7WL5 | pdb_00007wl5

Structure of an avian influenza H5 hemagglutinin from the influenza virus A/Equine/Guangxi/25/2010(H5N1) and A/Equine/Guangxi/68/2010(H5N1)

• PDB DOI: https://doi.org/10.2210/pdb7WL5/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Influenza A virus
• Expression System: Baculovirus expression vector pFastBac1-HM
• Mutation(s): No 


• Deposited: 2022-01-12 Released: 2023-01-18 
• Deposition Author(s): Wei, X., Yang, X., Chen, Q., Meng, G.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 
  0.285 (Depositor), 0.280 (DCC) 
• R-Value Work: 
  0.233 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.235 (Depositor) 

Starting Model: experimental

Literature

Structure of an avian influenza H5 hemagglutinin from the influenza virus A/Equine/Guangxi/25/2010(H5N1) and A/Equine/Guangxi/68/2010(H5N1)

Wei, X., Yang, X., Chen, Q., Meng, G.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Hetero 6-mer - A3B3 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 173.64 kDa 
• Atom Count: 12,185 
• Modeled Residue Count: 1,470 
• Deposited Residue Count: 1,470 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin	A, B [auth C], C [auth E]	321	Influenza A virus	Mutation(s): 0  Gene Names: HA
UniProt
Find proteins for D1LPE3 (Influenza A virus) Explore D1LPE3  Go to UniProtKB:  D1LPE3
Glycosylation
Glycosylation Sites: 5

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin	D [auth B], E [auth D], F	169	Influenza A virus	Mutation(s): 0  Gene Names: HA
UniProt
Find proteins for A0A8K1XY81 (Influenza A virus) Explore A0A8K1XY81  Go to UniProtKB:  A0A8K1XY81

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	G, I, J, K, M, N, O, Q, R	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	H, L, P	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE GlyCosmos:  G15407YE GlyGen:  G15407YE

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free:  0.285 (Depositor), 0.280 (DCC) 
• R-Value Work:  0.233 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.235 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 215.425	α = 90
b = 99.092	β = 95.03
c = 102.06	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-01-18 
Deposition Author(s): Wei, X., Yang, X., Chen, Q., Meng, G.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2023-01-18
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description
• Version 1.2: 2024-10-23
  Changes: Structure summary