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- PDB-9ost: Structure of human Fab HB34 in complex with influenza H1N1 A/Solo... -

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Basic information

Entry
Database: PDB / ID: 9ost
TitleStructure of human Fab HB34 in complex with influenza H1N1 A/Solomon Island/3/2006 hemagglutinin
Components
  • (Heavy chain of ...) x 2
  • (Hemagglutinin ...) x 2
  • (Light chain of ...) x 2
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / Influenza / Hemagglutinin / Antibody / Immune response / 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 speciesInfluenza A virus
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.64 Å
AuthorsLv, H. / Pholcharee, T. / 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: Structures of three IGHV3-23 broadly neutralizing antibodies targeting the HA stem of H1N1 and H5N1 influenza viruses
Authors: Lv, H. / Pholcharee, T. / Wu, N.C.
History
DepositionMay 26, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 17, 2026Provider: repository / Type: Initial release
Revision 1.0Jun 17, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jun 17, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 17, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 17, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 17, 2026Data 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 HA1
B: Hemagglutinin HA2
C: Hemagglutinin HA1
D: Hemagglutinin HA2
E: Hemagglutinin HA1
F: Hemagglutinin HA2
H: Heavy chain of Fab from human antibody HB34
I: Light chain of Fab from human antibody HB31
J: Heavy chain of Fab from human antibody HB34
K: Light chain of Fab from human antibody HB31
M: Heavy chain of Fab from human antibody HB34
N: Light chain of Fab from human antibody HB31
O: Heavy chain of FISW84 Fab
P: Light chain of FISW84
R: Heavy chain of FISW84 Fab
S: Light chain of FISW84
X: Heavy chain of FISW84 Fab
Y: Light chain of FISW84


Theoretical massNumber of molelcules
Total (without water)335,64318
Polymers335,64318
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

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Hemagglutinin ... , 2 types, 6 molecules ACEBDF

#1: Protein Hemagglutinin HA1


Mass: 36379.801 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Gene: HA / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A0A0G2RTI0
#2: Protein Hemagglutinin HA2


Mass: 25066.264 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Gene: HA / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: D9TZS3

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Antibody , 4 types, 12 molecules HJMIKNORXPSY

#3: Antibody Heavy chain of Fab from human antibody HB34


Mass: 13816.316 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#4: Antibody Light chain of Fab from human antibody HB31


Mass: 11442.464 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#5: Antibody Heavy chain of FISW84 Fab


Mass: 13197.892 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#6: Antibody Light chain of FISW84


Mass: 11978.316 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

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Details

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: A complex of hemagglutinin from influenza A strain A/Solomon Island/3/2006 with human Fab HB31
Type: COMPLEX
Details: Hemagglutinin was expressed recombinantly in SF9 cells. Fab HB31 was expressed recombinantly in Expi293F cells.
Entity ID: #1-#4 / Source: MULTIPLE SOURCES
Molecular weightValue: 0.489 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
SpecimenConc.: 3 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
2PHENIX1.20.1_4487model refinement
11cryoSPARC4.5final Euler assignment
13cryoSPARC4.53D reconstruction
CTF correctionType: NONE
3D reconstructionResolution: 2.64 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 304985 / Symmetry type: POINT

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