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- PDB-9n4f: Structure of 240-14-IgA_2F02 Fab in complex with influenza H3N8 A... -

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Basic information

Entry
Database: PDB / ID: 9n4f
TitleStructure of 240-14-IgA_2F02 Fab in complex with influenza H3N8 A/Mallard/Alberta/362/2017 Hemagglutinin
Components
  • Hemagglutinin
  • Variable domain of the heavy chain of 240-14-IgA_2F02 Fab
  • Variable domain of the light chain of 240-14-IgA_2F02 Fab
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / Influenza / Antibody / Immune system / Hemagglutinin / VIRAL PROTEIN-IMMUNE SYSTEM 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
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.71 Å
AuthorsGopal, A.B. / Wu, N.C. / Lv, H. / Pholcharee, T.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI167910 United States
CitationJournal: To Be Published
Title: Structure of 240-14-IgA_2F02 Fab in complex with influenza H3N8 A/Mallard/Alberta/362/2017 Hemagglutinin
Authors: Gopal, A.B. / Wu, N.C. / Lv, H. / Pholcharee, T.
History
DepositionFeb 2, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 8, 2025Provider: repository / Type: Initial release
Revision 1.0Oct 8, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Oct 8, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Oct 8, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Oct 8, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Oct 8, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hemagglutinin
B: Hemagglutinin
H: Variable domain of the heavy chain of 240-14-IgA_2F02 Fab
L: Variable domain of the light chain of 240-14-IgA_2F02 Fab
C: Hemagglutinin
D: Hemagglutinin
M: Variable domain of the heavy chain of 240-14-IgA_2F02 Fab
N: Variable domain of the light chain of 240-14-IgA_2F02 Fab
E: Hemagglutinin
F: Hemagglutinin
O: Variable domain of the heavy chain of 240-14-IgA_2F02 Fab
P: Variable domain of the light chain of 240-14-IgA_2F02 Fab


Theoretical massNumber of molelcules
Total (without water)407,46612
Polymers407,46612
Non-polymers00
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: 55449.852 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/Mallard/Alberta/362/2017 / Gene: HA / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A0A2Z4WF96
#2: Antibody Variable domain of the heavy chain of 240-14-IgA_2F02 Fab


Mass: 13487.812 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): EXPI 293F / Production host: Homo sapiens (human)
#3: Antibody Variable domain of the light chain of 240-14-IgA_2F02 Fab


Mass: 11434.602 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): EXPI 293F / Production host: Homo sapiens (human)
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: 240-14-IgA_2F02 Fab in complex with influenza H3N8 A/Mallard/Alberta/362/2017 hemagglutinin
Type: COMPLEX
Details: Hemagglutinin was expressed recombinantly in SF9 cells. 240-14-IgA_2F02 Fab was expressed recombinantly in Expi293F cells.
Entity ID: all / Source: MULTIPLE SOURCES
Molecular weightValue: 0.42 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 8 / Details: 20 mM Tris-HCl, 100 mM NaCl, 10 mM CaCl2, pH 8.0
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: The sample was also mixed with octyl glucoside to 0.1% w/v of the detergent final concentration prior to applying to the grid.
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 277.15 K

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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: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm
Image recordingElectron dose: 57.35 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.5particle selection
10cryoSPARC4.5initial Euler assignment
11cryoSPARC4.5final Euler assignment
13cryoSPARC4.53D reconstruction
CTF correctionType: NONE
3D reconstructionResolution: 2.71 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 120986 / Symmetry type: POINT

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