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- PDB-9e6j: DH726-1 Fab bound to hemagglutinin from influenza A/Solomon Islan... -

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Basic information

Entry
Database: PDB / ID: 9e6j
TitleDH726-1 Fab bound to hemagglutinin from influenza A/Solomon Islands/3/2006
Components
  • DH726-1 Fab heavy chain
  • DH726-1 Fab light chain
  • Hemagglutinin
KeywordsVIRAL PROTEIN / immunoglobulin / antibody / 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 speciesAlphainfluenzavirus influenzae
Macaca mulatta (Rhesus monkey)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.98 Å
AuthorsFinney, J. / Harrison, S.C.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI089618 United States
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: To Be Published
Title: IGHV3 encoded hemagglutinin stem rhesus antibodies protects against H1N1 virus by targeting a conserved epitope
Authors: Gu, S. / Finney, J. / Schmidt, A.G. / Vandergrift, N.A. / Luo, K. / Valencia, S.M. / Mielke, D. / Pollara, J. / Zhang, R. / Gurley, T.C. / Armand, L.C. / Von Holle, T.A. / Marshall, D.J. / ...Authors: Gu, S. / Finney, J. / Schmidt, A.G. / Vandergrift, N.A. / Luo, K. / Valencia, S.M. / Mielke, D. / Pollara, J. / Zhang, R. / Gurley, T.C. / Armand, L.C. / Von Holle, T.A. / Marshall, D.J. / Parks, R. / Sutherland, L.L. / Scearce, R.M. / Wiehe, K. / Santra, S. / McGee, C.E. / Yassine, H. / Graham, B.S. / Golding, H. / Kepler, T.B. / Liao, H.-X. / Nair, S.K. / Ferrari, G. / Haynes, B.F. / Harrison, S.C. / Moody, M.A.
History
DepositionOct 30, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 21, 2026Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jan 21, 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
H: DH726-1 Fab heavy chain
L: DH726-1 Fab light chain
B: Hemagglutinin
I: DH726-1 Fab heavy chain
M: DH726-1 Fab light chain
C: Hemagglutinin
J: DH726-1 Fab heavy chain
N: DH726-1 Fab light chain


Theoretical massNumber of molelcules
Total (without water)321,3299
Polymers321,3299
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Hemagglutinin


Mass: 58436.199 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Alphainfluenzavirus influenzae / Strain: A/Solomon Islands/3/2006 / Gene: HA / Cell line (production host): High Five / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A7UPX0
#2: Antibody DH726-1 Fab heavy chain


Mass: 25467.539 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Cell line (production host): Expi293 / Production host: Homo sapiens (human)
#3: Antibody DH726-1 Fab light chain


Mass: 23205.787 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Cell line (production host): High Five / 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: Complex of three DH726-1 Fabs with homotrimeric hemagglutinin
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Alphainfluenzavirus influenzae / Strain: A/Solomon Islands/3/2006
Source (recombinant)Organism: Trichoplusia ni (cabbage looper) / Strain: High Five
Buffer solutionpH: 7.4
SpecimenConc.: 1.5 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

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Electron microscopy imaging

MicroscopyModel: TFS TALOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 36000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 49.99 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
7UCSF ChimeraX1.8model fitting
8Coot0.9.8.91model fitting
14PHENIX1.21.1_5286model refinement
15Coot0.9.8.91model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C3 (3 fold cyclic)
3D reconstructionResolution: 2.98 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 180435 / Symmetry type: POINT
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeSource nameType
15UGY

5ugy

15UGYPDBexperimental model
26XSK

6xsk

16XSKPDBexperimental model
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 46.97 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.002417163
ELECTRON MICROSCOPYf_angle_d0.442223256
ELECTRON MICROSCOPYf_chiral_restr0.04032499
ELECTRON MICROSCOPYf_plane_restr0.00323036
ELECTRON MICROSCOPYf_dihedral_angle_d5.332349

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