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- EMDB-21328: Full-length HIV-1 Envelope glycoprotein clone AMC011 in complex w... -

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Basic information

Entry
Database: EMDB / ID: EMD-21328
TitleFull-length HIV-1 Envelope glycoprotein clone AMC011 in complex with PGT151 Fab and 10E8v4-5R+100cF Fab
Map dataFull-length HIV-1 Envelope glycoprotein clone AMC011 in complex with PGT151 Fab and 10E8v4-5R 100cF Fab
Sample
  • Complex: Full-length HIV-1 Envelope glycoprotein clone AMC011 in complex with PGT151 Fab and 10E8v4-5R+100cF Fab
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.8 Å
AuthorsRantalainen K / Lee WS / Ward ABW
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)UM1AI100663 United States
Bill & Melinda Gates FoundationOPP1115782 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)UM1AI144462 United States
CitationJournal: Cell Rep / Year: 2020
Title: HIV-1 Envelope and MPER Antibody Structures in Lipid Assemblies.
Authors: Kimmo Rantalainen / Zachary T Berndsen / Aleksandar Antanasijevic / Torben Schiffner / Xi Zhang / Wen-Hsin Lee / Jonathan L Torres / Lei Zhang / Adriana Irimia / Jeffrey Copps / Kenneth H ...Authors: Kimmo Rantalainen / Zachary T Berndsen / Aleksandar Antanasijevic / Torben Schiffner / Xi Zhang / Wen-Hsin Lee / Jonathan L Torres / Lei Zhang / Adriana Irimia / Jeffrey Copps / Kenneth H Zhou / Young D Kwon / William H Law / Chaim A Schramm / Raffaello Verardi / Shelly J Krebs / Peter D Kwong / Nicole A Doria-Rose / Ian A Wilson / Michael B Zwick / John R Yates / William R Schief / Andrew B Ward /
Abstract: Structural and functional studies of HIV envelope glycoprotein (Env) as a transmembrane protein have long been complicated by challenges associated with inherent flexibility of the molecule and the ...Structural and functional studies of HIV envelope glycoprotein (Env) as a transmembrane protein have long been complicated by challenges associated with inherent flexibility of the molecule and the membrane-embedded hydrophobic regions. Here, we present approaches for incorporating full-length, wild-type HIV-1 Env, as well as C-terminally truncated and stabilized versions, into lipid assemblies, providing a modular platform for Env structural studies by single particle electron microscopy. We reconstitute a full-length Env clone into a nanodisc, complex it with a membrane-proximal external region (MPER) targeting antibody 10E8, and structurally define the full quaternary epitope of 10E8 consisting of lipid, MPER, and ectodomain contacts. By aligning this and other Env-MPER antibody complex reconstructions with the lipid bilayer, we observe evidence of Env tilting as part of the neutralization mechanism for MPER-targeting antibodies. We also adapt the platform toward vaccine design purposes by introducing stabilizing mutations that allow purification of unliganded Env with a peptidisc scaffold.
History
DepositionFeb 4, 2020-
Header (metadata) releaseApr 22, 2020-
Map releaseApr 22, 2020-
UpdateNov 25, 2020-
Current statusNov 25, 2020Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.00827
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.00827
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_21328.png

Downloads & links

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Map

FileDownload / File: emd_21328.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFull-length HIV-1 Envelope glycoprotein clone AMC011 in complex with PGT151 Fab and 10E8v4-5R 100cF Fab
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.03 Å/pix.
x 320 pix.
= 329.6 Å		1.03 Å/pix.
x 320 pix.
= 329.6 Å		1.03 Å/pix.
x 320 pix.
= 329.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.03 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.00827 / Movie #1: 0.00827
Minimum - Maximum-0.012558982 - 0.03636367
Average (Standard dev.)0.00021102391 (±0.0020923552)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 329.59998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.031.031.03
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z329.600329.600329.600
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-0.0130.0360.000

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Supplemental data

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Half map: Full-length HIV-1 Envelope glycoprotein clone AMC011 in complex...

Fileemd_21328_half_map_1.map
AnnotationFull-length HIV-1 Envelope glycoprotein clone AMC011 in complex with PGT151 Fab and 10E8v4-5R 100cF Fab
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Full-length HIV-1 Envelope glycoprotein clone AMC011 in complex...

Fileemd_21328_half_map_2.map
AnnotationFull-length HIV-1 Envelope glycoprotein clone AMC011 in complex with PGT151 Fab and 10E8v4-5R 100cF Fab
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Full-length HIV-1 Envelope glycoprotein clone AMC011 in complex w...

EntireName: Full-length HIV-1 Envelope glycoprotein clone AMC011 in complex with PGT151 Fab and 10E8v4-5R+100cF Fab
Components
  • Complex: Full-length HIV-1 Envelope glycoprotein clone AMC011 in complex with PGT151 Fab and 10E8v4-5R+100cF Fab

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Supramolecule #1: Full-length HIV-1 Envelope glycoprotein clone AMC011 in complex w...

SupramoleculeName: Full-length HIV-1 Envelope glycoprotein clone AMC011 in complex with PGT151 Fab and 10E8v4-5R+100cF Fab
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#11
Details: AMC011 Env purified with stabilizing PGT151 Fab. Complexed with 10E8v4-5R+100cF Fab during detergent-lipid exchange and prior to grid preparation.
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)

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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

Concentration5.2 mg/mL
BufferpH: 7.4
GridModel: C-flat-1.2/1.3 / Material: COPPER / Mesh: 400
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV
DetailsAMC011 Env purified with stabilizing PGT151 Fab. Complexed with 10E8v4-5R+100cF Fab during detergent-lipid exchange and prior to grid preparation. Sample is in detergent-lipid micelle.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number real images: 6751 / Average electron dose: 54.3 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 599629
CTF correctionSoftware - Name: Gctf (ver. 1.06)
Startup modelType of model: OTHER / Details: Unliganded Env ectodomain low-pass filtered to 15A
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 7.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 23653
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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