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- PDB-7dkj: Hemagglutinin Influenza A virus (A/Okuda/1957(H2N2) bound with a ... -

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Basic information

Entry
Database: PDB / ID: 7dkj
TitleHemagglutinin Influenza A virus (A/Okuda/1957(H2N2) bound with a neutralizing antibody
Components
  • Fv-clasp heavy chain
  • Fv-clasp light chain
  • Hemagglutinin
KeywordsVIRAL PROTEIN / neutralizing antibody / Influenza A virus / Hemagglutinin / Fv-clasp / Okuda
Function / homology
Function and homology information


viral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / host cell surface receptor binding / apical plasma membrane / 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
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
Mus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsShirouzu, M.
CitationJournal: To Be Published
Title: Hemagglutinin Influenza A virus (A/Okuda/1957(H2N2) bound with a neutralizing antibody
Authors: Makino-Okamura, C. / Hata, H. / Watanabe, T. / Kim, S. / Hebrard, M. / Sato, R. / Yan, M. / Onodera, T. / Takahashi, Y. / Li, Q. / Taylor, T. / Okuno, Y. / Kurosaki, T. / Tomabechi, Y. / ...Authors: Makino-Okamura, C. / Hata, H. / Watanabe, T. / Kim, S. / Hebrard, M. / Sato, R. / Yan, M. / Onodera, T. / Takahashi, Y. / Li, Q. / Taylor, T. / Okuno, Y. / Kurosaki, T. / Tomabechi, Y. / Uchikubo-Kamo, T. / Kamada, K. / Shirouzu, M. / Fukuyama, H.
History
DepositionNov 24, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 24, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 14, 2022Group: Refinement description / Structure summary / Category: audit_author / pdbx_initial_refinement_model
Revision 1.2Jun 14, 2023Group: Data collection / Derived calculations ...Data collection / Derived calculations / Refinement description / Structure summary
Category: em_3d_fitting_list / em_imaging ...em_3d_fitting_list / em_imaging / em_software / pdbx_contact_author / pdbx_struct_oper_list / software
Item: _em_3d_fitting_list.accession_code / _em_3d_fitting_list.source_name ..._em_3d_fitting_list.accession_code / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _em_imaging.nominal_defocus_max / _em_imaging.nominal_defocus_min / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 20, 2024Group: Data collection / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_3d_fitting_list / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_3d_fitting_list.initial_refinement_model_id / _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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Structure visualization

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Structure viewerMolecule:
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Assembly

Deposited unit
A: Hemagglutinin
C: Fv-clasp heavy chain
D: Fv-clasp light chain
E: Hemagglutinin
G: Fv-clasp heavy chain
H: Fv-clasp light chain
I: Hemagglutinin
K: Fv-clasp heavy chain
L: Fv-clasp light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)340,89624
Polymers335,3869
Non-polymers5,51015
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Hemagglutinin


Mass: 67423.797 Da / Num. of mol.: 3 / Mutation: L35C, Y106F, N111S, G387C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/Okuda/1957(H2N2)) / Strain: A/Okuda/1957(H2N2) / Gene: HA / Plasmid: pFastBac1
Details (production host): gp67 secretion signal sequence on N-terminal. Thrombin-Foldon-AviTag-6xHis on C-terminal.
Cell line (production host): Hi-Five / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A0A0A7E4R0
#2: Antibody Fv-clasp heavy chain


Mass: 23083.908 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pCR2.1-dT7P / Production host: Escherichia coli (E. coli)
#3: Antibody Fv-clasp light chain


Mass: 21287.729 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pCR2.1-dT7P / Production host: Escherichia coli (E. coli)
#4: Polysaccharide
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#5: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
Has ligand of interestN
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: Hemagglutinin Influenza A virus (A/Okuda/1957(H2N2) bound with a neutralizing antibody
Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT
Molecular weightValue: 0.29 MDa / Experimental value: YES
Source (natural)Organism: Influenza A virus (A/Okuda/1957(H2N2))
Source (recombinant)Organism: Trichoplusia n
Buffer solutionpH: 7.5
SpecimenConc.: 0.03 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationCryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm
Specimen holderSpecimen holder model: OTHER
Image recordingAverage exposure time: 12 sec. / Electron dose: 50 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of real images: 2043
Image scansMovie frames/image: 40

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Processing

EM software
IDNameVersionCategory
1Gautomatchparticle selection
2SerialEMimage acquisition
4CTFFIND4CTF correction
7Cootmodel fitting
9PHENIX1.18model refinement
10RELION3.0.8initial Euler assignment
11RELION3.0.8final Euler assignment
12RELION3.0.8classification
13RELION3.0.83D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1768385
SymmetryPoint symmetry: C3 (3 fold cyclic)
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 52314 / Symmetry type: POINT
Atomic model buildingB value: 141.37 / Protocol: AB INITIO MODEL / Space: REAL / Target criteria: Corelation coefficient
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
14HLZ

4hlz

14HLZ1PDBexperimental model
25XCX

5xcx

15XCX2PDBexperimental model
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 32.32 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.007220550
ELECTRON MICROSCOPYf_angle_d0.823427795
ELECTRON MICROSCOPYf_chiral_restr0.05113048
ELECTRON MICROSCOPYf_plane_restr0.00533567
ELECTRON MICROSCOPYf_dihedral_angle_d18.48142886

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