6A4K | pdb_00006a4k

Human antibody 32D6 Fab in complex with H1N1 influenza A virus HA1

• PDB DOI: https://doi.org/10.2210/pdb6A4K/pdb

• Classification: VIRAL PROTEIN/IMMUNE SYSTEM
• Organism(s): Influenza A virus (A/California/7/2009(H1N1)), Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2018-06-20 Released: 2019-03-27 
• Deposition Author(s): Lee, C.C., Ko, T.P., Lin, L.L., Wang, A.H.J.
• Funding Organization(s): Academia Sinica (Taiwan)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.15 Å
• R-Value Free: 
  0.233 (Depositor), 0.235 (DCC) 
• R-Value Work: 
  0.175 (Depositor), 0.178 (DCC) 
• R-Value Observed: 
  0.178 (Depositor) 

Starting Models: experimental

Literature

An Effective Neutralizing Antibody Against Influenza Virus H1N1 from Human B Cells.

Lee, C.C., Yang, C.Y., Lin, L.L., Ko, T.P., Chang, A.H., Chang, S.S., Wang, A.H.

(2019) Sci Rep 9: 4546-4546

• PubMed: 30872685 
• DOI: https://doi.org/10.1038/s41598-019-40937-4
• Primary Citation Related Structures: 
  6A4K


• PubMed Abstract: 
  

  Influenza is a contagious acute respiratory disease caused by the influenza virus infection. Hemagglutinin (HA) is an important target in the therapeutic treatment and diagnostic detection of the influenza virus. Influenza A virus encompasses several different HA subtypes with different strains, which are constantly changing. In this study, we identified a fully human H1N1 neutralizing antibody (32D6) via an Epstein-Barr virus-immortalized B cell-based technology. 32D6 specifically neutralizes the clinically isolated H1N1 strains after the 2009 pandemic but not the earlier strains. The epitope was identified through X-ray crystallographic analysis of the 32D6-Fab/HA1 complex structure, which revealed a unique loop conformation located on the top surface of HA. The major region is composed of two peptide segments (residues 172-177 and 206-213), which form an abreast loop conformation. The residue T262 between the two loops forms a conformational epitope for recognition by 32D6. Three water molecules were observed at the interface of HA and the heavy chain, and they may constitute a stabilizing element for the 32D6-HA association. In addition, each 32D6-Fab is likely capable of blocking one HA trimer. This study provides important information on the strain specificity of 32D6 for the therapeutic treatment and detection of viral infection.

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Organizational Affiliation: 
• Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan.
Core Facility for Protein Production and X-ray Structural Analysis, Academia Sinica, Taipei, Taiwan.
Department of Science and Innovation, Medigen Biotech Corporation, Taipei, Taiwan.
Department of Science and Innovation, Medigen Biotech Corporation, Taipei, Taiwan. [e-mail].
Institute of Biotechnology, National Taiwan University, Taipei, Taiwan. [e-mail].
Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan. [e-mail].
Core Facility for Protein Production and X-ray Structural Analysis, Academia Sinica, Taipei, Taiwan. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: surface plasmon resonance

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 3 assigned by authors.

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 4 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 301.09 kDa 
• Atom Count: 20,618 
• Modeled Residue Count: 2,672 
• Deposited Residue Count: 2,756 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin	A, D [auth B], G [auth C], J [auth D]	235	Influenza A virus (A/California/7/2009(H1N1))	Mutation(s): 0
UniProt
Find proteins for C3W5X2 (Influenza A virus) Explore C3W5X2  Go to UniProtKB:  C3W5X2
Glycosylation
Glycosylation Sites: 1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
immunoglobulin Fab heavy chain	B [auth H], E [auth I], H [auth J], K	238	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
immunoglobulin Fab light chain	C [auth L], F [auth M], I [auth N], L [auth O]	216	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	M [auth A], O [auth B], R [auth C], T [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
ACT	Q [auth B], V [auth D]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
CA	N [auth A], P [auth B], S [auth C], U [auth D], W [auth O]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.15 Å
• R-Value Free:  0.233 (Depositor), 0.235 (DCC) 
• R-Value Work:  0.175 (Depositor), 0.178 (DCC) 
• R-Value Observed: 0.178 (Depositor) 

Space Group: P 3₁ 1 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 181.743	α = 90
b = 181.743	β = 90
c = 248.091	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-03-27 
Deposition Author(s): Lee, C.C., Ko, T.P., Lin, L.L., Wang, A.H.J.

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Funding Organization	Location	Grant Number
Academia Sinica (Taiwan)	Taiwan	--

Revision History  

• Version 1.0: 2019-03-27
  Type: Initial release
  
• Version 1.1: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.2: 2023-11-22
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 1.3: 2024-10-23
  Changes: Structure summary