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- EMDB-70657: Influenza A Virus Group 2 Hemagglutinin (H7, Strain SH13) in Comp... -

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Basic information

Entry
Database: EMDB / ID: EMD-70657
TitleInfluenza A Virus Group 2 Hemagglutinin (H7, Strain SH13) in Complex with the Potent Small-Molecule Entry Inhibitor SA-67
Map dataEM map for model building and refinement
Sample
  • Virus: Influenza A virus
    • Protein or peptide: Hemagglutinin HA1
    • Protein or peptide: Hemagglutinin HA2
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: (4R)-N-cyclohexyl-2-(4-fluorophenyl)imidazo[1,2-a]pyrimidin-3-amine
KeywordsInfluenza A Virus / Hemagglutinin / Complex / Small-Molecule Inhibitor / Entry / SA-67 / VIRAL PROTEIN-INHIBITOR complex
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 speciesInfluenza A virus
Methodsingle particle reconstruction / cryo EM / Resolution: 2.77 Å
AuthorsXu Y / Xu K
Funding support United States, 1 items
OrganizationGrant numberCountry
Not funded United States
CitationJournal: To Be Published
Title: Mechanistic Insights into the Small Molecule Inhibition of Influenza A Virus Entry
Authors: Xu Y / Anirudhan V / Rong L / Xu K
History
DepositionMay 15, 2025-
Header (metadata) releaseJul 16, 2025-
Map releaseJul 16, 2025-
UpdateJul 16, 2025-
Current statusJul 16, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_70657.png

Downloads & links

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Map

FileDownload / File: emd_70657.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationEM map for model building and refinement
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.9 Å/pix.
x 360 pix.
= 323.64 Å		0.9 Å/pix.
x 360 pix.
= 323.64 Å		0.9 Å/pix.
x 360 pix.
= 323.64 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.899 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-0.2956314 - 0.66462237
Average (Standard dev.)0.0003084206 (±0.014581223)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 323.63998 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_70657_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map A

Fileemd_70657_half_map_1.map
Annotationhalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map B

Fileemd_70657_half_map_2.map
Annotationhalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Influenza A virus

EntireName: Influenza A virus
Components
  • Virus: Influenza A virus
    • Protein or peptide: Hemagglutinin HA1
    • Protein or peptide: Hemagglutinin HA2
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: (4R)-N-cyclohexyl-2-(4-fluorophenyl)imidazo[1,2-a]pyrimidin-3-amine

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Supramolecule #1: Influenza A virus

SupramoleculeName: Influenza A virus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 / NCBI-ID: 11320 / Sci species name: Influenza A virus / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: Yes

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Macromolecule #1: Hemagglutinin HA1

MacromoleculeName: Hemagglutinin HA1 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Influenza A virus
Molecular weightTheoretical: 36.526305 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MNTQILVFAL IAIIPTNADK ICLGHHAVSN GTKVNTLCER GVEVVNATET VERTNIPRIC SKGKRTVDLG QCGLLGTITG PPQCDQFLE FSADLIIERR EGSDVCYPGK FVNEEALRQI LRESGGIDKE AMGFTYSGIR TNGATSSCRR SGSSFYAEMK W LLSNTDNA ...String:
MNTQILVFAL IAIIPTNADK ICLGHHAVSN GTKVNTLCER GVEVVNATET VERTNIPRIC SKGKRTVDLG QCGLLGTITG PPQCDQFLE FSADLIIERR EGSDVCYPGK FVNEEALRQI LRESGGIDKE AMGFTYSGIR TNGATSSCRR SGSSFYAEMK W LLSNTDNA AFPQMTKSYK NTRKNPALIV WGIHHSGSTA EQTKLYGSGN KLVTVGSSNY QQSFVPSPGA RTQVNGQSGR ID FHWLMLN PNDTVTFSFN GAFIAPDRAS FLRGKSMGIQ SGVQVDADCE GDCYYSGGTI ISNLPFQNID SRAVGKCPRY VKQ RSLLLA TGMKNVPEI

UniProtKB: Hemagglutinin

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Macromolecule #2: Hemagglutinin HA2

MacromoleculeName: Hemagglutinin HA2 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Influenza A virus
Molecular weightTheoretical: 19.850803 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
GLFGAIAGFI ENGWEGLIDG WYGFRHQNAQ GEGTAADYKS TQSAIDCITG KLNRLIEKTN QQFELIDNEF TEVEKQIGNV INWTRDSIT EVWSYNAELL VAMENQHTID LADSEMDKLY ERVKRQLREN AEEDGTGCFE IFHKCDDDCM ASIRNNTYDH S KYREEAMQ NRIQ

UniProtKB: Hemagglutinin

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Macromolecule #4: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / Number of copies: 9 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

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Macromolecule #5: (4R)-N-cyclohexyl-2-(4-fluorophenyl)imidazo[1,2-a]pyrimidin-3-amine

MacromoleculeName: (4R)-N-cyclohexyl-2-(4-fluorophenyl)imidazo[1,2-a]pyrimidin-3-amine
type: ligand / ID: 5 / Number of copies: 3 / Formula: A1CC2
Molecular weightTheoretical: 310.369 Da

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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: 7.2 / Details: 5mM HEPES buffer pH7.2, 150nM NaCl
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 273 K / Instrument: FEI VITROBOT MARK IV
Details1mg/ml in HBS buffer, purfied from HEK293 recombinant expression and purified with NiNTA resin via Hisx6 tag

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 81000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 6403039
CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.77 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 155278
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
Final 3D classificationNumber classes: 3

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Atomic model buiding 1

Initial modelPDB ID:

8tnl


Chain - Source name: PDB / Chain - Initial model type: experimental model / Details: complete model of PDB 8TNL
RefinementProtocol: OTHER / Overall B value: 112
Output model

PDB-9onz:
Influenza A Virus Group 2 Hemagglutinin (H7, Strain SH13) in Complex with the Potent Small-Molecule Entry Inhibitor SA-67

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