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- EMDB-0236: Structure of Full-length Influenza Hemagglutinin (A/duck/Alberta/... -

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Entry
Database: EMDB / ID: EMD-0236
TitleStructure of Full-length Influenza Hemagglutinin (A/duck/Alberta/35/76) in complex with FISW84 Fab Fragment
Map dataSharpened map of full-length Hemagglutinin of A/duck/Alberta/35/76(H1N1) in complex with FISW84 Fab fragment
Sample
  • Complex: Complex of Full-length A/duck/Alberta/35/76 Hemagglutinin and FISW84 Fab Fragment
    • Complex: A/duck/Alberta/35/76 Hemagglutinin
      • Protein or peptide: Hemagglutinin
      • Protein or peptide: Hemagglutinin
    • Complex: FISW84 Fab Fragment
      • Protein or peptide: Heavy chain of FISW84 Fab
      • Protein or peptide: Light chain of FISW84 Fab
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 / apical plasma membrane / 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) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.1 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 9, 2024-
Current statusOct 9, 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
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  • Surface view colored by cylindrical radius
  • Surface level: 1
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6hjq
  • Surface level: 1
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0236.png

Downloads & links

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Map

FileDownload / File: emd_0236.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map of full-length Hemagglutinin of A/duck/Alberta/35/76(H1N1) in complex with FISW84 Fab fragment
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-2.234049 - 4.7277756
Average (Standard dev.)0.0032642235 (±0.17477667)
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-2.2344.7280.003

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Supplemental data

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Mask #1

Fileemd_0236_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 full-length Hemagglutinin of A/duck/Alberta/35/76(H1N1) in...

Fileemd_0236_additional_1.map
AnnotationUnsharpened map of full-length Hemagglutinin of A/duck/Alberta/35/76(H1N1) in complex with FISW84 Fab fragment
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Sharpened map used to build linker region of...

Fileemd_0236_additional_2.map
AnnotationSharpened map used to build linker region of full-length Hemagglutinin of A/duck/Alberta/35/76(H1N1) in complex with FISW84 Fab fragment
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map 1 of full-length Hemagglutinin of A/duck/Alberta/35/76(H1N1) in...

Fileemd_0236_half_map_1.map
AnnotationHalf-map 1 of full-length Hemagglutinin of A/duck/Alberta/35/76(H1N1) in complex with FISW84 Fab fragment
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map 2 of full-length Hemagglutinin of A/duck/Alberta/35/76(H1N1) in...

Fileemd_0236_half_map_2.map
AnnotationHalf-map 2 of full-length Hemagglutinin of A/duck/Alberta/35/76(H1N1) in complex with FISW84 Fab fragment
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Complex of Full-length A/duck/Alberta/35/76 Hemagglutinin and FIS...

EntireName: Complex of Full-length A/duck/Alberta/35/76 Hemagglutinin and FISW84 Fab Fragment
Components
  • Complex: Complex of Full-length A/duck/Alberta/35/76 Hemagglutinin and FISW84 Fab Fragment
    • Complex: A/duck/Alberta/35/76 Hemagglutinin
      • Protein or peptide: Hemagglutinin
      • Protein or peptide: Hemagglutinin
    • Complex: FISW84 Fab Fragment
      • Protein or peptide: Heavy chain of FISW84 Fab
      • Protein or peptide: Light chain of FISW84 Fab

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Supramolecule #1: Complex of Full-length A/duck/Alberta/35/76 Hemagglutinin and FIS...

SupramoleculeName: Complex of Full-length A/duck/Alberta/35/76 Hemagglutinin and FISW84 Fab Fragment
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Molecular weightTheoretical: 300 KDa

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Supramolecule #2: A/duck/Alberta/35/76 Hemagglutinin

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

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Supramolecule #3: FISW84 Fab Fragment

SupramoleculeName: FISW84 Fab Fragment / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3-#4
Source (natural)Organism: Homo sapiens (human)

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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: 35.684852 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 VPSI

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: 22.991572 KDa
SequenceString: GLFGAIAGFI EGGWTGMIDG WYGYHHQNEQ GSGYAADQKS TQNAIDGITS KVNSVIEKMN TQFTAVGKEF NNLERRIENL NKKVDDGFL DVWTYNAELL VLLENERTLD FHDSNVRNLY EKVKSQLRNN AKEIGNGCFE FYHKCDDECM ESVKNGTYDY P KYSEESKL ...String:
GLFGAIAGFI EGGWTGMIDG WYGYHHQNEQ GSGYAADQKS TQNAIDGITS KVNSVIEKMN TQFTAVGKEF NNLERRIENL NKKVDDGFL DVWTYNAELL VLLENERTLD FHDSNVRNLY EKVKSQLRNN AKEIGNGCFE FYHKCDDECM ESVKNGTYDY P KYSEESKL NREEIDGVKL ESMGVYQILA IYSTVASSLV LLVSL

UniProtKB: Hemagglutinin

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Macromolecule #3: Heavy chain of FISW84 Fab

MacromoleculeName: Heavy chain of FISW84 Fab / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 22.925875 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: EVQLLESGGG LVQPGGSLRL SCAASGFTFS SYGMAWVRQA PGKGLEWVSF ISATGLSTYF ADSVKGRFTI SRDTTKNTLY LQMNSLRAD DTAVYFCARM RRTMIAFGGN DFWGQGTLVT VSSASTKGPS VFPLAPSGTA ALGCLVKDYF PEPVTVSWNS G ALTSGVHT ...String:
EVQLLESGGG LVQPGGSLRL SCAASGFTFS SYGMAWVRQA PGKGLEWVSF ISATGLSTYF ADSVKGRFTI SRDTTKNTLY LQMNSLRAD DTAVYFCARM RRTMIAFGGN DFWGQGTLVT VSSASTKGPS VFPLAPSGTA ALGCLVKDYF PEPVTVSWNS G ALTSGVHT FPAVLQSSGL YSLSSVVTVP SSSLGTQTYI CNVNHKPSNT KVDKRVEP

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Macromolecule #4: Light chain of FISW84 Fab

MacromoleculeName: Light chain of FISW84 Fab / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.277766 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: EVVMTQSPAT LSVSPGEGAT LSCRASQSVN TNVAWYQQKP GQAPRLLIYG ASTRATGIPA RFSGSGSGTE FTLTISTLQS EDFAVYYCQ QYSNWPPITF GQGTRLEIKR TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD ...String:
EVVMTQSPAT LSVSPGEGAT LSCRASQSVN TNVAWYQQKP GQAPRLLIYG ASTRATGIPA RFSGSGSGTE FTLTISTLQS EDFAVYYCQ QYSNWPPITF GQGTRLEIKR TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD SKDSTYSLSS TLTLSKADYE KHKVYACEVT HQGLSSPVTK SFNRGE

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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

Concentration1.5 mg/mL
BufferpH: 8
Component:
ConcentrationName
25.0 mMTris
150.0 mMNaCl
1.0 mMTCEP
0.01 % (w/v)Azide
0.002 % (w/v)MNA-C12
0.1 % (w/v)octyl-b-glucoside
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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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: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 23286
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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