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- PDB-9osr: Structure of Fab HB420 in complex with influenza H3N2 A/Moscow/10... -

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Basic information

Entry
Database: PDB / ID: 9osr
TitleStructure of Fab HB420 in complex with influenza H3N2 A/Moscow/10/1999 neuraminidase
Components
  • Neuraminidase
  • Variable domain of the heavy chain of Fab hb420
  • Variable domain of the light chain of Fab HB420
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / Influenza / Neuraminidase / Antibody / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


exo-alpha-sialidase / exo-alpha-sialidase activity / viral budding from plasma membrane / carbohydrate metabolic process / host cell plasma membrane / virion membrane / metal ion binding / membrane
Similarity search - Function
Sialidase, Influenza viruses A/B / Glycoside hydrolase, family 34 / Neuraminidase / Sialidase superfamily
Similarity search - Domain/homology
Biological speciesInfluenza A virus
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.16 Å
AuthorsLv, H. / Wu, N.C.
Funding support United States, 1items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI)Emerging Pathogens Initiative United States
CitationJournal: To Be Published
Title: Evolution of antibody cross-reactivity to influenza H5N1 neuraminidase from an N2-specific germline
Authors: Lv, H. / Wu, N.C.
History
DepositionMay 25, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 1, 2025Provider: repository / Type: Initial release
Revision 1.0Oct 1, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Oct 1, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Oct 1, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Oct 1, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Oct 1, 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

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Assembly

Deposited unit
A: Neuraminidase
B: Neuraminidase
C: Neuraminidase
D: Neuraminidase
J: Variable domain of the heavy chain of Fab hb420
H: Variable domain of the heavy chain of Fab hb420
N: Variable domain of the light chain of Fab HB420
K: Variable domain of the heavy chain of Fab hb420
L: Variable domain of the light chain of Fab HB420
R: Variable domain of the light chain of Fab HB420
I: Variable domain of the heavy chain of Fab hb420
M: Variable domain of the light chain of Fab HB420


Theoretical massNumber of molelcules
Total (without water)271,09312
Polymers271,09312
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
Neuraminidase


Mass: 42767.715 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Gene: NA / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q8AZ87, exo-alpha-sialidase
#2: Antibody
Variable domain of the heavy chain of Fab hb420


Mass: 13544.985 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Antibody
Variable domain of the light chain of Fab HB420


Mass: 11460.441 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / 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: Structure of Fab HB420 in complex with influenza H3N2 A/Moscow/10/1999 neuraminidase
Type: COMPLEX
Details: Neuraminidase was expressed recombinantly in SF9 cells. Fab HB420 was expressed recombinantly in Expi293F cells.
Entity ID: all / Source: MULTIPLE SOURCES
Molecular weightValue: 0.35 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
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 piror to applying on 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: 2.16 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 355667 / Symmetry type: POINT

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