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- EMDB-20106: Full length HIV-1 Env AMC011 in complex with PGT151 Fab - DOPC bicelle -

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Basic information

Entry
Database: EMDB / ID: EMD-20106
TitleFull length HIV-1 Env AMC011 in complex with PGT151 Fab - DOPC bicelle
Map dataHIV-1 Env AMC011 in complex with PGT151 Fab - DOPC bicelle
Sample
  • Complex: PGT151 Fab in complex with full length AMC011 HIV-1 Env
    • Complex: AMC011 Glycoprotein 120
    • Complex: AMC011 Glycoprotein 41
    • Complex: PGT151 Fab
Biological speciesHuman immunodeficiency virus 1 / Homo sapiens (human)
Methodsingle particle reconstruction / negative staining / Resolution: 28.0 Å
AuthorsRantalainen K / Torrents de la Pena A / Ward AB
Funding support United States, 5 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesP01 AI110657 United States
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesF31 AI131873 United States
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesUM1 AI100663 United States
Bill & Melinda Gates FoundationOPP1115782 United States
Bill & Melinda Gates FoundationOPP1084519 United States
CitationJournal: PLoS Pathog / Year: 2019
Title: Similarities and differences between native HIV-1 envelope glycoprotein trimers and stabilized soluble trimer mimetics.
Authors: Alba Torrents de la Peña / Kimmo Rantalainen / Christopher A Cottrell / Joel D Allen / Marit J van Gils / Jonathan L Torres / Max Crispin / Rogier W Sanders / Andrew B Ward /
Abstract: The HIV-1 envelope glycoprotein (Env) trimer is located on the surface of the virus and is the target of broadly neutralizing antibodies (bNAbs). Recombinant native-like soluble Env trimer mimetics, ...The HIV-1 envelope glycoprotein (Env) trimer is located on the surface of the virus and is the target of broadly neutralizing antibodies (bNAbs). Recombinant native-like soluble Env trimer mimetics, such as SOSIP trimers, have taken a central role in HIV-1 vaccine research aimed at inducing bNAbs. We therefore performed a direct and thorough comparison of a full-length unmodified Env trimer containing the transmembrane domain and the cytoplasmic tail, with the sequence matched soluble SOSIP trimer, both based on an early Env sequence (AMC011) from an HIV+ individual that developed bNAbs. The structures of the full-length AMC011 trimer bound to either bNAb PGT145 or PGT151 were very similar to the structures of SOSIP trimers. Antigenically, the full-length and SOSIP trimers were comparable, but in contrast to the full-length trimer, the SOSIP trimer did not bind at all to non-neutralizing antibodies, most likely as a consequence of the intrinsic stabilization of the SOSIP trimer. Furthermore, the glycan composition of full-length and SOSIP trimers was similar overall, but the SOSIP trimer possessed slightly less complex and less extensively processed glycans, which may relate to the intrinsic stabilization as well as the absence of the membrane tether. These data provide insights into how to best use and improve membrane-associated full-length and soluble SOSIP HIV-1 Env trimers as immunogens.
History
DepositionApr 15, 2019-
Header (metadata) releaseJul 31, 2019-
Map releaseJul 31, 2019-
UpdateJul 31, 2019-
Current statusJul 31, 2019Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.03
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_20106.png

Downloads & links

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Map

FileDownload / File: emd_20106.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHIV-1 Env AMC011 in complex with PGT151 Fab - DOPC bicelle
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.05 Å/pix.
x 192 pix.
= 393.6 Å		2.05 Å/pix.
x 192 pix.
= 393.6 Å		2.05 Å/pix.
x 192 pix.
= 393.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.05 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.03 / Movie #1: 0.03
Minimum - Maximum-0.0567589 - 0.17929535
Average (Standard dev.)0.000020914204 (±0.008703149)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions192192192
Spacing192192192
CellA=B=C: 393.59998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.052.052.05
M x/y/z192192192
origin x/y/z0.0000.0000.000
length x/y/z393.600393.600393.600
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS192192192
D min/max/mean-0.0570.1790.000

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Supplemental data

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Sample components

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Entire : PGT151 Fab in complex with full length AMC011 HIV-1 Env

EntireName: PGT151 Fab in complex with full length AMC011 HIV-1 Env
Components
  • Complex: PGT151 Fab in complex with full length AMC011 HIV-1 Env
    • Complex: AMC011 Glycoprotein 120
    • Complex: AMC011 Glycoprotein 41
    • Complex: PGT151 Fab

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Supramolecule #1: PGT151 Fab in complex with full length AMC011 HIV-1 Env

SupramoleculeName: PGT151 Fab in complex with full length AMC011 HIV-1 Env
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4

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Supramolecule #2: AMC011 Glycoprotein 120

SupramoleculeName: AMC011 Glycoprotein 120 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Human immunodeficiency virus 1
Recombinant expressionOrganism: Homo sapiens (human)

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Supramolecule #3: AMC011 Glycoprotein 41

SupramoleculeName: AMC011 Glycoprotein 41 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Human immunodeficiency virus 1
Recombinant expressionOrganism: Homo sapiens (human)

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Supramolecule #4: PGT151 Fab

SupramoleculeName: PGT151 Fab / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #3-#4
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)

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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

Concentration0.03 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
50.0 mMTrisTris base
150.0 mMNaClSodium Chloride
0.1 mMDOPCDipalmitoylphosphatidylcholine
StainingType: NEGATIVE / Material: Uranyl formate

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Electron microscopy

MicroscopeFEI TECNAI SPIRIT
Image recordingFilm or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Average electron dose: 25.0 e/Å2
Electron beamAcceleration voltage: 120 kV / Electron source: LAB6
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Sample stageSpecimen holder model: OTHER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Tecnai Spirit / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: Gctf (ver. 1.06)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 28.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 1.3) / Number images used: 10943
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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