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- EMDB-20912: Group 1 H1 influenza stem nanoparticle with an H38R mutation -

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Basic information

Entry
Database: EMDB / ID: EMD-20912
TitleGroup 1 H1 influenza stem nanoparticle with an H38R mutation
Map dataMap after postprocessing
Sample
  • Complex: H1ssF R38
    • Protein or peptide: H1ssF R38
Biological speciesInfluenza A virus
Methodsingle particle reconstruction / cryo EM / Resolution: 6.4 Å
AuthorsTsybovsky Y / Stephens T / Kanekiyo M / Graham BS
CitationJournal: Nat Commun / Year: 2020
Title: Glycan repositioning of influenza hemagglutinin stem facilitates the elicitation of protective cross-group antibody responses.
Authors: Seyhan Boyoglu-Barnum / Geoffrey B Hutchinson / Jeffrey C Boyington / Syed M Moin / Rebecca A Gillespie / Yaroslav Tsybovsky / Tyler Stephens / John R Vaile / Julia Lederhofer / Kizzmekia S ...Authors: Seyhan Boyoglu-Barnum / Geoffrey B Hutchinson / Jeffrey C Boyington / Syed M Moin / Rebecca A Gillespie / Yaroslav Tsybovsky / Tyler Stephens / John R Vaile / Julia Lederhofer / Kizzmekia S Corbett / Brian E Fisher / Hadi M Yassine / Sarah F Andrews / Michelle C Crank / Adrian B McDermott / John R Mascola / Barney S Graham / Masaru Kanekiyo /
Abstract: The conserved hemagglutinin (HA) stem has been a focus of universal influenza vaccine efforts. Influenza A group 1 HA stem-nanoparticles have been demonstrated to confer heterosubtypic protection in ...The conserved hemagglutinin (HA) stem has been a focus of universal influenza vaccine efforts. Influenza A group 1 HA stem-nanoparticles have been demonstrated to confer heterosubtypic protection in animals; however, the protection does not extend to group 2 viruses, due in part to differences in glycosylation between group 1 and 2 stems. Here, we show that introducing the group 2 glycan at Asn38 to a group 1 stem-nanoparticle (gN38 variant) based on A/New Caledonia/20/99 (H1N1) broadens antibody responses to cross-react with group 2 HAs. Immunoglobulins elicited by the gN38 variant provide complete protection against group 2 H7N9 virus infection, while the variant loses protection against a group 1 H5N1 virus. The N38 glycan thus is pivotal in directing antibody responses by controlling access to group-determining stem epitopes. Precise targeting of stem-directed antibody responses to the site of vulnerability by glycan repositioning may be a step towards achieving cross-group influenza protection.
History
DepositionNov 4, 2019-
Header (metadata) releaseDec 18, 2019-
Map releaseFeb 19, 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: 0.04
  • 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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Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_20912.png

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Map

FileDownload / File: emd_20912.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMap after postprocessing
Projections & slices

Image control

Size
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.58 Å/pix.
x 200 pix.
= 316. Å		1.58 Å/pix.
x 200 pix.
= 316. Å		1.58 Å/pix.
x 200 pix.
= 316. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.58 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.04 / Movie #1: 0.04
Minimum - Maximum-0.04356234 - 0.1972675
Average (Standard dev.)0.0026152565 (±0.014781063)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 316.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.581.581.58
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z316.000316.000316.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ400400400
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS200200200
D min/max/mean-0.0440.1970.003

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Supplemental data

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Mask #1

Fileemd_20912_msk_1.map
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Additional map: Map before postprocessing

Fileemd_20912_additional.map
AnnotationMap before postprocessing
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Additional map: Map before postprocessing

Fileemd_20912_additional_1.map
AnnotationMap before postprocessing
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Half map: Half-map 1

Fileemd_20912_half_map_1.map
AnnotationHalf-map 1
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AxesZYX

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Half map: Half-map 2

Fileemd_20912_half_map_2.map
AnnotationHalf-map 2
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Sample components

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Entire : H1ssF R38

EntireName: H1ssF R38
Components
  • Complex: H1ssF R38
    • Protein or peptide: H1ssF R38

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Supramolecule #1: H1ssF R38

SupramoleculeName: H1ssF R38 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Ferritin-based nanoparticle displaying Influenza hemagglutinin stems
Source (natural)Organism: Influenza A virus
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant cell: 293 Expi
Molecular weightTheoretical: 1.031 MDa

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Macromolecule #1: H1ssF R38

MacromoleculeName: H1ssF R38 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Influenza A virus
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MKAKLLVLLC TFTATYADTI CIGYHANNST DTVDTVLEKN VTVTRSVNLG SGLRMVTGLR NIPQRETRGL FGAIAGFIEG GWTGMVDGWY GYHHQNEQGS GYAADQKSTQ NAINGITNMV NSVIEKMGSG GSGTDLAELL VLLLNERTLD FHDSNVKNLY EKVKSQLKNN ...String:
MKAKLLVLLC TFTATYADTI CIGYHANNST DTVDTVLEKN VTVTRSVNLG SGLRMVTGLR NIPQRETRGL FGAIAGFIEG GWTGMVDGWY GYHHQNEQGS GYAADQKSTQ NAINGITNMV NSVIEKMGSG GSGTDLAELL VLLLNERTLD FHDSNVKNLY EKVKSQLKNN AKEIGNGCFE FYHKCNNECM ESVKNGTYDY PKYSEESKLN REKIDSGGDI IKLLNEQVNK EMQSSNLYMS MSSWCYTHSL DGAGLFLFDH AAEEYEHAKK LIIFLNENNV PVQLTSISAP EHKFEGLTQI FQKAYEHEQH ISESINNIVD HAIKSKDHAT FNFLQWYVAE QHEEEVLFKD ILDKIELIGN ENHGLYLADQ YVKGIAKSRK SGS

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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 / Details: PBS
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 297 K / Instrument: FEI VITROBOT MARK IV / Details: Drop volume: 2.7 microliters.

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Electron microscopy

MicroscopeTFS TALOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Number grids imaged: 1 / Number real images: 106 / Average exposure time: 2.0 sec. / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 92000
Sample stageSpecimen holder model: GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER
Cooling holder cryogen: NITROGEN

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Image processing

Particle selectionNumber selected: 68863
CTF correctionSoftware - Name: CTFFIND (ver. 4.1)
Startup modelType of model: OTHER
Details: The initial model was obtained using EMAN2 from selected 2D class averages.
Final reconstructionApplied symmetry - Point group: O (octahedral) / Resolution.type: BY AUTHOR / Resolution: 6.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1) / Number images used: 13539
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.1)
FSC plot (resolution estimation)

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