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- PDB-9cu7: Structure of 16.ND.92 Fab in complex with A/Solomon Islands/3/200... -

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Basic information

Entry
Database: PDB / ID: 9cu7
TitleStructure of 16.ND.92 Fab in complex with A/Solomon Islands/3/2006(H1N1) influenza virus Hemagglutinin
Components
  • Hemagglutinin HA1
  • Hemagglutinin HA2
  • Variable Heavy Chain of 16.ND.92 Fab
  • Variable Light Chain of 16.ND.92 Fab
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / Antibody / Influenza / 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
Hemagglutinin / Hemagglutinin
Similarity search - Component
Biological speciesHomo sapiens (human)
Influenza A virus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.82 Å
AuthorsOuyang, W.O. / Pholcharee, T. / Wu, N.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Center for Complementary and Integrative Health (NIH/NCCIH)DP2 AT011966 United States
CitationJournal: To Be Published
Title: Structure of 16.ND.92 Fab in complex with A/Solomon Islands/3/2006(H1N1) influenza virus Hemagglutinin
Authors: Ouyang, W.O. / Pholcharee, T. / Wu, N.C.
History
DepositionJul 25, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 30, 2025Provider: repository / Type: Initial release
Revision 1.0Jul 30, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 30, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jul 30, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 30, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 30, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 30, 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
H: Variable Heavy Chain of 16.ND.92 Fab
I: Variable Heavy Chain of 16.ND.92 Fab
J: Variable Heavy Chain of 16.ND.92 Fab
L: Variable Light Chain of 16.ND.92 Fab
M: Variable Light Chain of 16.ND.92 Fab
N: Variable Light Chain of 16.ND.92 Fab
A: Hemagglutinin HA1
C: Hemagglutinin HA1
E: Hemagglutinin HA1
B: Hemagglutinin HA2
D: Hemagglutinin HA2
F: Hemagglutinin HA2


Theoretical massNumber of molelcules
Total (without water)242,17012
Polymers242,17012
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, size exclusion chromatography indicated the correct assembly
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Antibody Variable Heavy Chain of 16.ND.92 Fab


Mass: 13659.272 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)
#2: Antibody Variable Light Chain of 16.ND.92 Fab


Mass: 11800.195 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: Protein Hemagglutinin HA1


Mass: 35851.199 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/Solomon Islands/3/2006(H1N1))
Gene: HA / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A0A0G2RTI0
#4: Protein Hemagglutinin HA2


Mass: 19412.537 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/Solomon Islands/3/2006(H1N1))
Gene: HA / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: C8CQF2
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: 16.ND.92 Fab in complex with A/Solomon Islands/3/2006 (H1N1) Hemagglutinin
Type: COMPLEX
Details: Both Hemagglutinin and Fab were recombinantly expressed and purified. The Fab was then mixed with Hemagglutinin at 3.5:1 ratio. The complex were then isolated using size exclusion chromatography.
Entity ID: all / Source: MULTIPLE SOURCES
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human) / Cell: Expi293F
Buffer solutionpH: 7.5 / Details: 20mM Tris-HCl, 150mM NaCl
SpecimenConc.: 3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 277 K
Details: Blot force: 0, Blot time: 3 s, Humidity 90%, and 4 C.

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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 defocus max: 5000 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 57.35 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.5.3particle selection
4cryoSPARC4.5.3CTF correction
10cryoSPARC4.5.3initial Euler assignment
11cryoSPARC4.5.3final Euler assignment
13cryoSPARC4.5.33D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.82 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 152449 / Symmetry type: POINT

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