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- EMDB-0234: Structure of Influenza Hemagglutinin ectodomain (A/duck/Alberta/35/76) -

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Basic information

Entry
Database: EMDB / ID: EMD-0234
TitleStructure of Influenza Hemagglutinin ectodomain (A/duck/Alberta/35/76)
Map dataSharpened map of A/duck/Alberta/35/76 Haemagglutinin Ectodomain
Sample
  • Complex: A/duck/Alberta/35/76 Hemagglutinin Ectodomain
    • Protein or peptide: Hemagglutinin
    • Protein or peptide: Hemagglutinin
  • Ligand: UNKNOWN BRANCHED FRAGMENT OF PHOSPHOLIPID
KeywordsInfluenza virus / Hemagglutinin / Membrane protein / Membrane fusion / 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
Hemagglutinin / Hemagglutinin
Similarity search - Component
Biological speciesInfluenza A virus (strain A/Duck/Alberta/35/1976 H1N1)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsBenton DJ / Rosenthal PB
Funding support United Kingdom, 7 items
OrganizationGrant numberCountry
Cancer Research UKFC001078 United Kingdom
Cancer Research UKFC001143 United Kingdom
Medical Research Council (United Kingdom)FC001078 United Kingdom
Medical Research Council (United Kingdom)FC001143 United Kingdom
Wellcome TrustFC001078 United Kingdom
Wellcome TrustFC001143 United Kingdom
European Research Council629829 United Kingdom
CitationJournal: Proc Natl Acad Sci U S A / Year: 2018
Title: Influenza hemagglutinin membrane anchor.
Authors: Donald J Benton / Andrea Nans / Lesley J Calder / Jack Turner / Ursula Neu / Yi Pu Lin / Esther Ketelaars / Nicole L Kallewaard / Davide Corti / Antonio Lanzavecchia / Steven J Gamblin / ...Authors: Donald J Benton / Andrea Nans / Lesley J Calder / Jack Turner / Ursula Neu / Yi Pu Lin / Esther Ketelaars / Nicole L Kallewaard / Davide Corti / Antonio Lanzavecchia / Steven J Gamblin / Peter B Rosenthal / John J Skehel /
Abstract: Viruses with membranes fuse them with cellular membranes, to transfer their genomes into cells at the beginning of infection. For Influenza virus, the membrane glycoprotein involved in fusion is the ...Viruses with membranes fuse them with cellular membranes, to transfer their genomes into cells at the beginning of infection. For Influenza virus, the membrane glycoprotein involved in fusion is the hemagglutinin (HA), the 3D structure of which is known from X-ray crystallographic studies. The soluble ectodomain fragments used in these studies lacked the "membrane anchor" portion of the molecule. Since this region has a role in membrane fusion, we have determined its structure by analyzing the intact, full-length molecule in a detergent micelle, using cryo-EM. We have also compared the structures of full-length HA-detergent micelles with full-length HA-Fab complex detergent micelles, to describe an infectivity-neutralizing monoclonal Fab that binds near the ectodomain membrane anchor junction. We determine a high-resolution HA structure which compares favorably in detail with the structure of the ectodomain seen by X-ray crystallography; we detect, clearly, all five carbohydrate side chains of HA; and we find that the ectodomain is joined to the membrane anchor by flexible, eight-residue-long, linkers. The linkers extend into the detergent micelle to join a central triple-helical structure that is a major component of the membrane anchor.
History
DepositionSep 4, 2018-
Header (metadata) releaseSep 26, 2018-
Map releaseSep 26, 2018-
UpdateOct 16, 2024-
Current statusOct 16, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 1
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6hjn
  • Surface level: 1
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0234.png

Downloads & links

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Map

FileDownload / File: emd_0234.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map of A/duck/Alberta/35/76 Haemagglutinin Ectodomain
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 512 pix.
= 551.936 Å		1.08 Å/pix.
x 512 pix.
= 551.936 Å		1.08 Å/pix.
x 512 pix.
= 551.936 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.078 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.0 / Movie #1: 1
Minimum - Maximum-2.2043006 - 6.213726
Average (Standard dev.)-0.000038092523 (±0.122444466)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 551.936 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0781.0781.078
M x/y/z512512512
origin x/y/z0.0000.0000.000
length x/y/z551.936551.936551.936
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS512512512
D min/max/mean-2.2046.214-0.000

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Supplemental data

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Mask #1

Fileemd_0234_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Unsharpened map of A/duck/Alberta/35/76 Hemagglutinin Ectodomain

