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- PDB-9mq1: Cryo-EM map of H5 HA (A/Jiangsu/NJ210/2023) in complex with monoc... -

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Basic information

Entry
Database: PDB / ID: 9mq1
TitleCryo-EM map of H5 HA (A/Jiangsu/NJ210/2023) in complex with monoclonal fab 20D10
Components
  • 20D10 Heavy Chain Fab
  • 20D10 Light Chain Fab
  • Hemagglutinin HA1
  • Hemagglutinin HA2
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / influenza / hemaglutinin / antibody-antigen complex / VIRAL PROTEIN / 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 speciesHomo sapiens (human)
Influenza A virus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.37 Å
AuthorsLeon, A.N. / Brouwer, P.J.M. / Rodriguez, A.J. / Han, J. / Ward, A.B.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)75N39019C00051 United States
CitationJournal: To Be Published
Title: Human Monoclonal Antibodies that Target Clade 2.3.4.4b H5N1 Hemagglutinin
Authors: Pena Alzua, G. / Leon, A.N. / Brouwer, P.J.M. / Yellin, T. / Bhavsar, D. / Loganathan, M. / Bushfield, K. / Marizzi, C. / Rodriguez, A.J. / Han, J. / Webby, R. / Ward, A.B. / Duty, J.A. / Krammer, F.
History
DepositionJan 1, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 5, 2025Provider: repository / Type: Initial release
Revision 1.0Nov 5, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Nov 5, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Nov 5, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Nov 5, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Nov 5, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Nov 5, 2025Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Nov 5, 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
H: 20D10 Heavy Chain Fab
L: 20D10 Light Chain Fab
B: Hemagglutinin HA1
b: Hemagglutinin HA2
A: Hemagglutinin HA1
a: Hemagglutinin HA2
C: Hemagglutinin HA1
c: Hemagglutinin HA2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)221,46620
Polymers218,8118
Non-polymers2,65412
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: Antibody 20D10 Heavy Chain Fab


Mass: 13253.739 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#2: Antibody 20D10 Light Chain Fab


Mass: 12232.831 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#3: Protein Hemagglutinin HA1


Mass: 39088.605 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/Jiangsu/NJ210/2023 / Gene: HA / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: A0A8E4ZAK5
#4: Protein Hemagglutinin HA2


Mass: 25352.949 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/Jiangsu/NJ210/2023 / Gene: HA / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: A0AAX6NNL9
#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.: 12 / 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: H5 HA (A/Jiangsu/NJ210/2023) in complex with monoclonal fab 20D10 and CR9114
Type: COMPLEX / Entity ID: #1-#4 / Source: NATURAL
Molecular weightValue: 0.28 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Buffer solutionpH: 7.4
SpecimenConc.: 0.56 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
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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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: 2000 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 44.74 e/Å2 / Film or detector model: FEI FALCON I (4k x 4k)

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Processing

EM software
IDNameVersionCategory
2PHENIX1.21.1_5286model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.37 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 44504 / Symmetry type: POINT
RefinementHighest resolution: 3.37 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00613825
ELECTRON MICROSCOPYf_angle_d0.96718752
ELECTRON MICROSCOPYf_dihedral_angle_d12.3625252
ELECTRON MICROSCOPYf_chiral_restr0.0532051
ELECTRON MICROSCOPYf_plane_restr0.0072418

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