8TXT

Crystal structure of 05.GC.w13.02 Fab in complex with H5 HA from A/Viet Nam/1203/2004(H5N1)

• PDB DOI: https://doi.org/10.2210/pdb8TXT/pdb

• Classification: VIRAL PROTEIN/IMMUNE SYSTEM
• Organism(s): Influenza A virus (A/Viet Nam/1203/2004(H5N1)), Homo sapiens
• Expression System: Trichoplusia ni, Cricetulus griseus
• Mutation(s): No 


• Deposited: 2023-08-24 Released: 2024-06-26 
• Deposition Author(s): Lin, T.H., Moore, N., Wilson, I.A.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.19 Å
• R-Value Free: 0.258 
• R-Value Work: 0.217 
• R-Value Observed: 0.220 

Literature

Maturation of germinal center B cells after influenza vaccination in humans

Lin, T.H., Moore, N., Wilson, I.A., Ellebedy, A.H., Kleinstein, S.H., Ward, A.B., Turner, J.S., Krammer, F., Presti, P.M., Teefey, S.A., Middleton, W.D., Suessen, T., Hoehn, K., Schmitz, A.J., Zhou, J.Q., Mohammed, B.M., Msllsdi, S.K., Wnag, M., McMahon, M., Han, J., Kim, W., Meng, H., McIntire, K.M.

(2024) J Exp Med 

• DOI: https://doi.org/10.1084/jem.20240668

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Hetero 12-mer - A3B3C3D3 Pseudo Symmetry: Cyclic - C3  (Explore in 3D)
Pseudo Stoichiometry: Hetero 12-mer - A6B3C3 

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

Macromolecule Content

• Total Structure Weight: 320.47 kDa 
• Atom Count: 22,149 
• Modelled Residue Count: 2,810 
• Deposited Residue Count: 2,850 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin	A, C, E	334	Influenza A virus (A/Viet Nam/1203/2004(H5N1))	Mutation(s): 0  Gene Names: HA
UniProt
Find proteins for Q5EP31 (Influenza A virus (strain A/Vietnam/1203/2004 H5N1)) Explore Q5EP31  Go to UniProtKB:  Q5EP31

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin	B, D, F	177	Influenza A virus (A/Viet Nam/1203/2004(H5N1))	Mutation(s): 0  Gene Names: HA
UniProt
Find proteins for A0A6B7HQ27 (Influenza A virus) Explore A0A6B7HQ27  Go to UniProtKB:  A0A6B7HQ27

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
GC_W13B_B, Fab heavy chain	G [auth H], I [auth G], K [auth J]	225	Homo sapiens	Mutation(s): 0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
GC_w13_B, Fab light chain	H [auth L], J [auth I], L [auth K]	214	Homo sapiens	Mutation(s): 0

Oligosaccharides

Help

Entity ID: 5
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	M, Q	3		N-Glycosylation

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	N, O, P, R	2		N-Glycosylation

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.19 Å
• R-Value Free: 0.258 
• R-Value Work: 0.217 
• R-Value Observed: 0.220 
• Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 159.461	α = 90
b = 232.604	β = 90
c = 233.67	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-06-26 
Deposition Author(s): Lin, T.H., Moore, N., Wilson, I.A.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	75N93019C00051

Revision History  

• Version 1.0: 2024-06-26
  Type: Initial release