5DUM | pdb_00005dum

Crystal structure of influenza A virus H5 hemagglutinin globular head in complex with the Fab of antibody 65C6

• PDB DOI: https://doi.org/10.2210/pdb5DUM/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens, Influenza A virus (A/Anhui/1/2005(H5N1))
• Expression System: Homo sapiens, Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2015-09-19 Released: 2015-12-16 
• Deposition Author(s): Sun, J., Zuo, T., Wang, G., Zhou, P., Zhang, L., Wang, X.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 
  0.269 (Depositor), 0.272 (DCC) 
• R-Value Work: 
  0.215 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.218 (Depositor) 

Literature

Comprehensive analysis of antibody recognition in convalescent humans from highly pathogenic avian influenza H5N1 infection

Zuo, T., Sun, J., Wang, G., Jiang, L., Zuo, Y., Li, D., Shi, X., Liu, X., Fan, S., Ren, H., Hu, H., Sun, L., Zhou, B., Liang, M., Zhou, P., Wang, X., Zhang, L.

(2015) Nat Commun 6: 8855-8855

• PubMed: 26635249 
• DOI: https://doi.org/10.1038/ncomms9855
• Primary Citation Related Structures: 
  5DUM, 5DUP, 5DUR, 5DUT


• PubMed Abstract: 
  

  Understanding the mechanism of protective antibody recognition against highly pathogenic avian influenza A virus H5N1 in humans is critical for the development of effective therapies and vaccines. Here we report the crystal structure of three H5-specific human monoclonal antibodies bound to the globular head of hemagglutinin (HA) with distinct epitope specificities, neutralization potencies and breadth. A structural and functional analysis of these epitopes combined with those reported elsewhere identifies four major vulnerable sites on the globular head of H5N1 HA. Chimeric and vulnerable site-specific mutant pseudoviruses are generated to delineate broad neutralization specificities of convalescent sera from two individuals who recovered from the infection with H5N1 virus. Our results show that the four vulnerable sites on the globular head rather than the stem region are the major neutralizing targets, suggesting that during natural H5N1 infection neutralizing antibodies against the globular head work in concert to provide protective antibody-mediated immunity.

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Organizational Affiliation: 
• Comprehensive AIDS Research Center, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, School of Medicine, Tsinghua University, Beijing 100084, China.
Ministry of Education Key Laboratory of Protein Science, Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China.
Collaborative Innovation Center for Biotherapy, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, Chengdu 610041, China.
Unit of Anti-Viral Immunity and Genetic Therapy, Key Laboratory of Molecular Virology and Immunology, Institute Pasteur of Shanghai, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China.
State Key Laboratory for Infectious Disease Control and Prevention, National Institute for Viral Disease Control and Prevention, China CDC, Beijing 102206, China.
Shenzhen Key Laboratory of Pathogen and Immunity, Shenzhen Third People's Hospital, Shenzhen 518112, China.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 76.11 kDa 
• Atom Count: 4,922 
• Modeled Residue Count: 627 
• Deposited Residue Count: 684 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
65C6 Heavy Chain	A [auth H]	237	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
65C6 Light Chain	B [auth L]	214	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin	C [auth A]	233	Influenza A virus (A/Anhui/1/2005(H5N1))	Mutation(s): 0  Gene Names: HA
UniProt
Find proteins for Q1WDM0 (Influenza A virus) Explore Q1WDM0  Go to UniProtKB:  Q1WDM0
Glycosylation
Glycosylation Sites: 2

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	D [auth A], E [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free:  0.269 (Depositor), 0.272 (DCC) 
• R-Value Work:  0.215 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.218 (Depositor) 

Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.539	α = 90
b = 92.981	β = 90
c = 134.005	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-12-16 
Deposition Author(s): Sun, J., Zuo, T., Wang, G., Zhou, P., Zhang, L., Wang, X.

Revision History  

• Version 1.0: 2015-12-16
  Type: Initial release
  
• Version 1.1: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.2: 2024-11-06
  Changes: Data collection, Database references, Structure summary