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- PDB-12iv: CryoEM structure of monoclonal Fab 047-09 1A02 binding the latera... -

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Basic information

Entry
Database: PDB / ID: 12iv
TitleCryoEM structure of monoclonal Fab 047-09 1A02 binding the lateral patch of influenza virus H1 HA (A/California/04/2009 H1N1)
Components
  • Heavy chain 1A02
  • Hemagglutinin HA1
  • Hemagglutinin HA2
  • Light chain 1A02
KeywordsIMMUNE SYSTEM/Viral Protein / Antibody / Hemagglutinin / IMMUNE SYSTEM / IMMUNE SYSTEM-Viral Protein 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 / metal ion binding / 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: 3.76 Å
AuthorsFernandez-Quintero, M.L. / Han, J. / Ward, A.B.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Temporal and cross-species convergence of influenza H1 lateral patch antigenic drift
Authors: Fernandez-Quintero, M.L. / Han, J. / Ward, A.B.
History
DepositionApr 7, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 23, 2026Provider: repository / Type: Initial release
Revision 1.0Sep 23, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hemagglutinin HA2
B: Hemagglutinin HA2
C: Hemagglutinin HA1
D: Hemagglutinin HA2
E: Hemagglutinin HA1
F: Hemagglutinin HA1
I: Heavy chain 1A02
J: Heavy chain 1A02
K: Heavy chain 1A02
R: Light chain 1A02
P: Light chain 1A02
Q: Light chain 1A02
hetero molecules


Theoretical massNumber of molelcules
Total (without water)239,75026
Polymers236,65312
Non-polymers3,09714
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 HA2


Mass: 18543.518 Da / Num. of mol.: 3 / Mutation: E47K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/California/04/2009(H1N1))
Gene: HA / Production host: Homo sapiens (human) / References: UniProt: C3W5S1
#2: Protein Hemagglutinin HA1


Mass: 35701.344 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/California/04/2009(H1N1))
Gene: HA / Production host: Homo sapiens (human) / References: UniProt: C3W5S1
#3: Antibody Heavy chain 1A02


Mass: 13095.723 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 1A02


Mass: 11543.765 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: 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.: 14 / 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: Fab 047-09 1A02 in complex with A/California/04/2009 / Type: COMPLEX / Entity ID: #4, #3, #1-#2 / Source: RECOMBINANT
Molecular weightValue: 330 kDa/nm / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: Quantifoil R1.2/1.3
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 45 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.7.1particle selection
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.76 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 87530 / Symmetry type: POINT

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