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- EMDB-7021: Structure of influenza hemagglutinin from A/New Caledonia/20/99 i... -

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Basic information

Entry
Database: EMDB / ID: 7021
TitleStructure of influenza hemagglutinin from A/New Caledonia/20/99 in complex with FAB 441D6.
Map dataHemagglutinin ectodomain derived from influenza A/New Caledonia/20/99 expressed with a trimerization domain (foldon), in complex with 3 molecules of FAB 441D6.
SampleInfluenza hemagglutinin from A/New Caledonia/20/99, in complex with 3 molecules of FAB 441D6.Hemagglutinin (influenza)
  • Influenza hemagglutinin from A/New Caledonia/20/99, with C-terminal trimerization domain (T4 fibritin foldon).Hemagglutinin (influenza)
SourceInfluenza A virus
Methodsingle particle reconstruction / cryo EM / 8 Å resolution
AuthorsGallagher JR / Harris AK
CitationJournal: To Be Published
Title: Induction of Cross-Reactive B Cell Responses by an Ordered Mosaic Array of Hemagglutinin from Diverse Influenza Strains
Authors: Kanekiyo M / Joyce MG / Gillespie RA / Gallagher JR / Andrews SF / Yassine HM / Wheatley AK / Fisher BE / Ambrozak DR / Creanga A / Leung K / Sung Yang E / Georgiev IS / Tsybovsky Y / Prabhakaran MS / Andersen H / Kong W / Baxa U / Koup RA / Kwong PD / Harris AK / McDermott AB / Mascola JR / Graham BS
DateDeposition: Sep 8, 2017 / Header (metadata) release: Nov 1, 2017 / Map release: Nov 21, 2018 / Last update: Nov 21, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0452
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0452
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_7021.map.gz (map file in CCP4 format, 70305 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
260 pix
1.38 Å/pix.
= 358.722 Å
260 pix
1.38 Å/pix.
= 358.722 Å
260 pix
1.38 Å/pix.
= 358.722 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.3797 Å
Density
Contour Level:0.0452 (by author), 0.0452 (movie #1):
Minimum - Maximum-0.05205744 - 0.20475802
Average (Standard dev.)-0.00022363848 (0.009204472)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions260260260
Origin0.00.00.0
Limit259.0259.0259.0
Spacing260260260
CellA=B=C: 1.0 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.37971.37971.3797
M x/y/z260260260
origin x/y/z0.0000.0000.000
length x/y/z358.722358.722358.722
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ240240240
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS260260260
D min/max/mean-0.0520.205-0.000

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Supplemental data

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Mask #1

Fileemd_7021_msk_1.map
Projections & Slices
AxesZYX
Projections
Slices (1/2)
Density Histograms

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Sample components

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Entire Influenza hemagglutinin from A/New Caledonia/20/99, in complex wi...

EntireName: Influenza hemagglutinin from A/New Caledonia/20/99, in complex with 3 molecules of FAB 441D6.
Number of components: 2

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Component #1: protein, Influenza hemagglutinin from A/New Caledonia/20/99, in c...

ProteinName: Influenza hemagglutinin from A/New Caledonia/20/99, in complex with 3 molecules of FAB 441D6.Hemagglutinin (influenza)
Recombinant expression: No
SourceSpecies: Influenza A virus / Strain: A/New Caledonia/20/99
Source (engineered)Expression System: Homo sapiens (human)

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Component #2: protein, Influenza hemagglutinin from A/New Caledonia/20/99, with...

ProteinName: Influenza hemagglutinin from A/New Caledonia/20/99, with C-terminal trimerization domain (T4 fibritin foldon).Hemagglutinin (influenza)
Recombinant expression: No
SourceSpecies: Influenza A virus / Strain: A/New Caledonia/20/99
Source (engineered)Expression System: Homo sapiens (human)

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionSpecimen conc.: 1 mg/ml / Buffer solution: PBS / pH: 7.4
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 298 K / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 34 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 59000.0 X (nominal) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 2000.0 - 8000.0 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: FEI FALCON II (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 464

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C3 (3 fold cyclic) / Number of projections: 75233
3D reconstructionAlgorithm: FOURIER SPACE / Software: RELION2
CTF correction: CTF values determined with CTFFIND4, and CTF correction was applied by RELION.
Resolution: 8 Å / Resolution method: FSC 0.143 CUT-OFF
Details: The final map was re-refined with RELION2 released 8/18/2017, after a bug was patched affecting fidelity of the "gold-standard" refinement procedure. No changes were found in the resulting map, which refined to an identical resolution.
FSC plot
(resolution estimation)

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