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- EMDB-20261: Single Particle Electron Cryo-Microscopy Reconstruction of BG505 ... -

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Basic information

Entry
Database: EMDB / ID: EMD-20261
TitleSingle Particle Electron Cryo-Microscopy Reconstruction of BG505 SOSIP-I53-50NP
Map dataBG505 SOSIP-I53-50NP
Sample
  • Complex: Two-component self-assembling nanoparticle consisting of BG505 SOSIP-I53-50A.1NT1 and I53-50B.4PT1
    • Complex: I53-50A.1NT1
      • Protein or peptide: I53-50A.1NT1
    • Complex: I53-50B.4PT1
      • Protein or peptide: I53-50B.4PT1
Keywordsnanoparticle / self-assembling / HIV / immunogen / SOSIP
Function / homology
Function and homology information


positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / 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 / virion attachment to host cell / host cell plasma membrane ...positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / 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 / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / identical protein binding / 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 speciessynthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.5 Å
AuthorsBerndsen ZT / Nieusma T / Ward AB
Funding support United States, 4 items
OrganizationGrant numberCountry
Bill & Melinda Gates FoundationOPP1111923 United States
Bill & Melinda Gates FoundationOPP1132237 United States
Bill & Melinda Gates FoundationOPP1115782 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)P01 AI110657 United States
CitationJournal: Nat Commun / Year: 2019
Title: Enhancing and shaping the immunogenicity of native-like HIV-1 envelope trimers with a two-component protein nanoparticle.
Authors: Philip J M Brouwer / Aleksandar Antanasijevic / Zachary Berndsen / Anila Yasmeen / Brooke Fiala / Tom P L Bijl / Ilja Bontjer / Jacob B Bale / William Sheffler / Joel D Allen / Anna Schorcht ...Authors: Philip J M Brouwer / Aleksandar Antanasijevic / Zachary Berndsen / Anila Yasmeen / Brooke Fiala / Tom P L Bijl / Ilja Bontjer / Jacob B Bale / William Sheffler / Joel D Allen / Anna Schorcht / Judith A Burger / Miguel Camacho / Daniel Ellis / Christopher A Cottrell / Anna-Janina Behrens / Marco Catalano / Iván Del Moral-Sánchez / Thomas J Ketas / Celia LaBranche / Marit J van Gils / Kwinten Sliepen / Lance J Stewart / Max Crispin / David C Montefiori / David Baker / John P Moore / Per Johan Klasse / Andrew B Ward / Neil P King / Rogier W Sanders /
Abstract: The development of native-like HIV-1 envelope (Env) trimer antigens has enabled the induction of neutralizing antibody (NAb) responses against neutralization-resistant HIV-1 strains in animal models. ...The development of native-like HIV-1 envelope (Env) trimer antigens has enabled the induction of neutralizing antibody (NAb) responses against neutralization-resistant HIV-1 strains in animal models. However, NAb responses are relatively weak and narrow in specificity. Displaying antigens in a multivalent fashion on nanoparticles (NPs) is an established strategy to increase their immunogenicity. Here we present the design and characterization of two-component protein NPs displaying 20 stabilized SOSIP trimers from various HIV-1 strains. The two-component nature permits the incorporation of exclusively well-folded, native-like Env trimers into NPs that self-assemble in vitro with high efficiency. Immunization studies show that the NPs are particularly efficacious as priming immunogens, improve the quality of the Ab response over a conventional one-component nanoparticle system, and are most effective when SOSIP trimers with an apex-proximate neutralizing epitope are displayed. Their ability to enhance and shape the immunogenicity of SOSIP trimers make these NPs a promising immunogen platform.
History
DepositionJun 3, 2019-
Header (metadata) releaseJun 19, 2019-
Map releaseJun 19, 2019-
UpdateOct 30, 2024-
Current statusOct 30, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6p6f
  • Surface level: 0.04
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6p6f
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_20261.png

Downloads & links

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Map

FileDownload / File: emd_20261.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationBG505 SOSIP-I53-50NP
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.31 Å/pix.
x 600 pix.
= 786. Å		1.31 Å/pix.
x 600 pix.
= 786. Å		1.31 Å/pix.
x 600 pix.
= 786. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.31 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.04 / Movie #1: 0.04
Minimum - Maximum-0.07415321 - 0.13343136
Average (Standard dev.)0.00011277083 (±0.0049399766)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions600600600
Spacing600600600
CellA=B=C: 785.99994 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.311.311.31
M x/y/z600600600
origin x/y/z0.0000.0000.000
length x/y/z786.000786.000786.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ320320320
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS600600600
D min/max/mean-0.0740.1330.000

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Supplemental data

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Mask #1

Fileemd_20261_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: BG505 SOSIP-I53-50NP, half map 1

Fileemd_20261_half_map_1.map
AnnotationBG505 SOSIP-I53-50NP, half map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: BG505 SOSIP-I53-50NP, half map 2

Fileemd_20261_half_map_2.map
AnnotationBG505 SOSIP-I53-50NP, 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 : Two-component self-assembling nanoparticle consisting of BG505 SO...

