8US0

Human antibody S8V1-157 in complex with the A/American black duck/New Brunswick/00464/2010(H4N6) HA head domain

• PDB DOI: https://doi.org/10.2210/pdb8US0/pdb

• Classification: Viral Protein/IMMUNE SYSTEM
• Organism(s): Influenza A virus, Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2023-10-27 Released: 2024-10-30 
• Deposition Author(s): McCarthy, K.R.
• 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: 3.70 Å
• R-Value Free: 0.293 
• R-Value Work: 0.246 
• R-Value Observed: 0.248 

Starting Models: experimental

Literature

Broadly protective antibodies engage influenza virus hemagglutinin at the head domain-HA2 interface

McCarthy, K.R.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Hetero 18-mer - A6B6C6 Pseudo Symmetry: Dihedral - D3  (Explore in 3D)
Pseudo Stoichiometry: Hetero 18-mer - A12B6 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 494.58 kDa 
• Atom Count: 33,101 
• Modelled Residue Count: 4,244 
• Deposited Residue Count: 4,464 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin	A, B [auth D], C [auth G], D [auth J], E [auth M], F [auth P]	292	Influenza A virus	Mutation(s): 0  Gene Names: HA
UniProt
Find proteins for M1UPL4 (Influenza A virus) Explore M1UPL4  Go to UniProtKB:  M1UPL4
Glycosylation
Glycosylation Sites: 2

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
human antibody S8V1-157 light chain	G [auth O], H [auth I], I [auth C], J [auth R], K [auth F], R [auth L]	221	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
human antibody S8V1-157 heavy chain	L [auth B], M [auth H], N [auth K], O [auth N], P [auth Q], Q [auth E]	231	Homo sapiens	Mutation(s): 0

Oligosaccharides

Help

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	AA [auth a], CA [auth c], S, T, U, V, W, X	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE GlyCosmos:  G15407YE GlyGen:  G15407YE

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	BA [auth b], Y, Z	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	HA [auth M]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
MES	DA [auth A], EA [auth D], FA [auth G], GA [auth J], IA [auth M], JA [auth P]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C6 H13 N O4 S SXGZJKUKBWWHRA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.70 Å
• R-Value Free: 0.293 
• R-Value Work: 0.246 
• R-Value Observed: 0.248 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 127.92	α = 90
b = 241.54	β = 101.619
c = 144.13	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-10-30 
Deposition Author(s): McCarthy, K.R.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	2P01AI089618-11A1

Revision History  

• Version 1.0: 2024-10-30
  Type: Initial release