Fileemd_0234_additional.map
AnnotationUnsharpened map of A/duck/Alberta/35/76 Hemagglutinin Ectodomain
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map 1 of A/duck/Alberta/35/76 Hemagglutinin Ectodomain

Fileemd_0234_half_map_1.map
AnnotationHalf Map 1 of A/duck/Alberta/35/76 Hemagglutinin Ectodomain
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map 2 of A/duck/Alberta/35/76 Hemagglutinin Ectodomain

Fileemd_0234_half_map_2.map
AnnotationHalf Map 2 of A/duck/Alberta/35/76 Hemagglutinin Ectodomain
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : A/duck/Alberta/35/76 Hemagglutinin Ectodomain

EntireName: A/duck/Alberta/35/76 Hemagglutinin Ectodomain
Components
  • Complex: A/duck/Alberta/35/76 Hemagglutinin Ectodomain
    • Protein or peptide: Hemagglutinin
    • Protein or peptide: Hemagglutinin
  • Ligand: UNKNOWN BRANCHED FRAGMENT OF PHOSPHOLIPID

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Supramolecule #1: A/duck/Alberta/35/76 Hemagglutinin Ectodomain

SupramoleculeName: A/duck/Alberta/35/76 Hemagglutinin Ectodomain / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Influenza A virus (strain A/Duck/Alberta/35/1976 H1N1)
Molecular weightTheoretical: 170 KDa

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Macromolecule #1: Hemagglutinin

MacromoleculeName: Hemagglutinin / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Influenza A virus (strain A/Duck/Alberta/35/1976 H1N1)
Molecular weightTheoretical: 35.571695 KDa
SequenceString: DTICVGYHAN NSTDTVDTVL EKNVTVTHSV NLLEDSHNGK LCSLNGIAPL QLGKCNVAGW LLGNPECDLL LTANSWSYII ETSNSENGT CYPGEFIDYE ELREQLSSVS SFEKFEIFPK ASSWPNHETT KGVTAACSYS GASSFYRNLL WITKKGTSYP K LSKSYTNN ...String:
DTICVGYHAN NSTDTVDTVL EKNVTVTHSV NLLEDSHNGK LCSLNGIAPL QLGKCNVAGW LLGNPECDLL LTANSWSYII ETSNSENGT CYPGEFIDYE ELREQLSSVS SFEKFEIFPK ASSWPNHETT KGVTAACSYS GASSFYRNLL WITKKGTSYP K LSKSYTNN KGKEVLVLWG VHHPPSVSEQ QSLYQNADAY VSVGSSKYNR RFAPEIAARP KVRGQAGRMN YYWTLLDQGD TI TFEATGN LIAPWYAFAL NKGSDSGIIT SDAPVHNCDT RCQTPHGALN SSLPFQNVHP ITIGECPKYV KSTKLRMATG LRN VPS

UniProtKB: Hemagglutinin

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Macromolecule #2: Hemagglutinin

MacromoleculeName: Hemagglutinin / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Influenza A virus (strain A/Duck/Alberta/35/1976 H1N1)
Molecular weightTheoretical: 19.838834 KDa
SequenceString:
GLFGAIAGFI EGGWTGMIDG WYGYHHQNEQ GSGYAADQKS TQNAIDGITS KVNSVIEKMN TQFTAVGKEF NNLERRIENL NKKVDDGFL DVWTYNAELL VLLENERTLD FHDSNVRNLY EKVKSQLRNN AKEIGNGCFE FYHKCDDECM ESVKNGTYDY P KYSEESKL NREEI

UniProtKB: Hemagglutinin

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Macromolecule #7: UNKNOWN BRANCHED FRAGMENT OF PHOSPHOLIPID

MacromoleculeName: UNKNOWN BRANCHED FRAGMENT OF PHOSPHOLIPID / type: ligand / ID: 7 / Number of copies: 3 / Formula: UPL
Molecular weightTheoretical: 478.92 Da
Chemical component information

ChemComp-UPL:
UNKNOWN BRANCHED FRAGMENT OF PHOSPHOLIPID

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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

Concentration2 mg/mL
BufferpH: 8
Component:
ConcentrationName
25.0 mMTris
150.0 mMNaCl
1.0 mMTCEP
0.01 % (w/v)Azide
0.01 % (w/v)LMNG
0.1 % (w/v)octyl-b-glucoside
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK III

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 43.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 365887
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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