5K9Q

Crystal structure of multidonor HV1-18-class broadly neutralizing Influenza A antibody 16.a.26 in complex with A/Hong Kong/1-4-MA21-1/1968 (H3N2) Hemagglutinin

• PDB DOI: https://doi.org/10.2210/pdb5K9Q/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Influenza A virus (A/Hong Kong/1/1968(H3N2)), Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2016-06-01 Released: 2016-11-30 
• Deposition Author(s): Joyce, M.G., Thomas, P.V., Wheatley, A.K., McDermott, A.B., Mascola, J.R., Kwong, P.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.218 
• R-Value Work: 0.182 
• R-Value Observed: 0.184 

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)

Biological Assembly 2  

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 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 626.61 kDa 
• Atom Count: 45,420 
• Modelled Residue Count: 5,582 
• Deposited Residue Count: 5,610 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin HA1	A, C, E, M, O, Q	320	Influenza A virus (A/Hong Kong/1/1968(H3N2))	Mutation(s): 0  Gene Names: HA
UniProt
Find proteins for Q91MA7 (Influenza A virus (strain A/Hong Kong/1/1968 H3N2)) Explore Q91MA7  Go to UniProtKB:  Q91MA7

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin HA2	B, D, F, N, P, R	170	Influenza A virus (A/Hong Kong/1/1968(H3N2))	Mutation(s): 0  Gene Names: HA
UniProt
Find proteins for Q91MA7 (Influenza A virus (strain A/Hong Kong/1/1968 H3N2)) Explore Q91MA7  Go to UniProtKB:  Q91MA7

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
16.a.26 Heavy chain	G, H, J, S, U, W [auth X]	231	Homo sapiens	Mutation(s): 0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
16.a.26 Light chain	I, K, L, T, V, X [auth Y]	214	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	AA [auth A], AB [auth O], BA [auth A], BB [auth P], CA [auth A], CB [auth Q], DA [auth B], DB [auth Q], EA [auth C], EB [auth Q], FA [auth C], FB [auth Q], GA [auth C], GB [auth Q], HA [auth C], HB [auth R], IA [auth C], JA [auth D], KA [auth E], LA [auth E], MA [auth E], NA [auth E], OA [auth E], PA [auth F], QA [auth M], RA [auth M], SA [auth M], TA [auth M], UA [auth M], VA [auth N], WA [auth O], XA [auth O], Y [auth A], YA [auth O], Z [auth A], ZA [auth O]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.218 
• R-Value Work: 0.182 
• R-Value Observed: 0.184 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 121.808	α = 90
b = 233.909	β = 90
c = 302.452	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-11-30 
Deposition Author(s): Joyce, M.G., Thomas, P.V., Wheatley, A.K., McDermott, A.B., Mascola, J.R., Kwong, P.D.

Revision History  

• Version 1.0: 2016-11-30
  Type: Initial release
  
• Version 1.1: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Database references, Derived calculations, Structure summary