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- EMDB-31916: 2.56 A structure of influenza hemagglutinin (HA) trimer -

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Basic information

Entry
Database: EMDB / ID: EMD-31916
Title2.56 A structure of influenza hemagglutinin (HA) trimer
Map data
Sample
  • Complex: Influenza hemagglutinin (HA) trimer
    • Protein or peptide: Hemagglutinin
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: beta-D-mannopyranose
KeywordsInfluenza hemagglutinin (HA) trimer / 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
Biological speciesH3N2 subtype (virus) / Influenza A virus (strain A/Hong Kong/1/1968 H3N2)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.56 Å
AuthorsFan HC / Zhang Y
Funding support China, 5 items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2017YFA0504700 China
National Natural Science Foundation of China (NSFC)31830020 China
Chinese Academy of SciencesXDB37040102 China
National Natural Science Foundation of China (NSFC)31925026 China
Ministry of Science and Technology (MoST, China)2015DFG32140 China
CitationJournal: Nat Commun / Year: 2021
Title: A cryo-electron microscopy support film formed by 2D crystals of hydrophobin HFBI.
Authors: Hongcheng Fan / Bo Wang / Yan Zhang / Yun Zhu / Bo Song / Haijin Xu / Yujia Zhai / Mingqiang Qiao / Fei Sun /
Abstract: Cryo-electron microscopy (cryo-EM) has become a powerful tool to resolve high-resolution structures of biomacromolecules in solution. However, air-water interface induced preferred orientations, ...Cryo-electron microscopy (cryo-EM) has become a powerful tool to resolve high-resolution structures of biomacromolecules in solution. However, air-water interface induced preferred orientations, dissociation or denaturation of biomacromolecules during cryo-vitrification remains a limiting factor for many specimens. To solve this bottleneck, we developed a cryo-EM support film using 2D crystals of hydrophobin HFBI. The hydrophilic side of the HFBI film adsorbs protein particles via electrostatic interactions and sequesters them from the air-water interface, allowing the formation of sufficiently thin ice for high-quality data collection. The particle orientation distribution can be regulated by adjusting the buffer pH. Using this support, we determined the cryo-EM structures of catalase (2.29 Å) and influenza haemagglutinin trimer (2.56 Å), which exhibited strong preferred orientations using a conventional cryo-vitrification protocol. We further show that the HFBI film is suitable to obtain high-resolution structures of small proteins, including aldolase (150 kDa, 3.28 Å) and haemoglobin (64 kDa, 3.6 Å). Our work suggests that HFBI films may have broad future applications in increasing the success rate and efficiency of cryo-EM.
History
DepositionSep 6, 2021-
Header (metadata) releaseDec 29, 2021-
Map releaseDec 29, 2021-
UpdateJun 25, 2025-
Current statusJun 25, 2025Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.7
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.7
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7vdf
  • Surface level: 0.7
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_31916.png

Downloads & links

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Map

FileDownload / File: emd_31916.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.76 Å/pix.
x 320 pix.
= 243.2 Å		0.76 Å/pix.
x 320 pix.
= 243.2 Å		0.76 Å/pix.
x 320 pix.
= 243.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.76 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.55 / Movie #1: 0.7
Minimum - Maximum-5.0341797 - 7.05403
Average (Standard dev.)0.0018207382 (±0.15143873)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 243.2 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.760.760.76
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z243.200243.200243.200
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ480480480
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-5.0347.0540.002

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Supplemental data

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Half map: #1

Fileemd_31916_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_31916_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : Influenza hemagglutinin (HA) trimer

EntireName: Influenza hemagglutinin (HA) trimer
Components
  • Complex: Influenza hemagglutinin (HA) trimer
    • Protein or peptide: Hemagglutinin
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: beta-D-mannopyranose

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Supramolecule #1: Influenza hemagglutinin (HA) trimer

SupramoleculeName: Influenza hemagglutinin (HA) trimer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: H3N2 subtype (virus)
Molecular weightTheoretical: 190 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/Hong Kong/1/1968 H3N2)
Strain: A/Hong Kong/1/1968 H3N2
Molecular weightTheoretical: 62.855215 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QDLPGNDNST ATLCLGHHAV PNGTLVKTIT DDQIEVTNAT ELVQSSSTGK ICNNPHRILD GIDCTLIDAL LGDPHCDVFQ NETWDLFVE RSKAFSNCYP YDVPDYASLR SLVASSGTLE FITEGFTWTG VTQNGGSNAC KRGPGSGFFS RLNWLTKSGS T YPVLNVTM ...String:
QDLPGNDNST ATLCLGHHAV PNGTLVKTIT DDQIEVTNAT ELVQSSSTGK ICNNPHRILD GIDCTLIDAL LGDPHCDVFQ NETWDLFVE RSKAFSNCYP YDVPDYASLR SLVASSGTLE FITEGFTWTG VTQNGGSNAC KRGPGSGFFS RLNWLTKSGS T YPVLNVTM PNNDNFDKLY IWGVHHPSTN QEQTSLYVQA SGRVTVSTRR SQQTIIPNIG SRPWVRGLSS RISIYWTIVK PG DVLVINS NGNLIAPRGY FKMRTGKSSI MRSDAPIDTC ISECITPNGS IPNDKPFQNV NKITYGACPK YVKQNTLKLA TGM RNVPEK QTRGLFGAIA GFIENGWEGM IDGWYGFRHQ NSEGTGQAAD LKSTQAAIDQ INGKLNRVIE KTNEKFHQIE KEFS EVEGR IQDLEKYVED TKIDLWSYNA ELLVALENQH TIDLTDSEMN KLFEKTRRQL RENAEDMGNG CFKIYHKCDN ACIES IRNG TYDHDVYRDE ALNNRFQIKG VELKSGYDGG GGTGGGGTGR MKQIEDKIEE ILSKIYHIEN EIARIKKLIG ERHHHH HH

UniProtKB: Hemagglutinin

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Macromolecule #2: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 2 / Number of copies: 12 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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Macromolecule #3: beta-D-mannopyranose

MacromoleculeName: beta-D-mannopyranose / type: ligand / ID: 3 / Number of copies: 3 / Formula: BMA
Molecular weightTheoretical: 180.156 Da
Chemical component information

ChemComp-BMA:
beta-D-mannopyranose

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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
GridMaterial: NICKEL/TITANIUM / Mesh: 300
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: SUPER-RESOLUTION / Number real images: 4574 / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal magnification: 165000
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1213983
CTF correctionSoftware: (Name: Gctf (ver. 1.06), cryoSPARC) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: EMDB MAP
EMDB ID:

21954

Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.56 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 196464
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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