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- PDB-9n8p: Subtomogram average of dimers of influenza HA trimers -

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Basic information

Entry
Database: PDB / ID: 9n8p
TitleSubtomogram average of dimers of influenza HA trimers
Components
  • Hemagglutinin
  • Hemagglutinin HA2 chain
KeywordsVIRAL PROTEIN / Hemagglutinin
Function / homology
Function and homology information


Transport of HA trimer, NA tetramer and M2 tetramer from the endoplasmic reticulum to the Golgi Apparatus / Assembly of Viral Components at the Budding Site / Influenza Infection / Fusion of the Influenza Virion to the Host Cell Endosome / Release / Budding / Packaging of Eight RNA Segments / Uncoating of the Influenza Virion / Entry of Influenza Virion into Host Cell via Endocytosis / Viral mRNA Translation ...Transport of HA trimer, NA tetramer and M2 tetramer from the endoplasmic reticulum to the Golgi Apparatus / Assembly of Viral Components at the Budding Site / Influenza Infection / Fusion of the Influenza Virion to the Host Cell Endosome / Release / Budding / Packaging of Eight RNA Segments / Uncoating of the Influenza Virion / Entry of Influenza Virion into Host Cell via Endocytosis / Viral mRNA Translation / viral budding from plasma membrane / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / 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 / extracellular region / plasma 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
MethodELECTRON MICROSCOPY / subtomogram averaging / cryo EM / Resolution: 9 Å
AuthorsHuang, Q.J. / Song, K. / Schiffer, C.A. / Somasundaran, M.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM143773 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM151996 United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2025
Title: Virion-associated influenza hemagglutinin clusters upon sialic acid binding visualized by cryoelectron tomography.
Authors: Qiuyu J Huang / Ryan Kim / Kangkang Song / Nikolaus Grigorieff / James B Munro / Celia A Schiffer / Mohan Somasundaran /
Abstract: Influenza viruses are enveloped, negative-sense single-stranded RNA viruses covered in a dense layer of glycoproteins. Hemagglutinin (HA) accounts for 80 to 90% of influenza glycoprotein and plays a ...Influenza viruses are enveloped, negative-sense single-stranded RNA viruses covered in a dense layer of glycoproteins. Hemagglutinin (HA) accounts for 80 to 90% of influenza glycoprotein and plays a role in host cell binding and membrane fusion. While previous studies have characterized structures of purified receptor-free and receptor-bound HA, the effect of receptor binding on HA organization and structure on virions remains unknown. Here, we used cryoelectron tomography to visualize influenza virions bound to a sialic acid receptor mimic. Overall, receptor binding did not result in significant changes in viral morphology; however, we observed rearrangements of HA trimer organization and orientation. Compared to the even interglycoprotein spacing of unliganded HA trimers, receptor binding promotes HA trimer clustering and the formation of a triplet of trimers. Subtomogram averaging and refinement yielded 8 to 10 Å reconstructions that allowed us to visualize specific contacts between HAs from neighboring trimers and identify molecular features that mediate clustering. Taken together, we present structural evidence that receptor binding triggers clustering of HA trimers, revealing an additional layer of HA dynamics and plasticity.
History
DepositionFeb 9, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 16, 2025Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hemagglutinin
B: Hemagglutinin HA2 chain
C: Hemagglutinin
D: Hemagglutinin HA2 chain
E: Hemagglutinin
F: Hemagglutinin HA2 chain
G: Hemagglutinin
H: Hemagglutinin HA2 chain
I: Hemagglutinin
J: Hemagglutinin HA2 chain
K: Hemagglutinin
L: Hemagglutinin HA2 chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)332,68218
Polymers329,85412
Non-polymers2,8286
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Hemagglutinin


Mass: 36733.402 Da / Num. of mol.: 6 / Source method: isolated from a natural source
Source: (natural) Influenza A virus (A/Puerto Rico/8/1934(H1N1))
Strain: A/Puerto Rico/8/1934 / References: UniProt: P03452
#2: Protein
Hemagglutinin HA2 chain


Mass: 18242.221 Da / Num. of mol.: 6 / Source method: isolated from a natural source
Source: (natural) Influenza A virus (A/Puerto Rico/8/1934(H1N1))
Strain: A/Puerto Rico/8/1934 / References: UniProt: P03452
#3: Polysaccharide
N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose


Type: oligosaccharide / Mass: 471.411 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DNeup5Aca2-6DGalpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCC/3=O]/1-2/a6-b2WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-Galp]{[(6+2)][a-D-Neup5Ac]{}}LINUCSPDB-CARE
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: subtomogram averaging

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Sample preparation

ComponentName: Influenza A virus (A/Puerto Rico/8/1934(H1N1)) / Type: VIRUS
Details: Virus produced in embryonated eggs and purified from allantoic fluid.
Entity ID: #1-#2 / Source: NATURAL
Source (natural)Organism: Influenza A virus (A/Puerto Rico/8/1934(H1N1)) / Strain: A/Puerto Rico/8/1934
Details of virusEmpty: NO / Enveloped: YES / Isolate: STRAIN / Type: VIRION
Buffer solutionpH: 7.4
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: Virus was incubated with Sialylneolacto-N-tetraose c (LSTc) at a final concentration of 100 um
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/2
VitrificationInstrument: EMS-002 RAPID IMMERSION FREEZER / Cryogen name: ETHANE-PROPANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 42000 X / Nominal defocus max: 6000 nm / Nominal defocus min: 3000 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 1.86 e/Å2 / Avg electron dose per subtomogram: 120 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1Warpvolume selection
2SerialEMimage acquisition
7UCSF ChimeraXmodel fitting
10RELION4final Euler assignment
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 9283 / Symmetry type: POINT
EM volume selectionNum. of tomograms: 16 / Num. of volumes extracted: 26500
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Details: Rigid body docking was performed in ChimeraX. Phenix was used for flexible real space refinement and Schrodinger Protein Preparation Wizard was used to perform final energy minimization.
Atomic model buildingPDB-ID: 1RVZ

1rvz


Accession code: 1RVZ / Source name: PDB / Type: experimental model

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