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- EMDB-5683: Molecular structure of the native influenza hemagglutinin H1 on v... -

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Basic information

Entry
Database: EMDB / ID: EMD-5683
TitleMolecular structure of the native influenza hemagglutinin H1 on virions
Map dataReconstruction of hemagglutinin H1 from influenza virion (filamentous morphology)
Sample
  • Sample: H1 hemagglutinin A/California/7/2009 (H1N1)
  • Protein or peptide: influenza envelope glycoprotein hemagglutinin (HA)
Keywordshemagglutinin / cryoelectron microscopy / influenza vaccine / epitope
Biological speciesInfluenza A virus (A/California/07/2009(H1N1))
Methodsubtomogram averaging / cryo EM
AuthorsHarris AK / Meyerson JR / Matsuoka Y / Kuybeda O / Moran A / Bliss D / Das SR / Yewdell JW / Sapiro G / Subbarao K / Subramaniam S
CitationJournal: Proc Natl Acad Sci U S A / Year: 2013
Title: Structure and accessibility of HA trimers on intact 2009 H1N1 pandemic influenza virus to stem region-specific neutralizing antibodies.
Authors: Audray K Harris / Joel R Meyerson / Yumiko Matsuoka / Oleg Kuybeda / Amy Moran / Donald Bliss / Suman R Das / Jonathan W Yewdell / Guillermo Sapiro / Kanta Subbarao / Sriram Subramaniam /
Abstract: Rapid antigenic variation of HA, the major virion surface protein of influenza A virus, remains the principal challenge to the development of broader and more effective vaccines. Some regions of HA, ...Rapid antigenic variation of HA, the major virion surface protein of influenza A virus, remains the principal challenge to the development of broader and more effective vaccines. Some regions of HA, such as the stem region proximal to the viral membrane, are nevertheless highly conserved across strains and among most subtypes. A fundamental question in vaccine design is the extent to which HA stem regions on the surface of the virus are accessible to broadly neutralizing antibodies. Here we report 3D structures derived from cryoelectron tomography of HA on intact 2009 H1N1 pandemic virions in the presence and absence of the antibody C179, which neutralizes viruses expressing a broad range of HA subtypes, including H1, H2, H5, H6, and H9. By fitting previously derived crystallographic structures of trimeric HA into the density maps, we deduced the locations of the molecular surfaces of HA involved in interaction with C179. Using computational methods to distinguish individual unliganded HA trimers from those that have bound C179 antibody, we demonstrate that ∼75% of HA trimers on the surface of the virus have C179 bound to the stem domain. Thus, despite their close packing on the viral membrane, the majority of HA trimers on intact virions are available to bind anti-stem antibodies that target conserved HA epitopes, establishing the feasibility of universal influenza vaccines that elicit such antibodies.
History
DepositionJun 3, 2013-
Header (metadata) releaseAug 21, 2013-
Map releaseAug 21, 2013-
UpdateAug 21, 2013-
Current statusAug 21, 2013Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.1
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 1.1
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_5683_1.jpg

Downloads & links

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Map

FileDownload / File: emd_5683.map.gz / Format: CCP4 / Size: 659.2 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of hemagglutinin H1 from influenza virion (filamentous morphology)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
4.1 Å/pix.
x 78 pix.
= 319.8 Å		4.1 Å/pix.
x 47 pix.
= 192.7 Å		4.1 Å/pix.
x 47 pix.
= 192.7 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 4.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.1 / Movie #1: 1.1
Minimum - Maximum0.00090503 - 2.45071435
Average (Standard dev.)0.67226559 (±0.45123512)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions474778
Spacing474778
CellA: 192.7 Å / B: 192.7 Å / C: 319.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.14.14.1
M x/y/z474778
origin x/y/z0.0000.0000.000
length x/y/z192.700192.700319.800
α/β/γ90.00090.00090.000
start NX/NY/NZ-132-122-147
NX/NY/NZ250274261
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS474778
D min/max/mean0.0012.4510.672

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Supplemental data

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Sample components

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Entire : H1 hemagglutinin A/California/7/2009 (H1N1)

EntireName: H1 hemagglutinin A/California/7/2009 (H1N1)
Components
  • Sample: H1 hemagglutinin A/California/7/2009 (H1N1)
  • Protein or peptide: influenza envelope glycoprotein hemagglutinin (HA)

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Supramolecule #1000: H1 hemagglutinin A/California/7/2009 (H1N1)

SupramoleculeName: H1 hemagglutinin A/California/7/2009 (H1N1) / type: sample / ID: 1000 / Oligomeric state: trimer / Number unique components: 2

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Macromolecule #1: influenza envelope glycoprotein hemagglutinin (HA)

MacromoleculeName: influenza envelope glycoprotein hemagglutinin (HA) / type: protein_or_peptide / ID: 1 / Name.synonym: influenza surface spike / Recombinant expression: No / Database: NCBI
Source (natural)Organism: Influenza A virus (A/California/07/2009(H1N1))

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4 / Details: PBS buffer
GridDetails: Quantifoil Multi-A, 200 mesh
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI POLARA 300
Specialist opticsEnergy filter - Name: Gatan / Energy filter - Lower energy threshold: 0.0 eV / Energy filter - Upper energy threshold: 20.0 eV
DateSep 6, 2010
Image recordingCategory: CCD / Film or detector model: GENERIC CCD / Average electron dose: 100 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 2.5 µm / Nominal magnification: 34000
Sample stageSpecimen holder model: GATAN LIQUID NITROGEN / Tilt series - Axis1 - Min angle: -60 ° / Tilt series - Axis1 - Max angle: 60 °
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

DetailsAverage number of tilts used in the 3D reconstructions: 61. Average tomographic tilt angle increment: 2.
Final reconstructionSoftware - Name: IMOD / Number subtomograms used: 416

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Atomic model buiding 1

Initial modelPDB ID:

3lzg

RefinementSpace: REAL / Protocol: RIGID BODY FIT

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