EntireName: Two-component self-assembling nanoparticle consisting of BG505 SOSIP-I53-50A.1NT1 and I53-50B.4PT1
Components
  • Complex: Two-component self-assembling nanoparticle consisting of BG505 SOSIP-I53-50A.1NT1 and I53-50B.4PT1
    • Complex: I53-50A.1NT1
      • Protein or peptide: I53-50A.1NT1
    • Complex: I53-50B.4PT1
      • Protein or peptide: I53-50B.4PT1

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Supramolecule #1: Two-component self-assembling nanoparticle consisting of BG505 SO...

SupramoleculeName: Two-component self-assembling nanoparticle consisting of BG505 SOSIP-I53-50A.1NT1 and I53-50B.4PT1
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all

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Supramolecule #2: I53-50A.1NT1

SupramoleculeName: I53-50A.1NT1 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: synthetic construct (others)

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Supramolecule #3: I53-50B.4PT1

SupramoleculeName: I53-50B.4PT1 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: synthetic construct (others)

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Macromolecule #1: I53-50A.1NT1

MacromoleculeName: I53-50A.1NT1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 99.386711 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDAMKRGLCC VLLLCGAVFV SPSQEIHARF RRGARAENLW VTVYYGVPVW KDAETTLFCA SDAKAYETKK HNVWATHCCV PTDPNPQEI HLENVTEEFN MWKNNMVEQM HTDIISLWDQ SLKPCVKLTP LCVTLQCTNV TNNITDDMRG ELKNCSFNMT T ELRDKKQK ...String:
MDAMKRGLCC VLLLCGAVFV SPSQEIHARF RRGARAENLW VTVYYGVPVW KDAETTLFCA SDAKAYETKK HNVWATHCCV PTDPNPQEI HLENVTEEFN MWKNNMVEQM HTDIISLWDQ SLKPCVKLTP LCVTLQCTNV TNNITDDMRG ELKNCSFNMT T ELRDKKQK VYSLFYRLDV VQINENQGNR SNNSNKEYRL INCNTSAITQ ACPKVSFEPI PIHYCAPAGF AILKCKDKKF NG TGPCPSV STVQCTHGIK PVVSTQLLLN GSLAEEEVMI RSENITNNAK NILVQFNTPV QINCTRPNNN TRKSIRIGPG QWF YATGDI IGDIRQAHCN VSKATWNETL GKVVKQLRKH FGNNTIIRFA NSSGGDLEVT THSFNCGGEF FYCNTSGLFN STWI SNTSV QGSNSTGSND SITLPCRIKQ IINMWQRIGQ AMYAPPIQGV IRCVSNITGL ILTRDGGSTN STTETFRPGG GDMRD NWRS ELYKYKVVKI EPLGVAPTRC KRRVVGRRRR RRAVGIGAVF LGFLGAAGST MGAASMTLTV QARNLLSGIV QQQSNL LRA PECQQHLLKL TVWGIKQLQA RVLAVERYLR DQQLLGIWGC SGKLICCTNV PWNSSWSNRN LSEIWDNMTW LQWDKEI SN YTQIIYGLLE ESQNQQEKNE QDLLALDGSG GSGGSGGSGG SEKAAKAEEA ARKMEELFKK HKIVAVLRAN SVEEAIEK A VAVFAGGVHL IEITFTVPDA DTVIKALSVL KEKGAIIGAG TVTSVEQCRK AVESGAEFIV SPHLDEEISQ FCKEKGVFY MPGVMTPTEL VKAMKLGHDI LKLFPGEVVG PEFVKAMKGP FPNVKFVPTG GVDLDNVCEW FDAGVLAVGV GDALVEGDPD EVREKAKEF VEKIRGCTE

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Macromolecule #2: I53-50B.4PT1

MacromoleculeName: I53-50B.4PT1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 18.236877 KDa
Recombinant expressionOrganism: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others)
SequenceString:
MNQHSHKDHE TVRIAVVRAR WHAEIVDACV SAFEAAMRDI GGDRFAVDVF DVPGAYEIPL HARTLAETGR YGAVLGTAFV VNGGIYRHE FVASAVINGM MNVQLNTGVP VLSAVLTPHN YDKSKAHTLL FLALFAVKGM EAARACVEIL AAREKIAAGS L EHHHHHH

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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 mg/mL
BufferpH: 7.4
GridSupport film - Material: CARBON / Support film - topology: HOLEY / Details: unspecified
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Average exposure time: 8.0 sec. / Average electron dose: 10.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD

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Image processing

Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2) / Number images used: 3590
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: FLEXIBLE FIT
Output model

PDB-6p6f:
BG505 SOSIP-I53-50NP

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