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- EMDB-3067: cryoEM reconstruction of 3BC315 Fab in complex with BG505 SOSIP.6... -

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Basic information

Entry
Database: EMDB / ID: EMD-3067
TitlecryoEM reconstruction of 3BC315 Fab in complex with BG505 SOSIP.664 Env trimer
Map dataReconstruction of 3BC315 Fab bound to BG505 SOSIP.664
Sample
  • Sample: 3BC315 Fab in complex with BG505 SOSIP.664 trimer
  • Protein or peptide: HIV-1 Envelope glycoprotein
  • Protein or peptide: 3BC315 Antibody Fab
KeywordsHIV-1 / Env / SOSIP / bnAb / broadly neutralizing antibody / 3BC315
Biological speciesHuman Immunodeficiency Virus-1 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 9.3 Å
AuthorsLee JH / Ward AB
CitationJournal: Nat Commun / Year: 2015
Title: Antibodies to a conformational epitope on gp41 neutralize HIV-1 by destabilizing the Env spike.
Authors: Jeong Hyun Lee / Daniel P Leaman / Arthur S Kim / Alba Torrents de la Peña / Kwinten Sliepen / Anila Yasmeen / Ronald Derking / Alejandra Ramos / Steven W de Taeye / Gabriel Ozorowski / ...Authors: Jeong Hyun Lee / Daniel P Leaman / Arthur S Kim / Alba Torrents de la Peña / Kwinten Sliepen / Anila Yasmeen / Ronald Derking / Alejandra Ramos / Steven W de Taeye / Gabriel Ozorowski / Florian Klein / Dennis R Burton / Michel C Nussenzweig / Pascal Poignard / John P Moore / Per Johan Klasse / Rogier W Sanders / Michael B Zwick / Ian A Wilson / Andrew B Ward /
Abstract: The recent identification of three broadly neutralizing antibodies (bnAbs) against gp120-gp41 interface epitopes has expanded the targetable surface on the HIV-1 envelope glycoprotein (Env) trimer. ...The recent identification of three broadly neutralizing antibodies (bnAbs) against gp120-gp41 interface epitopes has expanded the targetable surface on the HIV-1 envelope glycoprotein (Env) trimer. By using biochemical, biophysical and computational methods, we map the previously unknown trimer epitopes of two related antibodies, 3BC315 and 3BC176. A cryo-EM reconstruction of a soluble Env trimer bound to 3BC315 Fab at 9.3 Å resolution reveals that the antibody binds between two gp41 protomers, and neutralizes the virus by accelerating trimer decay. In contrast, bnAb 35O22 binding to a partially overlapping quaternary epitope at the gp120-gp41 interface does not induce decay. A conserved gp41-proximal glycan at N88 was also shown to play a role in the binding kinetics of 3BC176 and 3BC315. Finally, our data suggest that the dynamic structure of the Env trimer influences exposure of bnAb epitopes.
History
DepositionJun 29, 2015-
Header (metadata) releaseAug 12, 2015-
Map releaseOct 7, 2015-
UpdateFeb 17, 2016-
Current statusFeb 17, 2016Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0232
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.0232
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_3067.png

Downloads & links

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Map

FileDownload / File: emd_3067.map.gz / Format: CCP4 / Size: 41.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of 3BC315 Fab bound to BG505 SOSIP.664
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.21 Å/pix.
x 224 pix.
= 271.04 Å		1.21 Å/pix.
x 224 pix.
= 271.04 Å		1.21 Å/pix.
x 224 pix.
= 271.04 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.21 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0232 / Movie #1: 0.0232
Minimum - Maximum-0.00733771 - 0.04181812
Average (Standard dev.)0.00030375 (±0.00429353)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions224224224
Spacing224224224
CellA=B=C: 271.04 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.211.211.21
M x/y/z224224224
origin x/y/z0.0000.0000.000
length x/y/z271.040271.040271.040
α/β/γ90.00090.00090.000
start NX/NY/NZ-800-4
NX/NY/NZ1611358
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS224224224
D min/max/mean-0.0070.0420.000

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Supplemental data

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Sample components

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Entire : 3BC315 Fab in complex with BG505 SOSIP.664 trimer

EntireName: 3BC315 Fab in complex with BG505 SOSIP.664 trimer
Components
  • Sample: 3BC315 Fab in complex with BG505 SOSIP.664 trimer
  • Protein or peptide: HIV-1 Envelope glycoprotein
  • Protein or peptide: 3BC315 Antibody Fab

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Supramolecule #1000: 3BC315 Fab in complex with BG505 SOSIP.664 trimer

SupramoleculeName: 3BC315 Fab in complex with BG505 SOSIP.664 trimer / type: sample / ID: 1000 / Oligomeric state: Two 3BC315 Fabs bind one SOSIP.664 trimer / Number unique components: 2
Molecular weightTheoretical: 520 KDa

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Macromolecule #1: HIV-1 Envelope glycoprotein

MacromoleculeName: HIV-1 Envelope glycoprotein / type: protein_or_peptide / ID: 1 / Name.synonym: BG505 SOSIP.664
Details: BG505 Env trimer ectodomain with the SOSIP mutations and truncation at residue 664
Number of copies: 1 / Oligomeric state: trimer / Recombinant expression: Yes
Source (natural)Organism: Human Immunodeficiency Virus-1 / Strain: BG505 / synonym: HIV-1
Molecular weightTheoretical: 420 KDa
Recombinant expressionOrganism: Mammalian (mammals) / Recombinant cell: HEK293F / Recombinant plasmid: pPPI4

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Macromolecule #2: 3BC315 Antibody Fab

MacromoleculeName: 3BC315 Antibody Fab / type: protein_or_peptide / ID: 2 / Name.synonym: 3BC315 Fab / Details: Each Fab is a LC-HC heterodimer. / Number of copies: 2 / Oligomeric state: heterodimer / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human) / synonym: Human
Molecular weightTheoretical: 500 KDa
Recombinant expressionOrganism: Mammalian (mammals) / Recombinant cell: HEK293F

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1.5 mg/mL
BufferpH: 7.4 / Details: 20 mM Tris 150 mM NaCl
GridDetails: 400 mesh Cu grid with holey carbon
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: HOMEMADE PLUNGER
Method: DDM added to the sample prior to freezing, to final concentration of 0.003% (w/v)

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Electron microscopy

MicroscopeFEI TECNAI F20
Alignment procedureLegacy - Astigmatism: Objective lens astigmatism corrected at 50,000x mag
DateJan 9, 2014
Image recordingCategory: CCD / Film or detector model: GATAN K2 (4k x 4k) / Number real images: 2393 / Average electron dose: 27 e/Å2
Details: Every image is an average of 25 frames recorded by the direct electron detector.
Tilt angle min0
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus max: 4.5 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 29000
Sample stageSpecimen holder model: SIDE ENTRY, EUCENTRIC
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: Whole micrograph
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 9.3 Å / Resolution method: OTHER / Software - Name: Relion
Details: Frames 5-25 were used for the final particle reconstruction, due to large frame shifts in the first 4 frames.
Number images used: 20252

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