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- EMDB-42486: I53_dn5 nanoparticle displaying the trimeric HA heads with heptad... -

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Basic information

Entry
Database: EMDB / ID: EMD-42486
TitleI53_dn5 nanoparticle displaying the trimeric HA heads with heptad domain, TH-6heptad-I53_dn5 (local refinement of TH-6heptad)
Map data
Sample
  • Complex: I53_dn5 nanoparticle displaying the trimeric HA heads with heptad domain, TH-6heptad-I53_dn5
    • Complex: Trimer head HA
      • Protein or peptide: Trimer head HA,Hemagglutinin HA1 chain
    • Complex: Pentamer
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsInfluenza virus / Hemagglutinin nanoparticle vaccine / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID / VIRAL PROTEIN
Function / homology
Function and homology information


viral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / host cell surface receptor binding / 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 / membrane
Similarity search - Function
Haemagglutinin, influenzavirus A / Haemagglutinin, HA1 chain, alpha/beta domain superfamily / Haemagglutinin / Haemagglutinin, influenzavirus A/B / Viral capsid/haemagglutinin protein
Similarity search - Domain/homology
Biological speciessynthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsPark YJ / Veesler D
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)P01 AI167966 United States
CitationJournal: Cell Rep / Year: 2023
Title: Antigen spacing on protein nanoparticles influences antibody responses to vaccination.
Authors: Daniel Ellis / Annie Dosey / Seyhan Boyoglu-Barnum / Young-Jun Park / Rebecca Gillespie / Hubza Syeda / Geoffrey B Hutchinson / Yaroslav Tsybovsky / Michael Murphy / Deleah Pettie / Nick ...Authors: Daniel Ellis / Annie Dosey / Seyhan Boyoglu-Barnum / Young-Jun Park / Rebecca Gillespie / Hubza Syeda / Geoffrey B Hutchinson / Yaroslav Tsybovsky / Michael Murphy / Deleah Pettie / Nick Matheson / Sidney Chan / George Ueda / Jorge A Fallas / Lauren Carter / Barney S Graham / David Veesler / Masaru Kanekiyo / Neil P King /
Abstract: Immunogen design approaches aim to control the specificity and quality of antibody responses elicited by next-generation vaccines. Here, we use computational protein design to generate a nanoparticle ...Immunogen design approaches aim to control the specificity and quality of antibody responses elicited by next-generation vaccines. Here, we use computational protein design to generate a nanoparticle vaccine platform based on the receptor-binding domain (RBD) of influenza hemagglutinin (HA) that enables precise control of antigen conformation and spacing. HA RBDs are presented as either monomers or native-like closed trimers that are connected to the underlying nanoparticle by a rigid linker that is modularly extended to precisely control antigen spacing. Nanoparticle immunogens with decreased spacing between trimeric RBDs elicit antibodies with improved hemagglutination inhibition and neutralization potency as well as binding breadth across diverse H1 HAs. Our "trihead" nanoparticle immunogen platform provides insights into anti-HA immunity, establishes antigen spacing as an important parameter in structure-based vaccine design, and embodies several design features that could be used in next-generation vaccines against influenza and other viruses.
History
DepositionOct 25, 2023-
Header (metadata) releaseDec 27, 2023-
Map releaseDec 27, 2023-
UpdateDec 27, 2023-
Current statusDec 27, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_42486.png

Downloads & links

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Map

FileDownload / File: emd_42486.map.gz / Format: CCP4 / Size: 22.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.4281 Å
Density
Contour LevelBy AUTHOR: 0.6
Minimum - Maximum-3.2085853 - 5.5151687
Average (Standard dev.)0.0025270616 (±0.11520393)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions180180180
Spacing180180180
CellA=B=C: 257.05798 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_42486_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Histogram

Histogram (log scale)

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Half map: #1

Fileemd_42486_half_map_1.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: #2

Fileemd_42486_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : I53_dn5 nanoparticle displaying the trimeric HA heads with heptad...

EntireName: I53_dn5 nanoparticle displaying the trimeric HA heads with heptad domain, TH-6heptad-I53_dn5
Components
  • Complex: I53_dn5 nanoparticle displaying the trimeric HA heads with heptad domain, TH-6heptad-I53_dn5
    • Complex: Trimer head HA
      • Protein or peptide: Trimer head HA,Hemagglutinin HA1 chain
    • Complex: Pentamer
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: I53_dn5 nanoparticle displaying the trimeric HA heads with heptad...

SupramoleculeName: I53_dn5 nanoparticle displaying the trimeric HA heads with heptad domain, TH-6heptad-I53_dn5
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1

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Supramolecule #2: Trimer head HA

SupramoleculeName: Trimer head HA / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: synthetic construct (others)

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Supramolecule #3: Pentamer

SupramoleculeName: Pentamer / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: synthetic construct (others)

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Macromolecule #1: Trimer head HA,Hemagglutinin HA1 chain

MacromoleculeName: Trimer head HA,Hemagglutinin HA1 chain / type: protein_or_peptide / ID: 1 / Details: I53_dn5 nanoparticle,I53_dn5 nanoparticle / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 48.580578 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDSKGSSQKG SRLLLLLVVS NLLLPQGVLA IAPLQLGNCS VAGWILGNPE CELLISKESW SYIVETPNPE NGTCFPGYFA DYEELRCQL SSVSSFERFE IFPKESSWPN HTVTGVSASC SHNGKSSFYR NLLWLTGKNG LYPNLSKSYV NNKEKEVLVL W GVHHPPNI ...String:
MDSKGSSQKG SRLLLLLVVS NLLLPQGVLA IAPLQLGNCS VAGWILGNPE CELLISKESW SYIVETPNPE NGTCFPGYFA DYEELRCQL SSVSSFERFE IFPKESSWPN HTVTGVSASC SHNGKSSFYR NLLWLTGKNG LYPNLSKSYV NNKEKEVLVL W GVHHPPNI GNQRALYHTE NAYVLVVSSH YDRVFTPIIA KRPKVRDQEG RINYYWTLLE PGDTIIFEAN GNLIAPWYAF AL SRGFGSG SGSCIENINS KIYHIEDKIE EINRKIEHIL SKIYHIERKI EEILNEIAEL AYLLGELAYK LGEYRIAIRA YRI ALKSDP NNAEAWYNLG NAYYKQGRYR EAIEYYQKAL ELDPNNAEAW YNLGNAYYER GEYEEAIEYY RKALRLDPNN ADAM QNLLN AKMREEGGWE LQHHHHHH

UniProtKB: Hemagglutinin

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Macromolecule #2: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 2 / Number of copies: 9 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine

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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

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS GLACIOS
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 60.0 e/Å2

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Image processing

Startup modelType of model: OTHER / Details: cryoSPARC ab initio
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 399299

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