
Details: Fab fragment generated by recombinant expression and complexed with the B41 SOSIP.664 trimer
Recombinant expression: No
MassTheoretical: 540 kDa

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Component #2: protein, B41 SOSIP.664 trimer

ProteinName: B41 SOSIP.664 trimer / Recombinant expression: No
SourceSpecies: Human immunodeficiency virus 1
Source (engineered)Expression System: Cricetulus griseus (Chinese hamster)

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Component #3: protein, 10-1074 Fab

ProteinName: 10-1074 Fab / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human) / Vector: p3BNC / Strain: Expi293

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Component #4: protein, SF12 Fab

ProteinName: SF12 Fab / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human) / Vector: p3BNC / Strain: Expi293

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionSpecimen conc.: 0.8 mg/mL / pH: 8
Support filmunspecified
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 295 K / Humidity: 100 %
Details: 0 blot force, 3 second blot time, 3 uL sample added to freshly glow-discharged grids.

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 40 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 130000.0 X (nominal) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 1200.0 - 3000.0 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 2732

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 55136
3D reconstructionSoftware: RELION / Resolution: 4.36 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

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Atomic model buiding

Modeling #1Refinement protocol: rigid body / Target criteria: Correlation coefficient / Refinement space: REAL
Input PDB model: 6CH9, 6CH9
Chain ID: G, B

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