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- PDB-8tx3: Fab 3864-6 in complex with influenza HA H3-VIC11 -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 8tx3
TitleFab 3864-6 in complex with influenza HA H3-VIC11
Components
  • (Hemagglutinin) x 2
  • Fab 3864-6 Heavy Chain
  • Fab 3864-6 Light Chain
KeywordsANTIVIRAL PROTEIN / antibody / influenza
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: 2.99 Å
AuthorsMorano, N.C. / Shapiro, L.
Funding support United States, 1items
OrganizationGrant numberCountry
Bill & Melinda Gates FoundationFNIH SHAP19IUFV United States
CitationJournal: Structure / Year: 2025
Title: The N terminus of H3-influenza hemagglutinin as a site-of-vulnerability to neutralizing antibody
Authors: Rawi, R. / Morano, N.C. / Cheung, C.S.F. / Du, H. / Gorman, J. / Prabhakaran, M. / Becker, J.E. / Bylund, T. / Charaf, S. / Chen, X. / Lee, M. / Harris, D.R. / Olia, A.S. / Ou, L. / Wang, L. ...Authors: Rawi, R. / Morano, N.C. / Cheung, C.S.F. / Du, H. / Gorman, J. / Prabhakaran, M. / Becker, J.E. / Bylund, T. / Charaf, S. / Chen, X. / Lee, M. / Harris, D.R. / Olia, A.S. / Ou, L. / Wang, L. / Wang, S. / Zhang, B. / Kanekiyo, M. / McDermott, A.B. / Zhou, T. / Shapiro, L. / Kwong, P.D.
History
DepositionAug 22, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 11, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2024Group: Data collection / Structure summary
Category: em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update / _pdbx_entry_details.has_protein_modification
Revision 1.2Sep 24, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hemagglutinin
B: Hemagglutinin
C: Hemagglutinin
D: Hemagglutinin
G: Hemagglutinin
I: Hemagglutinin
H: Fab 3864-6 Heavy Chain
L: Fab 3864-6 Light Chain
E: Fab 3864-6 Heavy Chain
J: Fab 3864-6 Light Chain
F: Fab 3864-6 Heavy Chain
K: Fab 3864-6 Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)352,00738
Polymers338,95312
Non-polymers13,05426
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 2 types, 6 molecules ACGBDI

#1: Protein Hemagglutinin


Mass: 39303.648 Da / Num. of mol.: 3 / Fragment: residues 1-345
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/Victoria/361/2011(H3N2))
Strain: A/Victoria/361/2011(H3N2) / Gene: HA / Production host: Homo sapiens (human) / References: UniProt: L0HR89
#2: Protein Hemagglutinin


Mass: 25234.092 Da / Num. of mol.: 3 / Fragment: residues 346-521
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/Victoria/361/2011(H3N2))
Gene: HA / Production host: Homo sapiens (human) / References: UniProt: L0HR89

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Antibody , 2 types, 6 molecules HEFLJK

#3: Antibody Fab 3864-6 Heavy Chain


Mass: 24862.734 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 Fab 3864-6 Light Chain


Mass: 23583.883 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

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Sugars , 3 types, 26 molecules

#5: Polysaccharide
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 9
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#6: 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.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam 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
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE
#7: 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

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Details

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: Trimer / Type: COMPLEX / Entity ID: #1-#4 / Source: NATURAL
Source (natural)Organism: Homo sapiens (human)
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 58.06 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
2PHENIX1.19.2_4158:model refinement
3Leginonimage acquisition
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.99 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 590963 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00318306
ELECTRON MICROSCOPYf_angle_d0.64224816
ELECTRON MICROSCOPYf_dihedral_angle_d8.9432883
ELECTRON MICROSCOPYf_chiral_restr0.0462892
ELECTRON MICROSCOPYf_plane_restr0.0063110

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