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- PDB-9dbx: Structure of AG11-2F01 Fab in complex with A/Solomon Islands/3/20... -

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Basic information

Entry
Database: PDB / ID: 9dbx
TitleStructure of AG11-2F01 Fab in complex with A/Solomon Islands/3/2006 (H1N1) influenza virus hemagglutinin
Components
  • Heavy chain of influenza virus hemagglutinin antibody AG11-2F01
  • Hemagglutinin HA1 chain
  • Hemagglutinin HA2 chain
  • Light chain of influenza virus hemagglutinin antibody AG11-2F01
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / antibody-antigen complex / 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 speciesInfluenza A virus
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsMou, Z. / Lei, R. / Dai, X. / Wu, N.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI167910 United States
National Institutes of Health/National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIH/NIAMS)DP2 AT011966 United States
Michelson Medical Research FoundationPrize for Human Immunology and Vaccine Research United States
Searle Scholars Program United States
CitationJournal: To Be Published
Title: Structure of AG11-2F01 Fab in complex with A/Solomon Islands/3/2006 (H1N1) influenza virus hemagglutinin
Authors: Mou, Z. / Lei, R. / Ouyang, W. / Dai, X. / Wu, N.
History
DepositionAug 23, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 3, 2025Provider: repository / Type: Initial release
Revision 1.0Sep 3, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Sep 3, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Sep 3, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Sep 3, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Sep 3, 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: Hemagglutinin HA1 chain
B: Hemagglutinin HA2 chain
C: Hemagglutinin HA1 chain
D: Hemagglutinin HA2 chain
E: Hemagglutinin HA1 chain
F: Hemagglutinin HA2 chain
H: Heavy chain of influenza virus hemagglutinin antibody AG11-2F01
L: Light chain of influenza virus hemagglutinin antibody AG11-2F01
W: Heavy chain of influenza virus hemagglutinin antibody AG11-2F01
X: Light chain of influenza virus hemagglutinin antibody AG11-2F01
Y: Heavy chain of influenza virus hemagglutinin antibody AG11-2F01
Z: Light chain of influenza virus hemagglutinin antibody AG11-2F01
hetero molecules


Theoretical massNumber of molelcules
Total (without water)242,78518
Polymers241,45812
Non-polymers1,3276
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 Hemagglutinin HA1 chain


Mass: 35809.098 Da / Num. of mol.: 3 / Fragment: UNP residues 18-339
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/Solomon Islands/3/2006(H1N1) / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A7Y8I1
#2: Protein Hemagglutinin HA2 chain


Mass: 19395.527 Da / Num. of mol.: 3 / Fragment: UNP residues 349-516
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/Solomon Islands/3/2006(H1N1) / Gene: HA / Cell (production host): sf9 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A7Y8I1
#3: Antibody Heavy chain of influenza virus hemagglutinin antibody AG11-2F01


Mass: 13794.432 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: phCMV3 / Cell (production host): Expi293F / Production host: Homo sapiens (human)
#4: Antibody Light chain of influenza virus hemagglutinin antibody AG11-2F01


Mass: 11486.814 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: phCMV3 / Cell (production host): Expi293F / Production host: Homo sapiens (human)
#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.: 6 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
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 interestY
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 AG11-2F01 Fab in complex with A/Solomon Islands/3/2006 (H1N1) influenza virus hemagglutinin
Type: COMPLEX / Entity ID: #1-#4 / Source: MULTIPLE SOURCES
Source (natural)Organism: Influenza A virus / Strain: A/Solomon Islands/3/2006(H1N1)
Source (recombinant)Organism: Trichoplusia ni (cabbage looper) / Cell: sf9
Buffer solutionpH: 8 / Details: 20 mM Tris-HCl, 100 mM NaCl, 10 mM CaCl2, pH 8.0
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMTris Hydrochloric acid1
2100 mMSodium ChlorideNaCl1
310 mMCalcium ChlorideCaCl21
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: NITROGEN

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 130000 X / Nominal defocus max: 1800 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV

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Processing

EM software
IDNameCategory
2SerialEMimage acquisition
8PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 359720 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00317451
ELECTRON MICROSCOPYf_angle_d0.55123652
ELECTRON MICROSCOPYf_dihedral_angle_d5.1592442
ELECTRON MICROSCOPYf_chiral_restr0.0422562
ELECTRON MICROSCOPYf_plane_restr0.0043045

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