9DBX | pdb_00009dbx

Structure of AG11-2F01 Fab in complex with A/Solomon Islands/3/2006 (H1N1) influenza virus hemagglutinin


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

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This is version 1.1 of the entry. See complete history

Literature

High-throughput synthesis and specificity characterization of natively paired influenza hemagglutinin antibodies with oPool + display.

Ouyang, W.O.Lv, H.Liu, W.Lei, R.Mou, Z.Pholcharee, T.Talmage, L.Tong, M.Ji, W.Wang, Y.Dailey, K.E.Gopal, A.B.Choi, D.Ardagh, M.R.Rodriguez, L.A.Guthmiller, J.J.Dai, X.Wu, N.C.

(2025) Sci Transl Med 17: eadt4147-eadt4147

  • DOI: https://doi.org/10.1126/scitranslmed.adt4147
  • Primary Citation Related Structures: 
    9CU7, 9DBX

  • PubMed Abstract: 

    Antibody discovery is crucial for developing therapeutics and vaccines and for understanding adaptive immunity. However, the lack of approaches to synthesize antibodies with defined sequences in a high-throughput manner represents a major bottleneck in antibody discovery. Here, we present oPool + display, a high-throughput cell-free platform that combined oligo pool synthesis and mRNA display to rapidly construct and characterize hundreds to thousands of natively paired antibodies in parallel. As a proof of concept, we applied oPool + display to probe the binding specificity of more than 300 uncommon influenza hemagglutinin-specific antibodies against nine hemagglutinin variants through 16 screens. More than 5000 binding tests were performed in 3 to 5 days of hands-on time with further scaling potential. Follow-up structural and functional analysis of two antibodies revealed the versatility of the human immunoglobulin gene segment D3-3 ( IGHD-3-3 ) in recognizing the hemagglutinin stem. Overall, this study established an experimental platform that not only accelerates antibody characterization but also enables unbiased discovery of recurring molecular signatures among antibodies with the same specificity.


  • Organizational Affiliation
    • Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.

Macromolecule Content 

  • Total Structure Weight: 242.78 kDa 
  • Atom Count: 17,055 
  • Modeled Residue Count: 2,157 
  • Deposited Residue Count: 2,157 
  • Unique protein chains: 4

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Hemagglutinin HA1 chain
A, C, E
321Influenza A virus (A/Solomon Islands/3/2006(H1N1))Mutation(s): 0 
Gene Names: HA
UniProt
Find proteins for A7Y8I1 (Influenza A virus)
Explore A7Y8I1 
Go to UniProtKB:  A7Y8I1
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA7Y8I1
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Hemagglutinin HA2 chain
B, D, F
168Influenza A virus (A/Solomon Islands/3/2006(H1N1))Mutation(s): 0 
Gene Names: HA
UniProt
Find proteins for B9W1X0 (Influenza A virus)
Explore B9W1X0 
Go to UniProtKB:  B9W1X0
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB9W1X0
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Heavy chain of influenza virus hemagglutinin antibody AG11-2F01G [auth H],
I [auth W],
K [auth Y]
125Homo sapiensMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Light chain of influenza virus hemagglutinin antibody AG11-2F01H [auth L],
J [auth X],
L [auth Z]
105Homo sapiensMutation(s): 0 

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR01 AI167910
National Institutes of Health/National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIH/NIAMS)United StatesDP2 AT011966
Michelson Medical Research FoundationUnited StatesPrize for Human Immunology and Vaccine Research
Searle Scholars ProgramUnited States--

Revision History  (Full details and data files)

  • Version 1.0: 2025-09-03
    Type: Initial release
  • Version 1.1: 2025-11-05
    Changes: Data collection, Database references